# 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/T0308/ # command:# Making conformation for sequence T0308 numbered 1 through 165 Created new target T0308 from T0308.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0308/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0308//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0308/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0308//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0308/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0308/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0308/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1r8sA/merged-good-all-a2m # 1r8sA read from 1r8sA/merged-good-all-a2m # found chain 1r8sA in training set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNAQ 1r8sA 19 :RILMVGLDAAGKTTILYKLKLGEIV # choosing archetypes in rotamer library T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1r8sA 44 :TTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r8sA 119 :AVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 1r8sA read from 1r8sA/merged-good-all-a2m # found chain 1r8sA in training set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNAQSQ 1r8sA 19 :RILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1r8sA 46 :IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL T0308 105 :RRIPILFFANKMDLRDAV 1r8sA 117 :RDAVLLVFANKQDLPNAM T0308 128 :SQLLCLENIK 1r8sA 135 :NAAEITDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1r8sA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=8 Number of alignments=2 # 1r8sA read from 1r8sA/merged-good-all-a2m # found chain 1r8sA in training set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNA 1r8sA 19 :RILMVGLDAAGKTTILYKLKLGEI T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r8sA 43 :VTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQL 1r8sA 116 :LRDAVLLVFANKQDLPNAMNAAEITDK T0308 136 :IK 1r8sA 143 :LG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1r8sA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=13 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vg8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vg8A expands to /projects/compbio/data/pdb/1vg8.pdb.gz 1vg8A:Skipped atom 997, because occupancy 0.5 <= existing 0.500 in 1vg8A Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1vg8A Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1vg8A # T0308 read from 1vg8A/merged-good-all-a2m # 1vg8A read from 1vg8A/merged-good-all-a2m # adding 1vg8A to template set # found chain 1vg8A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1vg8A 1009 :LKVIILGDSGVGKTSLMNQYV T0308 24 :SNAQSQNILPTIG 1vg8A 1030 :NKKFSNQYKATIG T0308 37 :FSIEKFKSSS 1vg8A 1045 :FLTKEVMVDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1vg8A 1057 :VTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRD T0308 105 :RRIPILFFANKMDLRDA 1vg8A 1116 :ENFPFVVLGNKIDLENR T0308 126 :KVSQLLCLENIKD 1vg8A 1133 :QVATKRAQAWCYS T0308 139 :KPWHICASDAIKGEGLQEGVDWLQDQI 1vg8A 1147 :NNIPYFETSAKEAINVEQAFQTIARNA Number of specific fragments extracted= 7 number of extra gaps= 0 total=20 Number of alignments=4 # 1vg8A read from 1vg8A/merged-good-all-a2m # found chain 1vg8A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1vg8A 1009 :LKVIILGDSGVGKTSLMNQYVNKKF T0308 28 :SQNI 1vg8A 1034 :SNQY T0308 32 :LPTIGFSIEKFKSSS 1vg8A 1040 :TIGADFLTKEVMVDD T0308 47 :LSFTVFDMSGQGRY 1vg8A 1057 :VTMQIWDTAGQERF T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1vg8A 1076 :AFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASP T0308 103 :KHRRIPILFFANKMDLRDA 1vg8A 1114 :DPENFPFVVLGNKIDLENR T0308 126 :KVSQLLCLENIKDKP 1vg8A 1133 :QVATKRAQAWCYSKN T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1vg8A 1149 :IPYFETSAKEAINVEQAFQTIARNA Number of specific fragments extracted= 8 number of extra gaps= 0 total=28 Number of alignments=5 # 1vg8A read from 1vg8A/merged-good-all-a2m # found chain 1vg8A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1vg8A 1008 :LLKVIILGDSGVGKTSLMNQYVNKKF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIK 1vg8A 1037 :YKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPR T0308 104 :HRRIPILFFANKMDLRDAVTSV 1vg8A 1115 :PENFPFVVLGNKIDLENRQVAT T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1vg8A 1137 :KRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARN Number of specific fragments extracted= 4 number of extra gaps= 0 total=32 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xtqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xtqA expands to /projects/compbio/data/pdb/1xtq.pdb.gz 1xtqA:# T0308 read from 1xtqA/merged-good-all-a2m # 1xtqA read from 1xtqA/merged-good-all-a2m # adding 1xtqA to template set # found chain 1xtqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1xtqA 7 :RKIAILGYRSVGKSSLTIQFV T0308 24 :SNAQSQNILPTIG 1xtqA 28 :EGQFVDSYDPTIE T0308 37 :FSIEKFKSSS 1xtqA 42 :TFTKLITVNG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1xtqA 54 :YHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDM T0308 102 :IKHRRIPILFFANKMDLRDAV 1xtqA 107 :VGKVQIPIMLVGNKKDLHMER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1xtqA 128 :VISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=38 Number of alignments=7 # 1xtqA read from 1xtqA/merged-good-all-a2m # found chain 1xtqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1xtqA 7 :RKIAILGYRSVGKSSLTIQFVEGQF T0308 28 :SQNILPTI 1xtqA 32 :VDSYDPTI T0308 36 :GFSIEKFKSSS 1xtqA 41 :NTFTKLITVNG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1xtqA 54 :YHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGK T0308 105 :RRIPILFFANKMDLRDAV 1xtqA 110 :VQIPIMLVGNKKDLHMER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 1xtqA 128 :VISYEEGKALAESWNAAFLESSAKENQTAVDVFRRII Number of specific fragments extracted= 6 number of extra gaps= 0 total=44 Number of alignments=8 # 1xtqA read from 1xtqA/merged-good-all-a2m # found chain 1xtqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1xtqA 6 :SRKIAILGYRSVGKSSLTIQFVEGQF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1xtqA 34 :SYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVG T0308 104 :HRRIPILFFANKMDLRDAVTSV 1xtqA 109 :KVQIPIMLVGNKKDLHMERVIS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQ 1xtqA 131 :YEEGKALAESWNAAFLESSAKENQTAVDVFRRII Number of specific fragments extracted= 4 number of extra gaps= 0 total=48 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yzgA expands to /projects/compbio/data/pdb/1yzg.pdb.gz 1yzgA:# T0308 read from 1yzgA/merged-good-all-a2m # 1yzgA read from 1yzgA/merged-good-all-a2m # adding 1yzgA to template set # found chain 1yzgA in template set Warning: unaligning (T0308)A26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0308)Q27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzgA)V42 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSN 1yzgA 16 :EHKVIIVGLDNAGKTTILYQFLMNE T0308 28 :SQ 1yzgA 43 :HT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1yzgA 45 :SPTIGSNVEEIVVKNTHFLMWDIGGQESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDLRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 1yzgA 118 :AAVLIFANKQDMKGCMTAAEISKYLTLSSIKDHPWHIQSCCALTGEGLCQGLEWM Number of specific fragments extracted= 4 number of extra gaps= 1 total=52 Number of alignments=10 # 1yzgA read from 1yzgA/merged-good-all-a2m # found chain 1yzgA in template set Warning: unaligning (T0308)A26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0308)Q27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzgA)V42 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSN 1yzgA 16 :EHKVIIVGLDNAGKTTILYQFLMNE T0308 28 :SQN 1yzgA 43 :HTS T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1yzgA 46 :PTIGSNVEEIVVKNTHFLMWDIGGQESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDL T0308 105 :RRIPILFFANKMDLRDAV 1yzgA 116 :RKAAVLIFANKQDMKGCM T0308 128 :SQLLCLENIK 1yzgA 134 :TAAEISKYLT T0308 138 :DKPWHICASDAIKGEGLQEGVDWL 1yzgA 149 :DHPWHIQSCCALTGEGLCQGLEWM Number of specific fragments extracted= 6 number of extra gaps= 1 total=58 Number of alignments=11 # 1yzgA read from 1yzgA/merged-good-all-a2m # found chain 1yzgA in template set Warning: unaligning (T0308)A26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0308)Q27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzgA)V42 T0308 3 :HVLCLGLDNSGKTTIINKLKPSN 1yzgA 18 :KVIIVGLDNAGKTTILYQFLMNE T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1yzgA 43 :HTSPTIGSNVEEIVVKNTHFLMWDIGGQESLRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHED T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQ 1yzgA 115 :LRKAAVLIFANKQDMKGCMTAAEISK T0308 135 :NIK 1yzgA 141 :YLT T0308 138 :DKPWHICASDAIKGEGLQEGVDWL 1yzgA 149 :DHPWHIQSCCALTGEGLCQGLEWM Number of specific fragments extracted= 5 number of extra gaps= 1 total=63 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ukvY/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ukvY expands to /projects/compbio/data/pdb/1ukv.pdb.gz 1ukvY:Skipped atom 3755, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3757, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3759, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3761, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3763, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3765, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3775, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3777, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3779, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3781, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3783, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3785, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3787, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 3789, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4119, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4121, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4123, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4125, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4127, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4129, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4131, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4133, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4135, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4137, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4139, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4141, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4143, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4145, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4147, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4149, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4151, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4153, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4155, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4157, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4159, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4161, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4163, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4165, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4167, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4169, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4171, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4173, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4175, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4177, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4179, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4181, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4183, because occupancy 0.500 <= existing 0.500 in 1ukvY Skipped atom 4185, because occupancy 0.500 <= existing 0.500 in 1ukvY # T0308 read from 1ukvY/merged-good-all-a2m # 1ukvY read from 1ukvY/merged-good-all-a2m # adding 1ukvY to template set # found chain 1ukvY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1ukvY 9 :FKLLLIGNSGVGKSCLLLRFS T0308 24 :SNAQSQNILPTIG 1ukvY 30 :DDTYTNDYISTIG T0308 37 :FSIEKFKSSS 1ukvY 45 :FKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1ukvY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRY T0308 103 :KHRRIPILFFANKMDLRDAV 1ukvY 110 :ATSTVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ukvY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=69 Number of alignments=13 # 1ukvY read from 1ukvY/merged-good-all-a2m # found chain 1ukvY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ukvY 9 :FKLLLIGNSGVGKSCLLLRFSDDTY T0308 28 :SQNI 1ukvY 34 :TNDY T0308 32 :LPTIGFSIEKFKSSS 1ukvY 40 :TIGVDFKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ukvY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAV 1ukvY 112 :STVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ukvY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=75 Number of alignments=14 # 1ukvY read from 1ukvY/merged-good-all-a2m # found chain 1ukvY in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ukvY 8 :LFKLLLIGNSGVGKSCLLLRFSDDTY T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ukvY 37 :YISTIGVDFKIKTVELDGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAVTSV 1ukvY 112 :STVLKLLVGNKCDLKDKRVVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ukvY 133 :YDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 4 number of extra gaps= 0 total=79 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r4aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r4aA expands to /projects/compbio/data/pdb/1r4a.pdb.gz 1r4aA:# T0308 read from 1r4aA/merged-good-all-a2m # 1r4aA read from 1r4aA/merged-good-all-a2m # adding 1r4aA to template set # found chain 1r4aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQS 1r4aA 17 :EMRILILGLDGAGKTTILYRLQVGEVVT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1r4aA 45 :TIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r4aA 119 :AILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=82 Number of alignments=16 # 1r4aA read from 1r4aA/merged-good-all-a2m # found chain 1r4aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1r4aA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1r4aA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEEL T0308 105 :RRIPILFFANKMDLRDAV 1r4aA 117 :RKAILVVFANKQDMEQAM T0308 128 :SQLLCLENIK 1r4aA 135 :TPSEMANALG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1r4aA 150 :DRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=87 Number of alignments=17 # 1r4aA read from 1r4aA/merged-good-all-a2m # found chain 1r4aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1r4aA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r4aA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r4aA 116 :LRKAILVVFANKQDMEQAMTPSEMANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=90 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z2aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z2aA expands to /projects/compbio/data/pdb/1z2a.pdb.gz 1z2aA:# T0308 read from 1z2aA/merged-good-all-a2m # 1z2aA read from 1z2aA/merged-good-all-a2m # adding 1z2aA to template set # found chain 1z2aA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1z2aA 10 :IKMVVVGNGAVGKSSMIQRYC T0308 24 :SNAQSQNILPTIG 1z2aA 31 :KGIFTKDYKKTIG T0308 37 :FSIEKFKSSS 1z2aA 46 :FLERQIQVND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z2aA 58 :VRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAE T0308 103 :K 1z2aA 111 :V T0308 105 :RRIPILFFANKMDLRDAV 1z2aA 112 :GDIPTALVQNKIDLLDDS T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1z2aA 130 :CIKNEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=97 Number of alignments=19 # 1z2aA read from 1z2aA/merged-good-all-a2m # found chain 1z2aA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1z2aA 10 :IKMVVVGNGAVGKSSMIQRYCKGIFTKDYK T0308 32 :LPTIGFSIEKFKSSS 1z2aA 41 :TIGVDFLERQIQVND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1z2aA 58 :VRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEV T0308 105 :RRIPILFFANKMDLRDAV 1z2aA 112 :GDIPTALVQNKIDLLDDS T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1z2aA 130 :CIKNEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=102 Number of alignments=20 # 1z2aA read from 1z2aA/merged-good-all-a2m # found chain 1z2aA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1z2aA 9 :AIKMVVVGNGAVGKSSMIQRYCKGIF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z2aA 38 :YKKTIGVDFLERQIQVNDEDVRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEVG T0308 106 :RIPILFFANKMDLRDAVTSV 1z2aA 113 :DIPTALVQNKIDLLDDSCIK T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 1z2aA 133 :NEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=106 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fn4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fn4A expands to /projects/compbio/data/pdb/2fn4.pdb.gz 2fn4A:Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2fn4A Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2fn4A # T0308 read from 2fn4A/merged-good-all-a2m # 2fn4A read from 2fn4A/merged-good-all-a2m # adding 2fn4A to template set # found chain 2fn4A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 2fn4A 30 :HKLVVVGGGGVGKSALTIQFI T0308 24 :SNAQSQNILPTIG 2fn4A 51 :QSYFVSDYDPTIE T0308 37 :FSIEKFKSSS 2fn4A 65 :SYTKICSVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2fn4A 77 :ARLDILDTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 2fn4A 130 :KDRDDFPVVLVGNKADLESQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2fn4A 151 :QVPRSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRAV Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 Number of alignments=22 # 2fn4A read from 2fn4A/merged-good-all-a2m # found chain 2fn4A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2fn4A 30 :HKLVVVGGGGVGKSALTIQFIQSYF T0308 28 :SQNILPTI 2fn4A 55 :VSDYDPTI T0308 36 :GFSIEKFKSSS 2fn4A 64 :DSYTKICSVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2fn4A 77 :ARLDILDTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDR T0308 105 :RRIPILFFANKMDLRDAV 2fn4A 133 :DDFPVVLVGNKADLESQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2fn4A 151 :QVPRSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRAV Number of specific fragments extracted= 6 number of extra gaps= 0 total=118 Number of alignments=23 # 2fn4A read from 2fn4A/merged-good-all-a2m # found chain 2fn4A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2fn4A 29 :THKLVVVGGGGVGKSALTIQFIQSYF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2fn4A 57 :DYDPTIEDSYTKICSVDGIPARLDILDTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 2fn4A 132 :RDDFPVVLVGNKADLESQRQVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 2fn4A 154 :RSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=122 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kshA expands to /projects/compbio/data/pdb/1ksh.pdb.gz 1kshA:Skipped atom 280, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 282, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 284, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 286, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 288, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 290, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 292, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1099, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1101, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1150, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1152, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1154, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1156, because occupancy 0.300 <= existing 0.700 in 1kshA # T0308 read from 1kshA/merged-good-all-a2m # 1kshA read from 1kshA/merged-good-all-a2m # adding 1kshA to template set # found chain 1kshA in template set Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kshA)N136 Warning: unaligning (T0308)V125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kshA)N136 T0308 1 :EVHVLCLGLDNSGKTTIINKL 1kshA 16 :ELRLLMLGLDNAGKTTILKKF T0308 24 :SNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1kshA 37 :NGEDVDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAG T0308 107 :IPILFFANKMDLRDAV 1kshA 118 :ATLLIFANKQDLPGAL T0308 126 :KVSQL 1kshA 137 :AIQEA T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1kshA 145 :DSIRSHHWRIQGCSAVTGEDLLPGIDWLLDDI Number of specific fragments extracted= 5 number of extra gaps= 0 total=127 Number of alignments=25 # 1kshA read from 1kshA/merged-good-all-a2m # found chain 1kshA in template set Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kshA)N136 Warning: unaligning (T0308)L130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kshA)N136 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSN 1kshA 16 :ELRLLMLGLDNAGKTTILKKFNGED T0308 28 :SQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1kshA 41 :VDTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERL T0308 105 :RRIPILFFANKMDLRDA 1kshA 116 :AGATLLIFANKQDLPGA T0308 127 :V 1kshA 133 :L T0308 131 :LCLENIK 1kshA 137 :AIQEALE T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1kshA 149 :SHHWRIQGCSAVTGEDLLPGIDWLLDDI Number of specific fragments extracted= 6 number of extra gaps= 0 total=133 Number of alignments=26 # 1kshA read from 1kshA/merged-good-all-a2m # found chain 1kshA in template set Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kshA)N136 Warning: unaligning (T0308)V125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kshA)N136 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1kshA 16 :ELRLLMLGLDNAGKTTILKKFNGEDV T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1kshA 42 :DTISPTLGFNIKTLEHRGFKLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEER T0308 104 :HRRIPILFFANKMDLRDAV 1kshA 115 :LAGATLLIFANKQDLPGAL T0308 126 :KVSQ 1kshA 137 :AIQE T0308 135 :NIK 1kshA 141 :ALE T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1kshA 149 :SHHWRIQGCSAVTGEDLLPGIDWLLDDI Number of specific fragments extracted= 6 number of extra gaps= 0 total=139 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1byuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1byuA expands to /projects/compbio/data/pdb/1byu.pdb.gz 1byuA:# T0308 read from 1byuA/merged-good-all-a2m # 1byuA read from 1byuA/merged-good-all-a2m # adding 1byuA to template set # found chain 1byuA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1byuA)E46 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1byuA)E46 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1byuA 11 :FKLVLVGDGGTGKTTFVKRHL T0308 24 :SNAQ 1byuA 36 :EKKY T0308 32 :LPTIG 1byuA 40 :VPTLG T0308 39 :IEKFKS 1byuA 47 :VHPLVF T0308 45 :SS 1byuA 55 :NR T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1byuA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRV T0308 105 :RRIPILFFANKMDLRDAVTSVKVSQLL 1byuA 113 :ENIPIVLCGNKVDIKDRKVKAKSIVFH T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQI 1byuA 140 :RKKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 8 number of extra gaps= 1 total=147 Number of alignments=28 # 1byuA read from 1byuA/merged-good-all-a2m # found chain 1byuA in template set Warning: unaligning (T0308)I35 because of BadResidue code BAD_PEPTIDE in next template residue (1byuA)E46 Warning: unaligning (T0308)G36 because of BadResidue code BAD_PEPTIDE at template residue (1byuA)E46 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1byuA 11 :FKLVLVGDGGTGKTTFVKRHLTGEFEKKYV T0308 32 :LPT 1byuA 42 :TLG T0308 37 :FSIEKFKSSS 1byuA 47 :VHPLVFHTNR T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1byuA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC T0308 105 :RRIPILFFANKMDLRDAVTSVKVSQLLC 1byuA 113 :ENIPIVLCGNKVDIKDRKVKAKSIVFHR T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1byuA 141 :KKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 6 number of extra gaps= 1 total=153 Number of alignments=29 # 1byuA read from 1byuA/merged-good-all-a2m # found chain 1byuA in template set Warning: unaligning (T0308)P33 because of BadResidue code BAD_PEPTIDE in next template residue (1byuA)E46 Warning: unaligning (T0308)T34 because of BadResidue code BAD_PEPTIDE at template residue (1byuA)E46 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1byuA 10 :QFKLVLVGDGGTGKTTFVKRHLTGEF T0308 27 :QSQNIL 1byuA 39 :YVPTLG T0308 35 :IGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1byuA 47 :VHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE T0308 106 :RIPILFFANKMDLRD 1byuA 114 :NIPIVLCGNKVDIKD T0308 121 :AVTS 1byuA 133 :AKSI T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1byuA 137 :VFHRKKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 6 number of extra gaps= 1 total=159 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z0jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z0jA expands to /projects/compbio/data/pdb/1z0j.pdb.gz 1z0jA:# T0308 read from 1z0jA/merged-good-all-a2m # 1z0jA read from 1z0jA/merged-good-all-a2m # adding 1z0jA to template set # found chain 1z0jA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1z0jA 5 :ELKVCLLGDTGVGKSSIMWRFV T0308 24 :SNAQSQNILPTIG 1z0jA 27 :EDSFDPNINPTIG T0308 37 :FSIEKFKSSS 1z0jA 42 :FMTKTVQYQN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z0jA 54 :HKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQH T0308 103 :KHRRIPILFFANKMDLRDAV 1z0jA 107 :GPPSIVVAIAGNKCDLTDVR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z0jA 127 :EVMERDAKDYADSIHAIFVETSAKNAININELFIEISRRI Number of specific fragments extracted= 6 number of extra gaps= 0 total=165 Number of alignments=31 # 1z0jA read from 1z0jA/merged-good-all-a2m # found chain 1z0jA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1z0jA 6 :LKVCLLGDTGVGKSSIMWRFVEDSF T0308 28 :SQNI 1z0jA 31 :DPNI T0308 32 :LPTIGFSIEKFKSSS 1z0jA 37 :TIGASFMTKTVQYQN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z0jA 54 :HKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGP T0308 105 :RRIPILFFANKMDLRDAV 1z0jA 109 :PSIVVAIAGNKCDLTDVR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z0jA 127 :EVMERDAKDYADSIHAIFVETSAKNAININELFIEISRRI Number of specific fragments extracted= 6 number of extra gaps= 0 total=171 Number of alignments=32 # 1z0jA read from 1z0jA/merged-good-all-a2m # found chain 1z0jA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1z0jA 5 :ELKVCLLGDTGVGKSSIMWRFVEDSF T0308 27 :QSQNILPTIGFSIEKFKSSS 1z0jA 32 :PNINPTIGASFMTKTVQYQN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z0jA 54 :HKFLIWDTAGLERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVRELRQHGP T0308 105 :RRIPILFFANKMDLRDAVTSV 1z0jA 109 :PSIVVAIAGNKCDLTDVREVM T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z0jA 130 :ERDAKDYADSIHAIFVETSAKNAININELFIEISRRI Number of specific fragments extracted= 5 number of extra gaps= 0 total=176 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2erxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2erxA expands to /projects/compbio/data/pdb/2erx.pdb.gz 2erxA:Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2erxA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2erxA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2erxA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2erxA # T0308 read from 2erxA/merged-good-all-a2m # 2erxA read from 2erxA/merged-good-all-a2m # adding 2erxA to template set # found chain 2erxA in template set Warning: unaligning (T0308)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2erxA)S113 Warning: unaligning (T0308)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2erxA)S113 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2erxA 8 :YRVAVFGAGGVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 2erxA 29 :KGTFRESYIPTVE T0308 37 :FSIEKFKSSS 2erxA 43 :TYRQVISCDK T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 2erxA 55 :CTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK T0308 107 :IPILFFANKMDLRDAV 2erxA 114 :IPIMLVGNKCDESPSR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2erxA 130 :EVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=182 Number of alignments=34 # 2erxA read from 2erxA/merged-good-all-a2m # found chain 2erxA in template set Warning: unaligning (T0308)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2erxA)S113 Warning: unaligning (T0308)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2erxA)S113 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2erxA 8 :YRVAVFGAGGVGKSSLVLRFVKGTF T0308 28 :SQNILPTI 2erxA 33 :RESYIPTV T0308 36 :GFSIEKFKSSS 2erxA 42 :DTYRQVISCDK T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 2erxA 55 :CTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK T0308 107 :IPILFFANKMDLRDAV 2erxA 114 :IPIMLVGNKCDESPSR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2erxA 130 :EVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=188 Number of alignments=35 # 2erxA read from 2erxA/merged-good-all-a2m # found chain 2erxA in template set Warning: unaligning (T0308)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2erxA)S113 Warning: unaligning (T0308)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2erxA)S113 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSS 2erxA 7 :DYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISCDK T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 2erxA 55 :CTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK T0308 107 :IPILFFANKMDLRDAVTSV 2erxA 114 :IPIMLVGNKCDESPSREVQ T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQ 2erxA 133 :SSEAEALARTWKCAFMETSAKLNHNVKELFQELLNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=192 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gf9A expands to /projects/compbio/data/pdb/2gf9.pdb.gz 2gf9A:Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1410, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1414, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1418, because occupancy 0.500 <= existing 0.500 in 2gf9A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2gf9A # T0308 read from 2gf9A/merged-good-all-a2m # 2gf9A read from 2gf9A/merged-good-all-a2m # adding 2gf9A to template set # found chain 2gf9A in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf9A)E163 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf9A)E163 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2gf9A 23 :FKLLLIGNSSVGKTSFLFRYA T0308 24 :SNAQSQNILPTIG 2gf9A 44 :DDSFTPAFVSTVG T0308 37 :FSIEKFKSSS 2gf9A 59 :FKVKTVYRHD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2gf9A 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTY T0308 103 :KHRRIPILFFANKMDLRDAV 2gf9A 124 :SWDNAQVILVGNKCDLEDER T0308 126 :KVSQLLCLENIKDKPWHI 2gf9A 144 :VVPAEDGRRLADDLGFEF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2gf9A 164 :ASAKENINVKQVFERLVDVI Number of specific fragments extracted= 7 number of extra gaps= 1 total=199 Number of alignments=37 # 2gf9A read from 2gf9A/merged-good-all-a2m # found chain 2gf9A in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf9A)E163 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf9A)E163 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 2gf9A 23 :FKLLLIGNSSVGKTSFLFRYADDSFTPAFV T0308 32 :LPTIGFSIEKFKSSS 2gf9A 54 :TVGIDFKVKTVYRHD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2gf9A 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSW T0308 105 :RRIPILFFANKMDLRDAV 2gf9A 126 :DNAQVILVGNKCDLEDER T0308 126 :KVSQLLCLENIKDKPWHI 2gf9A 144 :VVPAEDGRRLADDLGFEF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2gf9A 164 :ASAKENINVKQVFERLVDVI Number of specific fragments extracted= 6 number of extra gaps= 1 total=205 Number of alignments=38 # 2gf9A read from 2gf9A/merged-good-all-a2m # found chain 2gf9A in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf9A)E163 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf9A)E163 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2gf9A 22 :MFKLLLIGNSSVGKTSFLFRYADDSF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2gf9A 51 :FVSTVGIDFKVKTVYRHDKRIKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQIKTYSW T0308 105 :RRIPILFFANKMDLRDAVTSV 2gf9A 126 :DNAQVILVGNKCDLEDERVVP T0308 129 :QLLCLENIKDKPWHI 2gf9A 147 :AEDGRRLADDLGFEF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2gf9A 164 :ASAKENINVKQVFERLVDVI Number of specific fragments extracted= 5 number of extra gaps= 1 total=210 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g6bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g6bA expands to /projects/compbio/data/pdb/2g6b.pdb.gz 2g6bA:Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 2g6bA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 2g6bA # T0308 read from 2g6bA/merged-good-all-a2m # 2g6bA read from 2g6bA/merged-good-all-a2m # adding 2g6bA to template set # found chain 2g6bA in template set Warning: unaligning (T0308)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6bA)A132 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6bA)A132 Warning: unaligning (T0308)V77 because of BadResidue code BAD_PEPTIDE in next template residue (2g6bA)Y144 Warning: unaligning (T0308)I78 because of BadResidue code BAD_PEPTIDE at template residue (2g6bA)Y144 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIG 2g6bA 64 :FKVMLVGDSGVGKTCLLVRFKDGAFLAGTFISTVG T0308 37 :FSIEKFKSSS 2g6bA 101 :FRNKVLDVDG T0308 47 :LSFTVFDMSG 2g6bA 113 :VKLQMWDTAG T0308 67 :YYKEGQAIIF 2g6bA 133 :YYRDAHALLL T0308 79 :DSSDRLRMVVAKEELDTLLNH 2g6bA 145 :DVTNKASFDNIQAWLTEIHEY T0308 103 :KHRRIPILFFANKMDLRDAV 2g6bA 166 :AQHDVALMLLGNKVDSAHER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2g6bA 186 :VVKREDGEKLAKEYGLPFMETSAKTGLNVDLAFTAIAKEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=217 Number of alignments=40 # 2g6bA read from 2g6bA/merged-good-all-a2m # found chain 2g6bA in template set Warning: unaligning (T0308)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6bA)A132 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6bA)A132 Warning: unaligning (T0308)V77 because of BadResidue code BAD_PEPTIDE in next template residue (2g6bA)Y144 Warning: unaligning (T0308)I78 because of BadResidue code BAD_PEPTIDE at template residue (2g6bA)Y144 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 2g6bA 64 :FKVMLVGDSGVGKTCLLVRFKDGAFLAGTF T0308 32 :LPTIGFSIEKFKSSS 2g6bA 96 :TVGIDFRNKVLDVDG T0308 47 :LSFTVFDMSG 2g6bA 113 :VKLQMWDTAG T0308 67 :YYKEGQAIIF 2g6bA 133 :YYRDAHALLL T0308 79 :DSSDRLRMVVAKEELDTLLNHPD 2g6bA 145 :DVTNKASFDNIQAWLTEIHEYAQ T0308 105 :RRIPILFFANKMDLRDAV 2g6bA 168 :HDVALMLLGNKVDSAHER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2g6bA 186 :VVKREDGEKLAKEYGLPFMETSAKTGLNVDLAFTAIAKEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=224 Number of alignments=41 # 2g6bA read from 2g6bA/merged-good-all-a2m # found chain 2g6bA in template set Warning: unaligning (T0308)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g6bA)A132 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g6bA)A132 Warning: unaligning (T0308)V77 because of BadResidue code BAD_PEPTIDE in next template residue (2g6bA)Y144 Warning: unaligning (T0308)I78 because of BadResidue code BAD_PEPTIDE at template residue (2g6bA)Y144 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2g6bA 63 :AFKVMLVGDSGVGKTCLLVRFKDGAF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSG 2g6bA 93 :FISTVGIDFRNKVLDVDGVKVKLQMWDTAG T0308 67 :YYKEGQAIIF 2g6bA 133 :YYRDAHALLL T0308 79 :DSSDRLRMVVAKEELDTLLNHPD 2g6bA 145 :DVTNKASFDNIQAWLTEIHEYAQ T0308 105 :RRIPILFFANKMDLRDAVTSV 2g6bA 168 :HDVALMLLGNKVDSAHERVVK T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2g6bA 189 :REDGEKLAKEYGLPFMETSAKTGLNVDLAFTAIAKEL Number of specific fragments extracted= 6 number of extra gaps= 1 total=230 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1agp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1agp expands to /projects/compbio/data/pdb/1agp.pdb.gz 1agp:Warning: there is no chain 1agp will retry with 1agpA # T0308 read from 1agp/merged-good-all-a2m # 1agp read from 1agp/merged-good-all-a2m # adding 1agp to template set # found chain 1agp in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1agp 3 :EYKLVVVGADGVGKSALTIQLI T0308 24 :SNAQSQNILPTIG 1agp 25 :QNHFVDEYDPTIE T0308 37 :FSIEKFKSSS 1agp 39 :SYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1agp 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1agp 104 :KDSDDVPMVLVGNKCDLAART T0308 127 :VSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1agp 125 :VESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=236 Number of alignments=43 # 1agp read from 1agp/merged-good-all-a2m # found chain 1agp in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1agp 4 :YKLVVVGADGVGKSALTIQLIQNHF T0308 28 :SQNILPTI 1agp 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 1agp 38 :DSYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1agp 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDS T0308 105 :RRIPILFFANKMDLRDA 1agp 107 :DDVPMVLVGNKCDLAAR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1agp 124 :TVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=242 Number of alignments=44 # 1agp read from 1agp/merged-good-all-a2m # found chain 1agp in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1agp 3 :EYKLVVVGADGVGKSALTIQLIQNHF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1agp 31 :EYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 1agp 106 :SDDVPMVLVGNKCDLAARTVES T0308 130 :LLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1agp 128 :RQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 4 number of extra gaps= 0 total=246 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fzqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fzqA expands to /projects/compbio/data/pdb/1fzq.pdb.gz 1fzqA:Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 426, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 1fzqA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 1fzqA # T0308 read from 1fzqA/merged-good-all-a2m # 1fzqA read from 1fzqA/merged-good-all-a2m # adding 1fzqA to template set # found chain 1fzqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1fzqA 17 :EVRILLLGLDNAGKTTLLKQLASEDISHI T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1fzqA 46 :TPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSC T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1fzqA 119 :VPVLIFANKQDLLTAAPASEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNV Number of specific fragments extracted= 3 number of extra gaps= 0 total=249 Number of alignments=46 # 1fzqA read from 1fzqA/merged-good-all-a2m # found chain 1fzqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1fzqA 17 :EVRILLLGLDNAGKTTLLKQLASEDI T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1fzqA 43 :SHITPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKL T0308 105 :RRIPILFFANKMDLRDAV 1fzqA 117 :SCVPVLIFANKQDLLTAA T0308 128 :SQLLCLENIK 1fzqA 135 :PASEIAEGLN T0308 140 :P 1fzqA 147 :T T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1fzqA 153 :WQIQSCSALTGEGVQDGMNWVCKNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=255 Number of alignments=47 # 1fzqA read from 1fzqA/merged-good-all-a2m # found chain 1fzqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1fzqA 17 :EVRILLLGLDNAGKTTLLKQLASEDI T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1fzqA 44 :HITPTQGFNIKSVQSQGFKLNVWDIGGQRKIRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEK T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQL 1fzqA 116 :LSCVPVLIFANKQDLLTAAPASEIAEG T0308 136 :I 1fzqA 143 :L T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQI 1fzqA 149 :RDRVWQIQSCSALTGEGVQDGMNWVCKNV Number of specific fragments extracted= 5 number of extra gaps= 0 total=260 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky3A expands to /projects/compbio/data/pdb/1ky3.pdb.gz 1ky3A:Skipped atom 307, because occupancy 0.320 <= existing 0.680 in 1ky3A Skipped atom 309, because occupancy 0.320 <= existing 0.680 in 1ky3A Skipped atom 311, because occupancy 0.320 <= existing 0.680 in 1ky3A # T0308 read from 1ky3A/merged-good-all-a2m # 1ky3A read from 1ky3A/merged-good-all-a2m # adding 1ky3A to template set # found chain 1ky3A in template set Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky3A)I41 Warning: unaligning (T0308)I35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)I41 Warning: unaligning (T0308)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)D53 Warning: unaligning (T0308)S45 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D53 Warning: unaligning (T0308)S46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ky3A)G54 Warning: unaligning (T0308)M54 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)A66 Warning: unaligning (T0308)S55 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)A66 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)A77 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1ky3A 9 :LKVIILGDSGVGKTSLMHRYV T0308 24 :SNAQSQN 1ky3A 30 :NDKYSQQ T0308 36 :G 1ky3A 42 :G T0308 37 :FSIEKFK 1ky3A 45 :FLTKEVT T0308 47 :LSFTVFD 1ky3A 58 :ATMQVWD T0308 67 :YYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1ky3A 78 :FYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANV T0308 103 :KHRRIPILFFANKMDLRDAVT 1ky3A 115 :SPETFPFVILGNKIDAEESKK T0308 126 :KVSQLLCLENIKDK 1ky3A 136 :IVSEKSAQELAKSL T0308 140 :PWHICASDAIKGEGLQEGVDWLQDQ 1ky3A 151 :DIPLFLTSAKNAINVDTAFEEIARS Number of specific fragments extracted= 9 number of extra gaps= 2 total=269 Number of alignments=49 # 1ky3A read from 1ky3A/merged-good-all-a2m # found chain 1ky3A in template set Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky3A)I41 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)I41 Warning: unaligning (T0308)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)D53 Warning: unaligning (T0308)S45 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D53 Warning: unaligning (T0308)S46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ky3A)G54 Warning: unaligning (T0308)M54 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)A66 Warning: unaligning (T0308)S55 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)A66 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)A77 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ky3A 9 :LKVIILGDSGVGKTSLMHRYVNDKY T0308 28 :SQN 1ky3A 34 :SQQ T0308 34 :TIGFSIEKFK 1ky3A 42 :GADFLTKEVT T0308 47 :LSFTVFD 1ky3A 58 :ATMQVWD T0308 67 :YYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1ky3A 78 :FYRGADCCVLVYDVTNASSFENIKSWRDEFLVHANV T0308 103 :KHRRIPILFFANKMDLRDAVT 1ky3A 115 :SPETFPFVILGNKIDAEESKK T0308 126 :KVSQLLCLENIKDKP 1ky3A 136 :IVSEKSAQELAKSLG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1ky3A 152 :IPLFLTSAKNAINVDTAFEEIARS Number of specific fragments extracted= 8 number of extra gaps= 2 total=277 Number of alignments=50 # 1ky3A read from 1ky3A/merged-good-all-a2m # found chain 1ky3A in template set Warning: unaligning (T0308)Q27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky3A)I41 Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)I41 Warning: unaligning (T0308)F42 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)D53 Warning: unaligning (T0308)K43 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D53 Warning: unaligning (T0308)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ky3A)G54 Warning: unaligning (T0308)S45 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)D55 Warning: unaligning (T0308)S46 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)K56 Warning: unaligning (T0308)M54 because of BadResidue code BAD_PEPTIDE in next template residue (1ky3A)A66 Warning: unaligning (T0308)S55 because of BadResidue code BAD_PEPTIDE at template residue (1ky3A)A66 Warning: unaligning (T0308)H66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky3A)A77 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ky3A 8 :ILKVIILGDSGVGKTSLMHRYVNDKY T0308 32 :LPTIGFSIEK 1ky3A 42 :GADFLTKEVT T0308 47 :LSFTVFD 1ky3A 58 :ATMQVWD T0308 67 :YYKEGQAIIFVIDSSDRLRMVVAKEELDTLL 1ky3A 78 :FYRGADCCVLVYDVTNASSFENIKSWRDEFL T0308 98 :NHPD 1ky3A 112 :NVNS T0308 104 :HRRIPILFFANKMDLRDAVTSVK 1ky3A 116 :PETFPFVILGNKIDAEESKKIVS T0308 129 :QLLCLENI 1ky3A 139 :EKSAQELA T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQ 1ky3A 148 :SLGDIPLFLTSAKNAINVDTAFEEIARS Number of specific fragments extracted= 8 number of extra gaps= 2 total=285 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1guaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1guaA expands to /projects/compbio/data/pdb/1gua.pdb.gz 1guaA:# T0308 read from 1guaA/merged-good-all-a2m # 1guaA read from 1guaA/merged-good-all-a2m # adding 1guaA to template set # found chain 1guaA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1guaA 3 :EYKLVVLGSGGVGKSALTVQFV T0308 24 :SNAQSQNILPTIG 1guaA 25 :QGIFVDEYDPTIE T0308 37 :FSIEKFKSSS 1guaA 39 :SYRKQVEVDC T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1guaA 51 :CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1guaA 104 :KDTEDVPMILVGNKCDLEDER T0308 126 :KVSQLLCLENIKD 1guaA 125 :VVGKEQGQNLARQ T0308 139 :KPWHICASDAIKGEGLQEGVDWLQDQI 1guaA 139 :CNCAFLESSAKSKINVNEIFYDLVRQI Number of specific fragments extracted= 7 number of extra gaps= 0 total=292 Number of alignments=52 # 1guaA read from 1guaA/merged-good-all-a2m # found chain 1guaA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1guaA 4 :YKLVVLGSGGVGKSALTVQFVQGIF T0308 28 :SQNILPTI 1guaA 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 1guaA 38 :DSYRKQVEVDC T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1guaA 51 :CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDT T0308 105 :RRIPILFFANKMDLRDAV 1guaA 107 :EDVPMILVGNKCDLEDER T0308 126 :KVSQLLCLENIKDKP 1guaA 125 :VVGKEQGQNLARQWC T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1guaA 141 :CAFLESSAKSKINVNEIFYDLVRQI Number of specific fragments extracted= 7 number of extra gaps= 0 total=299 Number of alignments=53 # 1guaA read from 1guaA/merged-good-all-a2m # found chain 1guaA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1guaA 3 :EYKLVVLGSGGVGKSALTVQFVQGIF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1guaA 31 :EYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 1guaA 106 :TEDVPMILVGNKCDLEDERVVG T0308 129 :QLLCLENIKD 1guaA 128 :KEQGQNLARQ T0308 139 :KPWHICASDAIKGEGLQEGVDWLQDQI 1guaA 139 :CNCAFLESSAKSKINVNEIFYDLVRQI Number of specific fragments extracted= 5 number of extra gaps= 0 total=304 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yzqA expands to /projects/compbio/data/pdb/1yzq.pdb.gz 1yzqA:# T0308 read from 1yzqA/merged-good-all-a2m # 1yzqA read from 1yzqA/merged-good-all-a2m # adding 1yzqA to template set # found chain 1yzqA in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1yzqA)F14 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzqA)S156 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzqA)S156 T0308 3 :HVLCLGLDNSGKTTIINKLK 1yzqA 15 :KLVFLGEQSVGKTSLITRFM T0308 24 :SNAQSQNILPTIG 1yzqA 35 :YDSFDNTYQATIG T0308 37 :FSIEKFKSSS 1yzqA 50 :FLSKTMYLED T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1yzqA 62 :IRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTE T0308 103 :KHRRIPILFFANKMDLRDAV 1yzqA 115 :RGSDVIIMLVGNKTDLADKR T0308 126 :KVSQLLCLENIKDKPWHICA 1yzqA 135 :QVSIEEGERKAKELNVMFIE T0308 148 :AIKGEGLQEGVDWLQDQI 1yzqA 157 :AKAGYNVKQLFRRVAAAL Number of specific fragments extracted= 7 number of extra gaps= 1 total=311 Number of alignments=55 # 1yzqA read from 1yzqA/merged-good-all-a2m # found chain 1yzqA in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1yzqA)F14 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzqA)S156 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzqA)S156 T0308 3 :HVLCLGLDNSGKTTIINKLKPSNAQSQNI 1yzqA 15 :KLVFLGEQSVGKTSLITRFMYDSFDNTYQ T0308 32 :LPTIGFSIEKFKSSS 1yzqA 45 :TIGIDFLSKTMYLED T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1yzqA 62 :IRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERG T0308 105 :RRIPILFFANKMDLRDAV 1yzqA 117 :SDVIIMLVGNKTDLADKR T0308 126 :KVSQLLCLENIKDKPWHICA 1yzqA 135 :QVSIEEGERKAKELNVMFIE T0308 148 :AIKGEGLQEGVDWLQDQI 1yzqA 157 :AKAGYNVKQLFRRVAAAL Number of specific fragments extracted= 6 number of extra gaps= 1 total=317 Number of alignments=56 # 1yzqA read from 1yzqA/merged-good-all-a2m # found chain 1yzqA in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1yzqA)F14 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yzqA)S156 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yzqA)S156 T0308 3 :HVLCLGLDNSGKTTIINKLKPSNA 1yzqA 15 :KLVFLGEQSVGKTSLITRFMYDSF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1yzqA 42 :YQATIGIDFLSKTMYLEDRTIRLQLWDTAGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERG T0308 105 :RRIPILFFANKMDLRDAVTSV 1yzqA 117 :SDVIIMLVGNKTDLADKRQVS T0308 129 :QLLCLENIKDKPWHICA 1yzqA 138 :IEEGERKAKELNVMFIE T0308 148 :AIKGEGLQEGVDWLQDQI 1yzqA 157 :AKAGYNVKQLFRRVAAAL Number of specific fragments extracted= 5 number of extra gaps= 1 total=322 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mr3F/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mr3F expands to /projects/compbio/data/pdb/1mr3.pdb.gz 1mr3F:Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 324, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 326, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 328, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 330, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 332, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 334, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 336, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 360, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 361, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 363, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 364, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 366, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 367, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 369, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 370, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 372, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 373, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 375, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 376, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 378, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 379, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 428, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 430, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 432, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 434, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 436, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 438, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 440, because occupancy 0.330 <= existing 0.330 in 1mr3F Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1mr3F Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1mr3F # T0308 read from 1mr3F/merged-good-all-a2m # 1mr3F read from 1mr3F/merged-good-all-a2m # adding 1mr3F to template set # found chain 1mr3F in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1mr3F 17 :EMRILMVGLDGAGKTTVLYKLKLGEVITT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1mr3F 46 :IPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDELRN T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1mr3F 119 :AVWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQSTCATSGEGLYEGLEWLSNNL Number of specific fragments extracted= 3 number of extra gaps= 0 total=325 Number of alignments=58 # 1mr3F read from 1mr3F/merged-good-all-a2m # found chain 1mr3F in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1mr3F 17 :EMRILMVGLDGAGKTTVLYKLKLGEVITT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1mr3F 46 :IPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDEL T0308 105 :RRIPILFFANKMDLRDAV 1mr3F 117 :RNAVWLVFANKQDLPEAM T0308 128 :SQLLCLENIK 1mr3F 135 :SAAEITEKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1mr3F 150 :NRPWFIQSTCATSGEGLYEGLEWLSNNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=330 Number of alignments=59 # 1mr3F read from 1mr3F/merged-good-all-a2m # found chain 1mr3F in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 1mr3F 18 :MRILMVGLDGAGKTTVLYKLKLGEVI T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1mr3F 44 :TTIPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRHYYRNTEGVIFVIDSNDRSRIGEAREVMQRMLNEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1mr3F 116 :LRNAVWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQSTCATSGEGLYEGLEWLSNNL Number of specific fragments extracted= 3 number of extra gaps= 0 total=333 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf3A expands to /projects/compbio/data/pdb/1nf3.pdb.gz 1nf3A:# T0308 read from 1nf3A/merged-good-all-a2m # 1nf3A read from 1nf3A/merged-good-all-a2m # adding 1nf3A to template set # found chain 1nf3A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1nf3A 4 :IKCVVVGDGAVGKTCLLISYT T0308 24 :SNAQSQNILPTIG 1nf3A 25 :TNKFPSEYVPTVF T0308 37 :FSIEKFKSSS 1nf3A 39 :NYAVTVMIGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1nf3A 51 :YTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE T0308 92 :ELDTLLNH 1nf3A 97 :WVPEITHH T0308 104 :HRRIPILFFANKMDLRDAVTSVK 1nf3A 105 :CPKTPFLLVGTQIDLRDDPSTIE T0308 127 :VSQLLCLENIKDKPWH 1nf3A 137 :ITPETAEKLARDLKAV T0308 143 :ICASDAIKGEGLQEGVDWLQDQ 1nf3A 154 :YVECSALTQKGLKNVFDEAILA Number of specific fragments extracted= 8 number of extra gaps= 0 total=341 Number of alignments=61 # 1nf3A read from 1nf3A/merged-good-all-a2m # found chain 1nf3A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1nf3A 4 :IKCVVVGDGAVGKTCLLISYTTNKF T0308 28 :SQNILPTI 1nf3A 29 :PSEYVPTV T0308 36 :GFSIEKFKSSS 1nf3A 38 :DNYAVTVMIGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1nf3A 51 :YTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE T0308 92 :ELDTLLNHP 1nf3A 97 :WVPEITHHC T0308 105 :RRIPILFFANKMDLRDAVTSVK 1nf3A 106 :PKTPFLLVGTQIDLRDDPSTIE T0308 127 :VSQLLCLENIKDKP 1nf3A 137 :ITPETAEKLARDLK T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1nf3A 152 :VKYVECSALTQKGLKNVFDEAILA Number of specific fragments extracted= 8 number of extra gaps= 0 total=349 Number of alignments=62 # 1nf3A read from 1nf3A/merged-good-all-a2m # found chain 1nf3A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQNILPTIGFSIEKFKSSS 1nf3A 3 :TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1nf3A 51 :YTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKE T0308 92 :ELDTLLNHPD 1nf3A 97 :WVPEITHHCP T0308 106 :RIPILFFANKMDLRDAVTSVK 1nf3A 107 :KTPFLLVGTQIDLRDDPSTIE T0308 127 :VSQLLCLENIKDKPW 1nf3A 137 :ITPETAEKLARDLKA T0308 142 :HICASDAIKGEGLQEGVDWLQD 1nf3A 153 :KYVECSALTQKGLKNVFDEAIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=355 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x1rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x1rA expands to /projects/compbio/data/pdb/1x1r.pdb.gz 1x1rA:# T0308 read from 1x1rA/merged-good-all-a2m # 1x1rA read from 1x1rA/merged-good-all-a2m # adding 1x1rA to template set # found chain 1x1rA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1x1rA 14 :YKLVVVGDGGVGKSALTIQFF T0308 24 :SNAQSQNILPTIG 1x1rA 35 :QKIFVPDYDPTIE T0308 37 :FSIEKFKSSS 1x1rA 49 :SYLKHTEIDN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1x1rA 61 :AILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1x1rA 114 :KDRESFPMILVANKVDLMHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKG 1x1rA 135 :KVTRDQGKEMATKYNIPYIETSAKDP T0308 152 :EGLQEGVDWLQDQI 1x1rA 162 :LNVDKTFHDLVRVI Number of specific fragments extracted= 7 number of extra gaps= 0 total=362 Number of alignments=64 # 1x1rA read from 1x1rA/merged-good-all-a2m # found chain 1x1rA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1x1rA 14 :YKLVVVGDGGVGKSALTIQFFQKIF T0308 28 :SQNILPTI 1x1rA 39 :VPDYDPTI T0308 36 :GFSIEKFKSSS 1x1rA 48 :DSYLKHTEIDN T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1x1rA 61 :AILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKDR T0308 105 :RRIPILFFANKMDLRDAV 1x1rA 117 :ESFPMILVANKVDLMHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKG 1x1rA 135 :KVTRDQGKEMATKYNIPYIETSAKDP T0308 152 :EGLQEGVDWLQDQI 1x1rA 162 :LNVDKTFHDLVRVI Number of specific fragments extracted= 7 number of extra gaps= 0 total=369 Number of alignments=65 # 1x1rA read from 1x1rA/merged-good-all-a2m # found chain 1x1rA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1x1rA 13 :TYKLVVVGDGGVGKSALTIQFFQKIF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1x1rA 41 :DYDPTIEDSYLKHTEIDNQWAILDVLDTAGQEEFSAMREQYMRTGDGFLIVYSVTDKASFEHVDRFHQLILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 1x1rA 116 :RESFPMILVANKVDLMHLRKVT T0308 129 :QLLCLENIKDKPWHICASDAIKG 1x1rA 138 :RDQGKEMATKYNIPYIETSAKDP T0308 152 :EGLQEGVDWLQDQI 1x1rA 162 :LNVDKTFHDLVRVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=374 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f9lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f9lA expands to /projects/compbio/data/pdb/2f9l.pdb.gz 2f9lA:# T0308 read from 2f9lA/merged-good-all-a2m # 2f9lA read from 2f9lA/merged-good-all-a2m # adding 2f9lA to template set # found chain 2f9lA in template set Warning: unaligning (T0308)Q29 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f9lA)S42 Warning: unaligning (T0308)P33 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f9lA)S42 Warning: unaligning (T0308)Y60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f9lA)R74 Warning: unaligning (T0308)R61 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f9lA)R74 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2f9lA 12 :FKVVLIGDSGVGKSNLLSRFT T0308 24 :SNAQS 2f9lA 33 :RNEFN T0308 34 :TIG 2f9lA 43 :TIG T0308 37 :FSIEKFKSSS 2f9lA 48 :FATRSIQVDG T0308 47 :LSFTVFDMSGQGR 2f9lA 60 :IKAQIWDTAGQER T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2f9lA 75 :RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH T0308 103 :KHRRIPILFFANKMDLRDAV 2f9lA 113 :ADSNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2f9lA 133 :AVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEI Number of specific fragments extracted= 8 number of extra gaps= 1 total=382 Number of alignments=67 # 2f9lA read from 2f9lA/merged-good-all-a2m # found chain 2f9lA in template set Warning: unaligning (T0308)S28 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f9lA)S42 Warning: unaligning (T0308)Y60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f9lA)R74 Warning: unaligning (T0308)R61 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f9lA)R74 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 2f9lA 12 :FKVVLIGDSGVGKSNLLSRFTRNEFN T0308 32 :LPTIGFSIEKFKSSS 2f9lA 43 :TIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGR 2f9lA 60 :IKAQIWDTAGQER T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2f9lA 75 :RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAV 2f9lA 115 :SNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2f9lA 133 :AVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEI Number of specific fragments extracted= 6 number of extra gaps= 1 total=388 Number of alignments=68 # 2f9lA read from 2f9lA/merged-good-all-a2m # found chain 2f9lA in template set Warning: unaligning (T0308)Q29 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f9lA)S42 Warning: unaligning (T0308)Y60 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f9lA)R74 Warning: unaligning (T0308)R61 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f9lA)R74 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2f9lA 11 :LFKVVLIGDSGVGKSNLLSRFTRNEF T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGR 2f9lA 43 :TIGVEFATRSIQVDGKTIKAQIWDTAGQER T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2f9lA 75 :RITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAVTSV 2f9lA 115 :SNIVIMLVGNKSDLRHLRAVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2f9lA 136 :TDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=393 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b6hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b6hA expands to /projects/compbio/data/pdb/2b6h.pdb.gz 2b6hA:Skipped atom 594, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 596, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 598, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 600, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 957, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 959, because occupancy 0.350 <= existing 0.650 in 2b6hA Skipped atom 961, because occupancy 0.350 <= existing 0.650 in 2b6hA # T0308 read from 2b6hA/merged-good-all-a2m # 2b6hA read from 2b6hA/merged-good-all-a2m # adding 2b6hA to template set # found chain 2b6hA in template set Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b6hA)R75 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b6hA)R75 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 2b6hA 17 :QMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDM 2b6hA 46 :IPTIGFNVETVEYKNICFTVWDV T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 2b6hA 76 :PLWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2b6hA 119 :AVLLVFANKQDMPNAMPVSELTDKLGLQHLRSRTWYVQATCATQGTGLYDGLDWLSHEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=397 Number of alignments=70 # 2b6hA read from 2b6hA/merged-good-all-a2m # found chain 2b6hA in template set Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b6hA)R75 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b6hA)R75 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 2b6hA 17 :QMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDM 2b6hA 46 :IPTIGFNVETVEYKNICFTVWDV T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2b6hA 76 :PLWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDEL T0308 105 :RRIPILFFANKMDLRDAV 2b6hA 117 :RDAVLLVFANKQDMPNAM T0308 128 :SQLLCLENIK 2b6hA 135 :PVSELTDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 2b6hA 150 :SRTWYVQATCATQGTGLYDGLDWLSHEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=403 Number of alignments=71 # 2b6hA read from 2b6hA/merged-good-all-a2m # found chain 2b6hA in template set Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b6hA)R75 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b6hA)R75 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 2b6hA 18 :MRILMVGLDAAGKTTILYKLKLGEIV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDM 2b6hA 44 :TTIPTIGFNVETVEYKNICFTVWDV T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2b6hA 76 :PLWRHYFQNTQGLIFVVDSNDRERVQESADELQKMLQEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQL 2b6hA 116 :LRDAVLLVFANKQDMPNAMPVSELTDK T0308 136 :IK 2b6hA 143 :LG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 2b6hA 150 :SRTWYVQATCATQGTGLYDGLDWLSHEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=409 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u8zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u8zA expands to /projects/compbio/data/pdb/1u8z.pdb.gz 1u8zA:# T0308 read from 1u8zA/merged-good-all-a2m # 1u8zA read from 1u8zA/merged-good-all-a2m # adding 1u8zA to template set # found chain 1u8zA in template set Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u8zA)Y75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u8zA)Y75 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1u8zA 15 :HKVIMVGSGGVGKSALTLQFM T0308 24 :SNAQSQNILPTIG 1u8zA 36 :YDEFVEDYEPTKA T0308 37 :FSIEKFKSSS 1u8zA 50 :SYRKKVVLDG T0308 47 :LSFTVFDMS 1u8zA 62 :VQIDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1u8zA 76 :AAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1u8zA 115 :KEDENVPFLLVGNKSDLEDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1u8zA 136 :QVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREI Number of specific fragments extracted= 7 number of extra gaps= 0 total=416 Number of alignments=73 # 1u8zA read from 1u8zA/merged-good-all-a2m # found chain 1u8zA in template set Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u8zA)Y75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u8zA)Y75 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1u8zA 15 :HKVIMVGSGGVGKSALTLQFMYDEF T0308 28 :SQNILPTI 1u8zA 40 :VEDYEPTK T0308 36 :GFSIEKFKSSS 1u8zA 49 :DSYRKKVVLDG T0308 47 :LSFTVFDMS 1u8zA 62 :VQIDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1u8zA 76 :AAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKED T0308 105 :RRIPILFFANKMDLRDAV 1u8zA 118 :ENVPFLLVGNKSDLEDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1u8zA 136 :QVSVEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREI Number of specific fragments extracted= 7 number of extra gaps= 0 total=423 Number of alignments=74 # 1u8zA read from 1u8zA/merged-good-all-a2m # found chain 1u8zA in template set Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u8zA)Y75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u8zA)Y75 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1u8zA 14 :LHKVIMVGSGGVGKSALTLQFMYDEF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMS 1u8zA 42 :DYEPTKADSYRKKVVLDGEEVQIDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1u8zA 76 :AAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKE T0308 104 :HRRIPILFFANKMDLRDAVTSV 1u8zA 117 :DENVPFLLVGNKSDLEDKRQVS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1u8zA 139 :VEEAKNRADQWNVNYVETSAKTRANVDKVFFDLMREI Number of specific fragments extracted= 5 number of extra gaps= 0 total=428 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zd9A expands to /projects/compbio/data/pdb/1zd9.pdb.gz 1zd9A:# T0308 read from 1zd9A/merged-good-all-a2m # 1zd9A read from 1zd9A/merged-good-all-a2m # adding 1zd9A to template set # found chain 1zd9A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1zd9A 19 :EMELTLVGLQYSGKTTFVNVIA T0308 24 :SNAQSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1zd9A 41 :SGQFNEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQG T0308 107 :IPILFFANKMDLRDAVTSVKVSQL 1zd9A 122 :IPVLVLGNKRDLPGALDEKELIEK T0308 136 :IK 1zd9A 146 :MN T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1zd9A 153 :DREICCYSISCKEKDNIDITLQWLIQHS Number of specific fragments extracted= 5 number of extra gaps= 0 total=433 Number of alignments=76 # 1zd9A read from 1zd9A/merged-good-all-a2m # found chain 1zd9A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1zd9A 20 :MELTLVGLQYSGKTTFVNVIASGQF T0308 28 :SQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1zd9A 45 :NEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQL T0308 105 :RRIPILFFANKMDLRDA 1zd9A 120 :QGIPVLVLGNKRDLPGA T0308 127 :VSQLLCLENIK 1zd9A 137 :LDEKELIEKMN T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1zd9A 153 :DREICCYSISCKEKDNIDITLQWLIQHS Number of specific fragments extracted= 5 number of extra gaps= 0 total=438 Number of alignments=77 # 1zd9A read from 1zd9A/merged-good-all-a2m # found chain 1zd9A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1zd9A 19 :EMELTLVGLQYSGKTTFVNVIASGQFN T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1zd9A 46 :EDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQ T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQ 1zd9A 119 :LQGIPVLVLGNKRDLPGALDEKELIE T0308 135 :NI 1zd9A 145 :KM T0308 137 :KDKPWHICASDAIKGEGLQEGVDWLQDQ 1zd9A 152 :QDREICCYSISCKEKDNIDITLQWLIQH Number of specific fragments extracted= 5 number of extra gaps= 0 total=443 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s8fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s8fA expands to /projects/compbio/data/pdb/1s8f.pdb.gz 1s8fA:Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 1s8fA Skipped atom 1225, because occupancy 0.400 <= existing 0.600 in 1s8fA Skipped atom 1227, because occupancy 0.400 <= existing 0.600 in 1s8fA # T0308 read from 1s8fA/merged-good-all-a2m # 1s8fA read from 1s8fA/merged-good-all-a2m # adding 1s8fA to template set # found chain 1s8fA in template set Warning: unaligning (T0308)S28 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)T1034 Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)T1034 Warning: unaligning (T0308)H104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s8fA)P1114 Warning: unaligning (T0308)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)R1170 Warning: unaligning (T0308)D163 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)R1170 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1s8fA 1008 :FKVILLGDGGVGKSSLMNRYV T0308 24 :SNAQ 1s8fA 1029 :TNKF T0308 30 :NILPTIG 1s8fA 1035 :QLFHTIG T0308 37 :FSIEKFKSSS 1s8fA 1044 :FLNKDLEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1s8fA 1056 :VTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYY T0308 105 :RRIPILFFANKMDLRDA 1s8fA 1115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDK 1s8fA 1132 :QVSTEEAQAWCRDN T0308 140 :PWHICASDAIKGEGLQEGVDWL 1s8fA 1147 :DYPYFETSAKDATNVAAAFEEA T0308 164 :QI 1s8fA 1171 :RV Number of specific fragments extracted= 9 number of extra gaps= 2 total=452 Number of alignments=79 # 1s8fA read from 1s8fA/merged-good-all-a2m # found chain 1s8fA in template set Warning: unaligning (T0308)S28 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)T1034 Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)T1034 Warning: unaligning (T0308)I102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s8fA)P1114 Warning: unaligning (T0308)H104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s8fA)P1114 Warning: unaligning (T0308)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)R1170 Warning: unaligning (T0308)D163 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)R1170 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1s8fA 1008 :FKVILLGDGGVGKSSLMNRYVTNKF T0308 30 :NILPTIG 1s8fA 1035 :QLFHTIG T0308 37 :FSIEKFKSSS 1s8fA 1044 :FLNKDLEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1s8fA 1056 :VTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYAD T0308 105 :RRIPILFFANKMDLRDA 1s8fA 1115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDKP 1s8fA 1132 :QVSTEEAQAWCRDNG T0308 141 :WHICASDAIKGEGLQEGVDWL 1s8fA 1148 :YPYFETSAKDATNVAAAFEEA T0308 164 :QI 1s8fA 1171 :RV Number of specific fragments extracted= 8 number of extra gaps= 2 total=460 Number of alignments=80 # 1s8fA read from 1s8fA/merged-good-all-a2m # found chain 1s8fA in template set Warning: unaligning (T0308)Q27 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)T1034 Warning: unaligning (T0308)H99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s8fA)P1114 Warning: unaligning (T0308)H104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s8fA)P1114 Warning: unaligning (T0308)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (1s8fA)R1170 Warning: unaligning (T0308)D163 because of BadResidue code BAD_PEPTIDE at template residue (1s8fA)R1170 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1s8fA 1007 :LFKVILLGDGGVGKSSLMNRYVTNKF T0308 28 :SQNILPTIGFSIEKFKSSS 1s8fA 1035 :QLFHTIGVEFLNKDLEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLL 1s8fA 1056 :VTMQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFI T0308 98 :N 1s8fA 1110 :D T0308 105 :RRIPILFFANKMDLRDAVTSV 1s8fA 1115 :ESFPFVILGNKIDISERQVST T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWL 1s8fA 1136 :EEAQAWCRDNGDYPYFETSAKDATNVAAAFEEA T0308 164 :QI 1s8fA 1171 :RV Number of specific fragments extracted= 7 number of extra gaps= 2 total=467 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1mh1/merged-good-all-a2m # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1mh1 4 :IKCVVVGDGAVGKTCLLISYT T0308 24 :SNAQSQNILPTIG 1mh1 25 :TNAFPGEYIPTVF T0308 37 :FSIEKFKSSS 1mh1 39 :NYSANVMVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1mh1 51 :VNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRA T0308 92 :ELDTLLNH 1mh1 97 :WYPEVRHH T0308 104 :HRRIPILFFANKMDL 1mh1 105 :CPNTPIILVGTKLDL T0308 119 :RDAV 1mh1 132 :KKLT T0308 126 :KVSQLLCLENIKDKP 1mh1 136 :PITYPQGLAMAKEIG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1mh1 152 :VKYLECSALTQRGLKTVFDEAIRA Number of specific fragments extracted= 9 number of extra gaps= 0 total=476 Number of alignments=82 # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1mh1 4 :IKCVVVGDGAVGKTCLLISYTTNAF T0308 28 :SQNILPTI 1mh1 29 :PGEYIPTV T0308 36 :GFSIEKFKSSS 1mh1 38 :DNYSANVMVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAK 1mh1 51 :VNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVR T0308 91 :EELDTLLNHP 1mh1 96 :KWYPEVRHHC T0308 105 :RRIPILFFANKMDLRDAVTSVK 1mh1 106 :PNTPIILVGTKLDLRDDKDTIE T0308 127 :VSQLLCLENIKDKP 1mh1 137 :ITYPQGLAMAKEIG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1mh1 152 :VKYLECSALTQRGLKTVFDEAIRAV Number of specific fragments extracted= 8 number of extra gaps= 0 total=484 Number of alignments=83 # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1mh1 3 :AIKCVVVGDGAVGKTCLLISYTTNAF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1mh1 31 :EYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRA T0308 92 :ELDTLLNHPD 1mh1 97 :WYPEVRHHCP T0308 106 :RIPILFFANKMDLRDAVTSV 1mh1 107 :NTPIILVGTKLDLRDDKDTI T0308 129 :QLLCL 1mh1 127 :EKLKE T0308 134 :ENIKDKPW 1mh1 144 :AMAKEIGA T0308 142 :HICASDAIKGEGLQEGVDWLQDQ 1mh1 153 :KYLECSALTQRGLKTVFDEAIRA Number of specific fragments extracted= 7 number of extra gaps= 0 total=491 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wmsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1wmsA/merged-good-all-a2m # 1wmsA read from 1wmsA/merged-good-all-a2m # found chain 1wmsA in training set Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wmsA)T39 Warning: unaligning (T0308)T34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wmsA)T39 Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1wmsA)Q66 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1wmsA)Q66 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1wmsA 8 :FKVILLGDGGVGKSSLMNRYV T0308 24 :SNAQS 1wmsA 29 :TNKFD T0308 35 :IG 1wmsA 40 :IG T0308 37 :FSIEKFKSSS 1wmsA 44 :FLNKDLEVDG T0308 47 :LSFTVFDMS 1wmsA 56 :VTMQIWDTA T0308 58 :GRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1wmsA 67 :ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKE T0308 105 :RRIPILFFANKMDLRDA 1wmsA 115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDK 1wmsA 132 :QVSTEEAQAWCRDN T0308 140 :PWHICASDAIKGEGLQEGVDWLQDQI 1wmsA 147 :DYPYFETSAKDATNVAAAFEEAVRRV Number of specific fragments extracted= 9 number of extra gaps= 1 total=500 Number of alignments=85 # 1wmsA read from 1wmsA/merged-good-all-a2m # found chain 1wmsA in training set Warning: unaligning (T0308)S28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wmsA)T39 Warning: unaligning (T0308)L32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wmsA)T39 Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1wmsA)Q66 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1wmsA)Q66 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 1wmsA 8 :FKVILLGDGGVGKSSLMNRYVTNKFD T0308 33 :PTIGFSIEKFKSSS 1wmsA 40 :IGVEFLNKDLEVDG T0308 47 :LSFTVFDMS 1wmsA 56 :VTMQIWDTA T0308 58 :GRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1wmsA 67 :ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKE T0308 105 :RRIPILFFANKMDLRDA 1wmsA 115 :ESFPFVILGNKIDISER T0308 126 :KVSQLLCLENIKDK 1wmsA 132 :QVSTEEAQAWCRDN T0308 140 :PWHICASDAIKGEGLQEGVDWLQDQI 1wmsA 147 :DYPYFETSAKDATNVAAAFEEAVRRV Number of specific fragments extracted= 7 number of extra gaps= 1 total=507 Number of alignments=86 # 1wmsA read from 1wmsA/merged-good-all-a2m # found chain 1wmsA in training set Warning: unaligning (T0308)N30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wmsA)T39 Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1wmsA)Q66 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1wmsA)Q66 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1wmsA 7 :LFKVILLGDGGVGKSSLMNRYVTNKF T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMS 1wmsA 40 :IGVEFLNKDLEVDGHFVTMQIWDTA T0308 58 :GRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLL 1wmsA 67 :ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFI T0308 98 :NHPD 1wmsA 110 :DVKE T0308 104 :HRRIPILFFANKMDLRDAVTSV 1wmsA 114 :PESFPFVILGNKIDISERQVST T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1wmsA 136 :EEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV Number of specific fragments extracted= 6 number of extra gaps= 1 total=513 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hurA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hurA expands to /projects/compbio/data/pdb/1hur.pdb.gz 1hurA:# T0308 read from 1hurA/merged-good-all-a2m # 1hurA read from 1hurA/merged-good-all-a2m # adding 1hurA to template set # found chain 1hurA in template set Warning: unaligning (T0308)G56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hurA)Q71 Warning: unaligning (T0308)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)Q71 Warning: unaligning (T0308)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)D72 Warning: unaligning (T0308)R59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)K73 Warning: unaligning (T0308)Y60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)I74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hurA)R75 Warning: unaligning (T0308)N62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)P76 Warning: unaligning (T0308)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)L77 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1hurA 17 :EMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMS 1hurA 46 :IPTIGFNVETVEYKNISFTVWDVG T0308 64 :WEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1hurA 78 :WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1hurA 119 :AVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=517 Number of alignments=88 # 1hurA read from 1hurA/merged-good-all-a2m # found chain 1hurA in template set Warning: unaligning (T0308)G56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hurA)Q71 Warning: unaligning (T0308)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)Q71 Warning: unaligning (T0308)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)D72 Warning: unaligning (T0308)R59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)K73 Warning: unaligning (T0308)Y60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)I74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hurA)R75 Warning: unaligning (T0308)N62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)P76 Warning: unaligning (T0308)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)L77 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1hurA 17 :EMRILMVGLDAAGKTTILYKLKLGEIVTT T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMS 1hurA 46 :IPTIGFNVETVEYKNISFTVWDVG T0308 64 :WEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1hurA 78 :WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL T0308 105 :RRIPILFFANKMDLRDAVTS 1hurA 117 :RDAVLLVFANKQDLPNAMNA T0308 130 :LLCLENIK 1hurA 137 :AEITDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1hurA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 6 number of extra gaps= 1 total=523 Number of alignments=89 # 1hurA read from 1hurA/merged-good-all-a2m # found chain 1hurA in template set Warning: unaligning (T0308)G56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hurA)Q71 Warning: unaligning (T0308)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)Q71 Warning: unaligning (T0308)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)D72 Warning: unaligning (T0308)R59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)K73 Warning: unaligning (T0308)Y60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)I74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hurA)R75 Warning: unaligning (T0308)N62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hurA)P76 Warning: unaligning (T0308)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hurA)L77 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1hurA 18 :MRILMVGLDAAGKTTILYKLKLGEI T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMS 1hurA 44 :TTIPTIGFNVETVEYKNISFTVWDVG T0308 64 :WEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1hurA 78 :WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1hurA 116 :LRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=527 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kao/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kao expands to /projects/compbio/data/pdb/1kao.pdb.gz 1kao:Warning: there is no chain 1kao will retry with 1kaoA # T0308 read from 1kao/merged-good-all-a2m # 1kao read from 1kao/merged-good-all-a2m # adding 1kao to template set # found chain 1kao in template set Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)K31 Warning: unaligning (T0308)N30 because of BadResidue code BAD_PEPTIDE at template residue (1kao)K31 Warning: unaligning (T0308)I35 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)E37 Warning: unaligning (T0308)G36 because of BadResidue code BAD_PEPTIDE at template residue (1kao)E37 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)F64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1kao)F64 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kao)S146 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kao)S146 T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1kao 3 :EYKVVVLGSGGVGKSALTVQFV T0308 24 :SNAQS 1kao 25 :TGTFI T0308 31 :ILPT 1kao 32 :YDPT T0308 37 :FSIEKFKSSS 1kao 39 :FYRKEIEVDS T0308 47 :LSFTVFDMSGQG 1kao 51 :SVLEILDTAGTE T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1kao 65 :ASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1kao 104 :KRYEKVPVILVGNKVDLESER T0308 126 :KVSQLLCLENIKDKPWHICA 1kao 125 :EVSSSEGRALAEEWGCPFME T0308 148 :AIKGEGLQEGVDWLQDQI 1kao 147 :AKSKTMVDELFAEIVRQM Number of specific fragments extracted= 9 number of extra gaps= 4 total=536 Number of alignments=91 # 1kao read from 1kao/merged-good-all-a2m # found chain 1kao in template set Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)K31 Warning: unaligning (T0308)N30 because of BadResidue code BAD_PEPTIDE at template residue (1kao)K31 Warning: unaligning (T0308)I35 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)E37 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)F64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1kao)F64 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kao)S146 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kao)S146 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1kao 4 :YKVVVLGSGGVGKSALTVQFVTGTF T0308 28 :S 1kao 29 :I T0308 31 :ILPT 1kao 32 :YDPT T0308 36 :GFSIEKFKSSS 1kao 38 :DFYRKEIEVDS T0308 47 :LSFTVFDMSGQG 1kao 51 :SVLEILDTAGTE T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1kao 65 :ASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRY T0308 105 :RRIPILFFANKMDLRDAV 1kao 107 :EKVPVILVGNKVDLESER T0308 126 :KVSQLLCLENIKDKPWHICA 1kao 125 :EVSSSEGRALAEEWGCPFME T0308 148 :AIKGEGLQEGVDWLQDQI 1kao 147 :AKSKTMVDELFAEIVRQM Number of specific fragments extracted= 9 number of extra gaps= 4 total=545 Number of alignments=92 # 1kao read from 1kao/merged-good-all-a2m # found chain 1kao in template set Warning: unaligning (T0308)Q27 because of BadResidue code BAD_PEPTIDE at template residue (1kao)K31 Warning: unaligning (T0308)L32 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)E37 Warning: unaligning (T0308)P33 because of BadResidue code BAD_PEPTIDE at template residue (1kao)E37 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1kao)F64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1kao)F64 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kao)S146 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kao)S146 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1kao 3 :EYKVVVLGSGGVGKSALTVQFVTGTF T0308 28 :SQNI 1kao 32 :YDPT T0308 34 :TIGFSIEKFKSSSLSFTVFDMSGQG 1kao 38 :DFYRKEIEVDSSPSVLEILDTAGTE T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1kao 65 :ASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKR T0308 104 :HRRIPILFFANKMDLRDAVTSV 1kao 106 :YEKVPVILVGNKVDLESEREVS T0308 129 :QLLCLENIKDKPWHICA 1kao 128 :SSEGRALAEEWGCPFME T0308 148 :AIKGEGLQEGVDWLQDQI 1kao 147 :AKSKTMVDELFAEIVRQM Number of specific fragments extracted= 7 number of extra gaps= 4 total=552 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d5cA expands to /projects/compbio/data/pdb/1d5c.pdb.gz 1d5cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0308 read from 1d5cA/merged-good-all-a2m # 1d5cA read from 1d5cA/merged-good-all-a2m # adding 1d5cA to template set # found chain 1d5cA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1d5cA 11 :KYKLVFLGEQAVGKTSIITRFM T0308 24 :SNAQSQNILPTIG 1d5cA 33 :YDTFDNNYQSTIG T0308 37 :FSIEKFKSSS 1d5cA 48 :FLSKTLYLDE T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1d5cA 60 :VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNE T0308 103 :KHRRIPILFFANKMDLRDAV 1d5cA 113 :RGKDVIIALVGNKTDLGDLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1d5cA 133 :KVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=558 Number of alignments=94 # 1d5cA read from 1d5cA/merged-good-all-a2m # found chain 1d5cA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1d5cA 11 :KYKLVFLGEQAVGKTSIITRFMYDTF T0308 28 :SQNI 1d5cA 37 :DNNY T0308 32 :LPTIGFSIEKFKSSS 1d5cA 43 :TIGIDFLSKTLYLDE T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1d5cA 60 :VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG T0308 105 :RRIPILFFANKMDLRDAV 1d5cA 115 :KDVIIALVGNKTDLGDLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1d5cA 133 :KVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=564 Number of alignments=95 # 1d5cA read from 1d5cA/merged-good-all-a2m # found chain 1d5cA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1d5cA 12 :YKLVFLGEQAVGKTSIITRFMYDTF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1d5cA 40 :YQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG T0308 105 :RRIPILFFANKMDLRDAVTSV 1d5cA 115 :KDVIIALVGNKTDLGDLRKVT T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQD 1d5cA 136 :YEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTAS Number of specific fragments extracted= 4 number of extra gaps= 0 total=568 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ctqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1ctqA/merged-good-all-a2m # 1ctqA read from 1ctqA/merged-good-all-a2m # found chain 1ctqA in training set Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Q61 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Q61 Warning: unaligning (T0308)G58 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)E62 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Y64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Y64 T0308 1 :EVHVLCLGLDNSGKTTIINKLK 1ctqA 3 :EYKLVVVGAGGVGKSALTIQLI T0308 24 :SNAQSQNILPTIG 1ctqA 25 :QNHFVDEYDPTIE T0308 37 :FSIEKFKSSS 1ctqA 39 :SYRKQVVIDG T0308 47 :LSFTVFDMS 1ctqA 51 :CLLDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1ctqA 65 :SAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRV T0308 102 :IKHRRIPILFFANKMDLRDAV 1ctqA 104 :KDSDDVPMVLVGNKCDLAART T0308 127 :VSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ctqA 125 :VESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 7 number of extra gaps= 1 total=575 Number of alignments=97 # 1ctqA read from 1ctqA/merged-good-all-a2m # found chain 1ctqA in training set Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Q61 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Q61 Warning: unaligning (T0308)G58 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)E62 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Y64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Y64 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ctqA 4 :YKLVVVGAGGVGKSALTIQLIQNHF T0308 28 :SQNILPTI 1ctqA 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 1ctqA 38 :DSYRKQVVIDG T0308 47 :LSFTVFDMS 1ctqA 51 :CLLDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1ctqA 65 :SAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDS T0308 105 :RRIPILFFANKMDLRDA 1ctqA 107 :DDVPMVLVGNKCDLAAR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ctqA 124 :TVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 7 number of extra gaps= 1 total=582 Number of alignments=98 # 1ctqA read from 1ctqA/merged-good-all-a2m # found chain 1ctqA in training set Warning: unaligning (T0308)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Q61 Warning: unaligning (T0308)Q57 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Q61 Warning: unaligning (T0308)G58 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)E62 Warning: unaligning (T0308)R59 because of BadResidue code BAD_PEPTIDE in next template residue (1ctqA)Y64 Warning: unaligning (T0308)Y60 because of BadResidue code BAD_PEPTIDE at template residue (1ctqA)Y64 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ctqA 3 :EYKLVVVGAGGVGKSALTIQLIQNHF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMS 1ctqA 31 :EYDPTIEDSYRKQVVIDGETCLLDILDTA T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ctqA 65 :SAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKD T0308 104 :HRRIPILFFANKMDLRDAVTS 1ctqA 106 :SDDVPMVLVGNKCDLAARTVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ctqA 127 :SRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 5 number of extra gaps= 1 total=587 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x3sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x3sA expands to /projects/compbio/data/pdb/1x3s.pdb.gz 1x3sA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0308 read from 1x3sA/merged-good-all-a2m # 1x3sA read from 1x3sA/merged-good-all-a2m # adding 1x3sA to template set # found chain 1x3sA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1x3sA 9 :LKILIIGESGVGKSSLLLRFT T0308 24 :SNAQSQNILPTIG 1x3sA 30 :DDTFDPELAATIG T0308 37 :FSIEKFKSSS 1x3sA 45 :FKVKTISVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1x3sA 57 :AKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYC T0308 103 :KHRRIPILFFANKMDLRDA 1x3sA 111 :TRNDIVNMLVGNKIDKENR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1x3sA 130 :EVDRNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKI Number of specific fragments extracted= 6 number of extra gaps= 0 total=593 Number of alignments=100 # 1x3sA read from 1x3sA/merged-good-all-a2m # found chain 1x3sA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1x3sA 9 :LKILIIGESGVGKSSLLLRFTDDTF T0308 28 :SQNI 1x3sA 34 :DPEL T0308 32 :LPTIGFSIEKFKSSS 1x3sA 40 :TIGVDFKVKTISVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1x3sA 57 :AKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTR T0308 105 :RRIPILFFANKMDLRDA 1x3sA 113 :NDIVNMLVGNKIDKENR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1x3sA 130 :EVDRNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKI Number of specific fragments extracted= 6 number of extra gaps= 0 total=599 Number of alignments=101 # 1x3sA read from 1x3sA/merged-good-all-a2m # found chain 1x3sA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1x3sA 8 :TLKILIIGESGVGKSSLLLRFTDDTF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1x3sA 37 :LAATIGVDFKVKTISVDGNKAKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCT T0308 104 :HRRIPILFFANKMDLRDAVTS 1x3sA 112 :RNDIVNMLVGNKIDKENREVD T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1x3sA 133 :RNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=603 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ek0A expands to /projects/compbio/data/pdb/1ek0.pdb.gz 1ek0A:Skipped atom 20, because occupancy 0.160 <= existing 0.840 in 1ek0A Skipped atom 22, because occupancy 0.160 <= existing 0.840 in 1ek0A Skipped atom 80, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 82, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 84, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 86, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 88, because occupancy 0.460 <= existing 0.540 in 1ek0A Skipped atom 608, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 610, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 612, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 614, because occupancy 0.230 <= existing 0.770 in 1ek0A Skipped atom 842, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 844, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 846, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 848, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 850, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 852, because occupancy 0.400 <= existing 0.610 in 1ek0A Skipped atom 1074, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1076, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1078, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1080, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1082, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1084, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1086, because occupancy 0.410 <= existing 0.590 in 1ek0A Skipped atom 1331, because occupancy 0.270 <= existing 0.730 in 1ek0A Skipped atom 1333, because occupancy 0.270 <= existing 0.730 in 1ek0A Skipped atom 1335, because occupancy 0.270 <= existing 0.730 in 1ek0A Skipped atom 1337, because occupancy 0.270 <= existing 0.730 in 1ek0A # T0308 read from 1ek0A/merged-good-all-a2m # 1ek0A read from 1ek0A/merged-good-all-a2m # adding 1ek0A to template set # found chain 1ek0A in template set Warning: unaligning (T0308)E65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)Y76 Warning: unaligning (T0308)Y67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)Y76 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)L125 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)L125 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1ek0A 8 :IKLVLLGEAAVGKSSIVLRFV T0308 24 :SNAQSQNILPTIG 1ek0A 29 :SNDFAENKEPTIG T0308 37 :FSIEKFKSSS 1ek0A 44 :FLTQRVTINE T0308 47 :LSFTVFDMSGQGRYRNLW 1ek0A 56 :VKFEIWDTAGQERFASLA T0308 68 :YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1ek0A 77 :YRNAQAALVVYDVTKPQSFIKARHWVKELHEQ T0308 103 :KHRRIPILFFANKM 1ek0A 109 :ASKDIIIALVGNKI T0308 120 :DAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ek0A 126 :QEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKI Number of specific fragments extracted= 7 number of extra gaps= 0 total=610 Number of alignments=103 # 1ek0A read from 1ek0A/merged-good-all-a2m # found chain 1ek0A in template set Warning: unaligning (T0308)E65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)Y76 Warning: unaligning (T0308)Y67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)Y76 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)L125 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)L125 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1ek0A 8 :IKLVLLGEAAVGKSSIVLRFVSNDF T0308 28 :SQNI 1ek0A 33 :AENK T0308 32 :LPTIGFSIEKFKSSS 1ek0A 39 :TIGAAFLTQRVTINE T0308 47 :LSFTVFDMSGQGRYRNLW 1ek0A 56 :VKFEIWDTAGQERFASLA T0308 68 :YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ek0A 77 :YRNAQAALVVYDVTKPQSFIKARHWVKELHEQAS T0308 105 :RRIPILFFANKM 1ek0A 111 :KDIIIALVGNKI T0308 120 :DAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ek0A 126 :QEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKI Number of specific fragments extracted= 7 number of extra gaps= 0 total=617 Number of alignments=104 # 1ek0A read from 1ek0A/merged-good-all-a2m # found chain 1ek0A in template set Warning: unaligning (T0308)E65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)Y76 Warning: unaligning (T0308)Y67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)Y76 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek0A)L125 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek0A)L125 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1ek0A 7 :SIKLVLLGEAAVGKSSIVLRFVSNDF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLW 1ek0A 36 :KEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLA T0308 68 :YKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1ek0A 77 :YRNAQAALVVYDVTKPQSFIKARHWVKELHEQAS T0308 105 :RRIPILFFANKM 1ek0A 111 :KDIIIALVGNKI T0308 120 :DAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1ek0A 126 :QEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVFLGIGEKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=622 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uptA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uptA expands to /projects/compbio/data/pdb/1upt.pdb.gz 1uptA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0308 read from 1uptA/merged-good-all-a2m # 1uptA read from 1uptA/merged-good-all-a2m # adding 1uptA to template set # found chain 1uptA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQS 1uptA 17 :EMRILILGLDGAGKTTILYRLQVGEVVT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1uptA 45 :TIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1uptA 119 :AILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=625 Number of alignments=106 # 1uptA read from 1uptA/merged-good-all-a2m # found chain 1uptA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1uptA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1uptA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEEL T0308 105 :RRIPILFFANKMDLRDAV 1uptA 117 :RKAILVVFANKQDMEQAM T0308 128 :SQLLCLENIK 1uptA 135 :TSSEMANSLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1uptA 150 :DRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=630 Number of alignments=107 # 1uptA read from 1uptA/merged-good-all-a2m # found chain 1uptA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1uptA 17 :EMRILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1uptA 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1uptA 116 :LRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETL Number of specific fragments extracted= 3 number of extra gaps= 0 total=633 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bcgY/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bcgY expands to /projects/compbio/data/pdb/2bcg.pdb.gz 2bcgY:Skipped atom 4684, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4686, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4688, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4690, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4692, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4706, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4708, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4710, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4712, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4714, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4786, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4788, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4790, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4792, because occupancy 0.500 <= existing 0.500 in 2bcgY Skipped atom 4794, because occupancy 0.500 <= existing 0.500 in 2bcgY # T0308 read from 2bcgY/merged-good-all-a2m # 2bcgY read from 2bcgY/merged-good-all-a2m # adding 2bcgY to template set # found chain 2bcgY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 2bcgY 9 :FKLLLIGNSGVGKSCLLLRFS T0308 24 :SNAQSQNILPTIG 2bcgY 30 :DDTYTNDYISTIG T0308 37 :FSIEKFKSSS 2bcgY 45 :FKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2bcgY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRY T0308 103 :KHRRIPILFFANKMDLRDAV 2bcgY 110 :ATSTVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2bcgY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=639 Number of alignments=109 # 2bcgY read from 2bcgY/merged-good-all-a2m # found chain 2bcgY in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2bcgY 9 :FKLLLIGNSGVGKSCLLLRFSDDTY T0308 28 :SQNI 2bcgY 34 :TNDY T0308 32 :LPTIGFSIEKFKSSS 2bcgY 40 :TIGVDFKIKTVELDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bcgY 57 :VKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAV 2bcgY 112 :STVLKLLVGNKCDLKDKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2bcgY 130 :VVEYDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=645 Number of alignments=110 # 2bcgY read from 2bcgY/merged-good-all-a2m # found chain 2bcgY in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2bcgY 8 :LFKLLLIGNSGVGKSCLLLRFSDDTY T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bcgY 37 :YISTIGVDFKIKTVELDGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMWLQEIDRYAT T0308 105 :RRIPILFFANKMDLRDAVTSV 2bcgY 112 :STVLKLLVGNKCDLKDKRVVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2bcgY 133 :YDVAKEFADANKMPFLETSALDSTNVEDAFLTMARQI Number of specific fragments extracted= 4 number of extra gaps= 0 total=649 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uptC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uptC expands to /projects/compbio/data/pdb/1upt.pdb.gz 1uptC:# T0308 read from 1uptC/merged-good-all-a2m # 1uptC read from 1uptC/merged-good-all-a2m # adding 1uptC to template set # found chain 1uptC in template set Warning: unaligning (T0308)H3 because first residue in template chain is (1uptC)R19 Warning: unaligning (T0308)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)L111 Warning: unaligning (T0308)L97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)L111 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E131 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E131 Warning: unaligning (T0308)A121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)T135 Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)T135 Warning: unaligning (T0308)K126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)A140 Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)A140 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uptC)S159 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uptC)S159 Warning: unaligning (T0308)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E171 Warning: unaligning (T0308)D159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E171 T0308 4 :VLCLGLDNSGKTTIINKLKPSNAQS 1uptC 20 :ILILGLDGAGKTTILYRLQVGEVVT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELD 1uptC 45 :TIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELV T0308 98 :NHPDIKH 1uptC 112 :EEEELRK T0308 107 :IPILFFANKM 1uptC 119 :AILVVFANKQ T0308 120 :D 1uptC 132 :Q T0308 124 :SV 1uptC 136 :SS T0308 129 :QLLCLENIKDKPWHICA 1uptC 141 :NSLGLPALKDRKWQIFK T0308 148 :AIKGEGLQE 1uptC 160 :ATKGTGLDE T0308 160 :WLQDQI 1uptC 172 :WLVETL Number of specific fragments extracted= 9 number of extra gaps= 1 total=658 Number of alignments=112 # 1uptC read from 1uptC/merged-good-all-a2m # found chain 1uptC in template set Warning: unaligning (T0308)H3 because first residue in template chain is (1uptC)R19 Warning: unaligning (T0308)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)L111 Warning: unaligning (T0308)L97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)L111 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E131 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E131 Warning: unaligning (T0308)A121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)T135 Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)T135 Warning: unaligning (T0308)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)A140 Warning: unaligning (T0308)L133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)A140 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uptC)S159 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uptC)S159 Warning: unaligning (T0308)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E171 Warning: unaligning (T0308)D159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E171 T0308 4 :VLCLGLDNSGKTTIINKLKPSNAQ 1uptC 20 :ILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELD 1uptC 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELV T0308 98 :NHPDI 1uptC 112 :EEEEL T0308 105 :RRIPILFFANKM 1uptC 117 :RKAILVVFANKQ T0308 120 :D 1uptC 132 :Q T0308 129 :QL 1uptC 136 :SS T0308 134 :ENIK 1uptC 141 :NSLG T0308 141 :WHICA 1uptC 153 :WQIFK T0308 148 :AIKGEGLQE 1uptC 160 :ATKGTGLDE T0308 160 :WLQDQI 1uptC 172 :WLVETL Number of specific fragments extracted= 10 number of extra gaps= 1 total=668 Number of alignments=113 # 1uptC read from 1uptC/merged-good-all-a2m # found chain 1uptC in template set Warning: unaligning (T0308)H3 because first residue in template chain is (1uptC)R19 Warning: unaligning (T0308)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)L111 Warning: unaligning (T0308)L97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)L111 Warning: unaligning (T0308)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E131 Warning: unaligning (T0308)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E131 Warning: unaligning (T0308)A121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)T135 Warning: unaligning (T0308)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)T135 Warning: unaligning (T0308)K126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)A140 Warning: unaligning (T0308)S128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)A140 Warning: unaligning (T0308)S146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1uptC)S159 Warning: unaligning (T0308)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uptC)S159 Warning: unaligning (T0308)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uptC)E171 Warning: unaligning (T0308)D159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uptC)E171 T0308 4 :VLCLGLDNSGKTTIINKLKPSNAQ 1uptC 20 :ILILGLDGAGKTTILYRLQVGEVV T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELD 1uptC 44 :TTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELV T0308 98 :NHPD 1uptC 112 :EEEE T0308 104 :HRRIPILFFANKM 1uptC 116 :LRKAILVVFANKQ T0308 120 :D 1uptC 132 :Q T0308 124 :SV 1uptC 136 :SS T0308 129 :QLLCLENIKDKPWHICA 1uptC 141 :NSLGLPALKDRKWQIFK T0308 148 :AIKGEGLQE 1uptC 160 :ATKGTGLDE T0308 160 :WLQDQI 1uptC 172 :WLVETL Number of specific fragments extracted= 9 number of extra gaps= 1 total=677 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n6hA expands to /projects/compbio/data/pdb/1n6h.pdb.gz 1n6hA:Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 272, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 274, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 276, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 285, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 893, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 895, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 1n6hA Skipped atom 1272, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1274, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1276, because occupancy 0.300 <= existing 0.700 in 1n6hA Skipped atom 1278, because occupancy 0.300 <= existing 0.700 in 1n6hA # T0308 read from 1n6hA/merged-good-all-a2m # 1n6hA read from 1n6hA/merged-good-all-a2m # adding 1n6hA to template set # found chain 1n6hA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1n6hA 21 :FKLVLLGESAVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 1n6hA 42 :KGQFHEFQESTIG T0308 37 :FSIEKFKSSS 1n6hA 57 :FLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1n6hA 69 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQ T0308 103 :KHRRIPILFFANKMDLRDAV 1n6hA 122 :ASPNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1n6hA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=683 Number of alignments=115 # 1n6hA read from 1n6hA/merged-good-all-a2m # found chain 1n6hA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1n6hA 21 :FKLVLLGESAVGKSSLVLRFVKGQF T0308 28 :SQNI 1n6hA 46 :HEFQ T0308 32 :LPTIGFSIEKFKSSS 1n6hA 52 :TIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1n6hA 69 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAV 1n6hA 124 :PNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1n6hA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=689 Number of alignments=116 # 1n6hA read from 1n6hA/merged-good-all-a2m # found chain 1n6hA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1n6hA 20 :QFKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1n6hA 49 :QESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAVTSV 1n6hA 124 :PNIVIALSGNKADLANKRAVD T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1n6hA 145 :FQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=693 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a5dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a5dA expands to /projects/compbio/data/pdb/2a5d.pdb.gz 2a5dA:Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 36, because occupancy 0.400 <= existing 0.600 in 2a5dA Skipped atom 38, because occupancy 0.400 <= existing 0.600 in 2a5dA # T0308 read from 2a5dA/merged-good-all-a2m # 2a5dA read from 2a5dA/merged-good-all-a2m # adding 2a5dA to template set # found chain 2a5dA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (2a5dA)N48 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (2a5dA)N48 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 2a5dA 13 :EMRILMLGLDAAGKTTILYKLKLGQSV T0308 30 :NILPTIG 2a5dA 40 :TTIPTVG T0308 39 :IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 2a5dA 49 :VETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5dA 115 :AIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY Number of specific fragments extracted= 4 number of extra gaps= 1 total=697 Number of alignments=118 # 2a5dA read from 2a5dA/merged-good-all-a2m # found chain 2a5dA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (2a5dA)N48 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (2a5dA)N48 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 2a5dA 14 :MRILMLGLDAAGKTTILYKLKLGQSV T0308 30 :NILPTIG 2a5dA 40 :TTIPTVG T0308 39 :IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2a5dA 49 :VETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREM T0308 105 :RRIPILFFANKMDLRDAV 2a5dA 113 :RDAIILIFANKQDLPDAM T0308 128 :SQLLCLENIK 2a5dA 131 :KPHEIQEKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 2a5dA 146 :DRNWYVQPSCATSGDGLYEGLTWLTSNY Number of specific fragments extracted= 6 number of extra gaps= 1 total=703 Number of alignments=119 # 2a5dA read from 2a5dA/merged-good-all-a2m # found chain 2a5dA in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (2a5dA)N48 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (2a5dA)N48 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2a5dA 13 :EMRILMLGLDAAGKTTILYKLKLGQS T0308 29 :QNILPTIG 2a5dA 39 :VTTIPTVG T0308 39 :IEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2a5dA 49 :VETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDRE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5dA 112 :MRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNY Number of specific fragments extracted= 4 number of extra gaps= 1 total=707 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3rabA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3rabA expands to /projects/compbio/data/pdb/3rab.pdb.gz 3rabA:# T0308 read from 3rabA/merged-good-all-a2m # 3rabA read from 3rabA/merged-good-all-a2m # adding 3rabA to template set # found chain 3rabA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 3rabA 23 :FKILIIGNSSVGKTSFLFRYA T0308 24 :SNAQSQNILPTIG 3rabA 44 :DDSFTPAFVSTVG T0308 37 :FSIEKFKSSS 3rabA 59 :FKVKTIYRND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 3rabA 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTY T0308 103 :KHRRIPILFFANKMDLRDAV 3rabA 124 :SWDNAQVLLVGNKCDMEDER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 3rabA 144 :VVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=713 Number of alignments=121 # 3rabA read from 3rabA/merged-good-all-a2m # found chain 3rabA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 3rabA 23 :FKILIIGNSSVGKTSFLFRYADDSFTPAFV T0308 32 :LPTIGFSIEKFKSSS 3rabA 54 :TVGIDFKVKTIYRND T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 3rabA 71 :IKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSW T0308 105 :RRIPILFFANKMDLRDAV 3rabA 126 :DNAQVLLVGNKCDMEDER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 3rabA 144 :VVSSERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=718 Number of alignments=122 # 3rabA read from 3rabA/merged-good-all-a2m # found chain 3rabA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 3rabA 22 :MFKILIIGNSSVGKTSFLFRYADDSF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 3rabA 51 :FVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSW T0308 105 :RRIPILFFANKMDLRDAVTSV 3rabA 126 :DNAQVLLVGNKCDMEDERVVS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 3rabA 147 :SERGRQLADHLGFEFFEASAKDNINVKQTFERLVDVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=722 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eryA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2eryA expands to /projects/compbio/data/pdb/2ery.pdb.gz 2eryA:Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 848, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2eryA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2eryA # T0308 read from 2eryA/merged-good-all-a2m # 2eryA read from 2eryA/merged-good-all-a2m # adding 2eryA to template set # found chain 2eryA in template set Warning: unaligning (T0308)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eryA)G23 Warning: unaligning (T0308)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eryA)G23 Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eryA)F75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eryA)F75 T0308 1 :EVHVLCLG 2eryA 14 :KYRLVVVG T0308 11 :NSGKTTIINKLK 2eryA 24 :GVGKSALTIQFI T0308 24 :SNAQSQNILPTIG 2eryA 36 :QSYFVTDYDPTIE T0308 37 :FSIEKFKSSS 2eryA 50 :SYTKQCVIDD T0308 47 :LSFTVFDM 2eryA 62 :ARLDILDT T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2eryA 76 :GAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRV T0308 102 :IKHRRIPILFFANKMDLRDAV 2eryA 115 :KDRDEFPMILIGNKADLDHQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2eryA 136 :QVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVI Number of specific fragments extracted= 8 number of extra gaps= 1 total=730 Number of alignments=124 # 2eryA read from 2eryA/merged-good-all-a2m # found chain 2eryA in template set Warning: unaligning (T0308)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eryA)G23 Warning: unaligning (T0308)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eryA)G23 Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eryA)F75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eryA)F75 T0308 2 :VHVLCLG 2eryA 15 :YRLVVVG T0308 11 :NSGKTTIINKLKPSNA 2eryA 24 :GVGKSALTIQFIQSYF T0308 28 :SQNILPTI 2eryA 40 :VTDYDPTI T0308 36 :GFSIEKFKSSS 2eryA 49 :DSYTKQCVIDD T0308 47 :LSFTVFDM 2eryA 62 :ARLDILDT T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 2eryA 76 :GAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKDR T0308 105 :RRIPILFFANKMDLRDAV 2eryA 118 :DEFPMILIGNKADLDHQR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2eryA 136 :QVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVI Number of specific fragments extracted= 8 number of extra gaps= 1 total=738 Number of alignments=125 # 2eryA read from 2eryA/merged-good-all-a2m # found chain 2eryA in template set Warning: unaligning (T0308)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eryA)G23 Warning: unaligning (T0308)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eryA)G23 Warning: unaligning (T0308)S55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2eryA)F75 Warning: unaligning (T0308)Y60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2eryA)F75 T0308 1 :EVHVLCLG 2eryA 14 :KYRLVVVG T0308 11 :NSGKTTIINKLKPSNA 2eryA 24 :GVGKSALTIQFIQSYF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDM 2eryA 42 :DYDPTIEDSYTKQCVIDDRAARLDILDT T0308 61 :RNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2eryA 76 :GAMREQYMRTGEGFLLVFSVTDRGSFEEIYKFQRQILRVKD T0308 104 :HRRIPILFFANKMDLRDAVTSV 2eryA 117 :RDEFPMILIGNKADLDHQRQVT T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2eryA 139 :QEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVI Number of specific fragments extracted= 6 number of extra gaps= 1 total=744 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z06A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z06A expands to /projects/compbio/data/pdb/1z06.pdb.gz 1z06A:# T0308 read from 1z06A/merged-good-all-a2m # 1z06A read from 1z06A/merged-good-all-a2m # adding 1z06A to template set # found chain 1z06A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1z06A 34 :FKIIVIGDSNVGKTCLTYRFC T0308 24 :SNAQSQNILPTIG 1z06A 55 :AGRFPDRTEATIG T0308 37 :FSIEKFKSSS 1z06A 70 :FRERAVDIDG T0308 47 :LSFTVFDMSGQGRYR 1z06A 82 :IKIQLWDTAGQERFR T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z06A 98 :SMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQH T0308 102 :IKHRRIPILFFANKMDLRDAV 1z06A 136 :LLANDIPRILVGNKCDLRSAI T0308 126 :KVSQLLCLENIKDKPWHICASDAI 1z06A 157 :QVPTDLAQKFADTHSMPLFETSAK T0308 150 :KGEGLQEGVDWL 1z06A 184 :DNDHVEAIFMTL Number of specific fragments extracted= 8 number of extra gaps= 0 total=752 Number of alignments=127 # 1z06A read from 1z06A/merged-good-all-a2m # found chain 1z06A in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1z06A 34 :FKIIVIGDSNVGKTCLTYRFCAGRF T0308 27 :QSQN 1z06A 60 :DRTE T0308 32 :LPTIGFSIEKFKSSS 1z06A 65 :TIGVDFRERAVDIDG T0308 47 :LSFTVFDMSGQGRYR 1z06A 82 :IKIQLWDTAGQERFR T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1z06A 98 :SMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLA T0308 105 :RRIPILFFANKMDLRDAV 1z06A 139 :NDIPRILVGNKCDLRSAI T0308 126 :KVSQLLCLENIKDKPWHICASDAI 1z06A 157 :QVPTDLAQKFADTHSMPLFETSAK T0308 150 :KGEGLQEGVDWL 1z06A 184 :DNDHVEAIFMTL Number of specific fragments extracted= 8 number of extra gaps= 0 total=760 Number of alignments=128 # 1z06A read from 1z06A/merged-good-all-a2m # found chain 1z06A in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1z06A 33 :IFKIIVIGDSNVGKTCLTYRFCAGRF T0308 27 :QSQNILPTIGFSIEKFKSSS 1z06A 60 :DRTEATIGVDFRERAVDIDG T0308 47 :LSFTVFDMSGQGRYRN 1z06A 82 :IKIQLWDTAGQERFRK T0308 63 :LWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z06A 99 :MVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLL T0308 104 :HRRIPILFFANKMDLRDAVTSV 1z06A 138 :ANDIPRILVGNKCDLRSAIQVP T0308 129 :QLLCLENIKDKPWHICASDAI 1z06A 160 :TDLAQKFADTHSMPLFETSAK T0308 150 :KGEGLQEGVDWL 1z06A 184 :DNDHVEAIFMTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=767 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m2oB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m2oB expands to /projects/compbio/data/pdb/1m2o.pdb.gz 1m2oB:# T0308 read from 1m2oB/merged-good-all-a2m # 1m2oB read from 1m2oB/merged-good-all-a2m # adding 1m2oB to template set # found chain 1m2oB in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1m2oB)G24 T0308 3 :HVLCLGLDNSGKTTIINKLK 1m2oB 25 :KLLFLGLDNAGKTTLLHMLK T0308 24 :SNAQSQ 1m2oB 45 :NDRLAT T0308 31 :ILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1m2oB 51 :LQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAELKD T0308 107 :IPILFFANKMDLRDAVT 1m2oB 125 :VPFVILGNKIDAPNAVS T0308 129 :QLLCLENIK 1m2oB 142 :EAELRSALG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1m2oB 163 :QRPVEVFMCSVVMRNGYLEAFQWLSQYI Number of specific fragments extracted= 6 number of extra gaps= 0 total=773 Number of alignments=130 # 1m2oB read from 1m2oB/merged-good-all-a2m # found chain 1m2oB in template set Warning: unaligning (T0308)V2 because first residue in template chain is (1m2oB)G24 T0308 3 :HVLCLGLDNSGKTTIINKLKPSN 1m2oB 25 :KLLFLGLDNAGKTTLLHMLKNDR T0308 28 :SQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1m2oB 48 :LATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAEL T0308 105 :RRIPILFFANKMDLRDA 1m2oB 123 :KDVPFVILGNKIDAPNA T0308 127 :VSQLLCLENIKDKP 1m2oB 140 :VSEAELRSALGLLN T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1m2oB 166 :VEVFMCSVVMRNGYLEAFQWLSQY Number of specific fragments extracted= 5 number of extra gaps= 0 total=778 Number of alignments=131 # 1m2oB read from 1m2oB/merged-good-all-a2m # found chain 1m2oB in template set T0308 3 :HVLCLGLDNSGKTTIINKLKPSNA 1m2oB 25 :KLLFLGLDNAGKTTLLHMLKNDRL T0308 29 :QNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1m2oB 49 :ATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDAADPERFDEARVELDALFNIAE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVS 1m2oB 122 :LKDVPFVILGNKIDAPNAVSEAELR T0308 134 :ENIK 1m2oB 147 :SALG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQ 1m2oB 163 :QRPVEVFMCSVVMRNGYLEAFQWLSQY Number of specific fragments extracted= 5 number of extra gaps= 0 total=783 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f6bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1f6bA/merged-good-all-a2m # 1f6bA read from 1f6bA/merged-good-all-a2m # found chain 1f6bA in training set Warning: unaligning (T0308)N25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)P55 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)P55 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)R83 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)R83 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1f6bA 26 :GKLVFLGLDNAGKTTLLHMLK T0308 24 :S 1f6bA 47 :D T0308 34 :TIGFSIEKFKSSSLSFTVFDMS 1f6bA 56 :TLHPTSEELTIAGMTFTTFDLG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1f6bA 84 :RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIAN T0308 107 :IPILFFANKMDLRDAVTSVKVSQLL 1f6bA 127 :VPILILGNKIDRPEAISEERLREMF T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1f6bA 166 :KELNARPLEVFMCSVLKRQGYGEGFRWMAQYI Number of specific fragments extracted= 6 number of extra gaps= 0 total=789 Number of alignments=133 # 1f6bA read from 1f6bA/merged-good-all-a2m # found chain 1f6bA in training set Warning: unaligning (T0308)S24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)P55 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)P55 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)R83 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)R83 T0308 2 :VHVLCLGLDNSGKTTIINKLKP 1f6bA 26 :GKLVFLGLDNAGKTTLLHMLKD T0308 34 :TIGFSIEKFKSSSLSFTVFDMS 1f6bA 56 :TLHPTSEELTIAGMTFTTFDLG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1f6bA 84 :RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETI T0308 105 :RRIPILFFANKMDLRDA 1f6bA 125 :ANVPILILGNKIDRPEA T0308 127 :VSQLLCLENIK 1f6bA 142 :ISEERLREMFG T0308 138 :DKP 1f6bA 167 :ELN T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1f6bA 173 :LEVFMCSVLKRQGYGEGFRWMAQYI Number of specific fragments extracted= 7 number of extra gaps= 0 total=796 Number of alignments=134 # 1f6bA read from 1f6bA/merged-good-all-a2m # found chain 1f6bA in training set Warning: unaligning (T0308)S24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)P55 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)P55 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f6bA)R83 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f6bA)R83 T0308 2 :VHVLCLGLDNSGKTTIINKLKP 1f6bA 26 :GKLVFLGLDNAGKTTLLHMLKD T0308 34 :TIGFSIEKFKSSSLSFTVFDMS 1f6bA 56 :TLHPTSEELTIAGMTFTTFDLG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1f6bA 84 :RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDET T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLL 1f6bA 124 :IANVPILILGNKIDRPEAISEERLREMF T0308 134 :ENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1f6bA 166 :KELNARPLEVFMCSVLKRQGYGEGFRWMAQYI Number of specific fragments extracted= 5 number of extra gaps= 0 total=801 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o3yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o3yA expands to /projects/compbio/data/pdb/1o3y.pdb.gz 1o3yA:# T0308 read from 1o3yA/merged-good-all-a2m # 1o3yA read from 1o3yA/merged-good-all-a2m # adding 1o3yA to template set # found chain 1o3yA in template set Warning: unaligning (T0308)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o3yA)I46 Warning: unaligning (T0308)L32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o3yA)I46 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQS 1o3yA 18 :MRILMVGLDAAGKTTILYKLKLGEIVT T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1o3yA 47 :PTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRD T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1o3yA 119 :AVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 3 number of extra gaps= 1 total=804 Number of alignments=136 # 1o3yA read from 1o3yA/merged-good-all-a2m # found chain 1o3yA in template set Warning: unaligning (T0308)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o3yA)I46 Warning: unaligning (T0308)L32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o3yA)I46 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQ 1o3yA 18 :MRILMVGLDAAGKTTILYKLKLGEIV T0308 30 :N 1o3yA 44 :T T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1o3yA 47 :PTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL T0308 105 :RRIPILFFANKMDLRDAV 1o3yA 117 :RDAVLLVFANKQDLPNAM T0308 128 :SQLLCLENIK 1o3yA 135 :NAAEITDKLG T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1o3yA 150 :HRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 6 number of extra gaps= 1 total=810 Number of alignments=137 # 1o3yA read from 1o3yA/merged-good-all-a2m # found chain 1o3yA in template set Warning: unaligning (T0308)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o3yA)I46 Warning: unaligning (T0308)L32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o3yA)I46 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQ 1o3yA 17 :SMRILMVGLDAAGKTTILYKLKLGEIV T0308 30 :N 1o3yA 44 :T T0308 33 :PTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1o3yA 47 :PTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDE T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1o3yA 116 :LRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=814 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bmeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bmeA expands to /projects/compbio/data/pdb/2bme.pdb.gz 2bmeA:Skipped atom 858, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 862, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2bmeA # T0308 read from 2bmeA/merged-good-all-a2m # 2bmeA read from 2bmeA/merged-good-all-a2m # adding 2bmeA to template set # found chain 2bmeA in template set Warning: unaligning (T0308)S28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bmeA)D37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bmeA)D37 Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E151 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2bmeA 11 :FKFLVIGNAGTGKSCLLHQFI T0308 24 :SNAQ 2bmeA 32 :EKKF T0308 30 :NILPTIG 2bmeA 38 :DSNHTIG T0308 37 :FSIEKFKSSS 2bmeA 47 :FGSKIINVGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2bmeA 59 :VKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARML T0308 103 :KHRRIPILFFANKMDLRDAV 2bmeA 112 :ASQNIVIILCGNKKDLDADR T0308 126 :KVSQLLCLENIKDKPWHI 2bmeA 132 :EVTFLEASRFAQENELMF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2bmeA 152 :TSALTGENVEEAFVQCARKI Number of specific fragments extracted= 8 number of extra gaps= 2 total=822 Number of alignments=139 # 2bmeA read from 2bmeA/merged-good-all-a2m # found chain 2bmeA in template set Warning: unaligning (T0308)S28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bmeA)D37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bmeA)D37 Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E151 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2bmeA 11 :FKFLVIGNAGTGKSCLLHQFIEKKF T0308 30 :NI 2bmeA 38 :DS T0308 32 :LPTIGFSIEKFKSSS 2bmeA 42 :TIGVEFGSKIINVGG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bmeA 59 :VKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLAS T0308 105 :RRIPILFFANKMDLRDAV 2bmeA 114 :QNIVIILCGNKKDLDADR T0308 126 :KVSQLLCLENIKDKPWHI 2bmeA 132 :EVTFLEASRFAQENELMF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2bmeA 152 :TSALTGENVEEAFVQCARKI Number of specific fragments extracted= 7 number of extra gaps= 2 total=829 Number of alignments=140 # 2bmeA read from 2bmeA/merged-good-all-a2m # found chain 2bmeA in template set Warning: unaligning (T0308)C144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0308)A145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E151 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2bmeA 10 :LFKFLVIGNAGTGKSCLLHQFIEKKF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2bmeA 39 :SNHTIGVEFGSKIINVGGKYVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNALTNWLTDARMLAS T0308 105 :RRIPILFFANKMDLRDAVTSV 2bmeA 114 :QNIVIILCGNKKDLDADREVT T0308 129 :QLLCLENIKDKPWHI 2bmeA 135 :FLEASRFAQENELMF T0308 146 :SDAIKGEGLQEGVDWLQDQI 2bmeA 152 :TSALTGENVEEAFVQCARKI Number of specific fragments extracted= 5 number of extra gaps= 1 total=834 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z08A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z08A expands to /projects/compbio/data/pdb/1z08.pdb.gz 1z08A:# T0308 read from 1z08A/merged-good-all-a2m # 1z08A read from 1z08A/merged-good-all-a2m # adding 1z08A to template set # found chain 1z08A in template set Warning: unaligning (T0308)N11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z08A)V30 Warning: unaligning (T0308)S12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z08A)V30 Warning: unaligning (T0308)Q57 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z08A)P86 Warning: unaligning (T0308)E65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z08A)P86 T0308 2 :VHVLCLGLD 1z08A 20 :FKVVLLGEG T0308 13 :GKTTIINKLK 1z08A 31 :GKTSLVLRYC T0308 24 :SNAQSQNILPTIG 1z08A 41 :ENKFNDKHITTLG T0308 37 :FSIEKFKSSS 1z08A 56 :FLTKKLNIGG T0308 47 :LSFTVFDMSG 1z08A 68 :VNLAIWDTAG T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1z08A 87 :IYYRDSNGAILVYDITDEDSFQKVKNWVKELRKM T0308 103 :KHRRIPILFFANKMDLRDAV 1z08A 121 :LGNEICLCIVGNKIDLEKER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z08A 141 :HVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRM Number of specific fragments extracted= 8 number of extra gaps= 1 total=842 Number of alignments=142 # 1z08A read from 1z08A/merged-good-all-a2m # found chain 1z08A in template set Warning: unaligning (T0308)N11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z08A)V30 Warning: unaligning (T0308)S12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z08A)V30 Warning: unaligning (T0308)Q57 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z08A)P86 Warning: unaligning (T0308)E65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z08A)P86 T0308 2 :VHVLCLGLD 1z08A 20 :FKVVLLGEG T0308 13 :GKTTIINKLKPSNAQSQNI 1z08A 31 :GKTSLVLRYCENKFNDKHI T0308 32 :LPTIGFSIEKFKSSS 1z08A 51 :TLGASFLTKKLNIGG T0308 47 :LSFTVFDMSG 1z08A 68 :VNLAIWDTAG T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z08A 87 :IYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLG T0308 105 :RRIPILFFANKMDLRDAV 1z08A 123 :NEICLCIVGNKIDLEKER T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z08A 141 :HVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRM Number of specific fragments extracted= 7 number of extra gaps= 1 total=849 Number of alignments=143 # 1z08A read from 1z08A/merged-good-all-a2m # found chain 1z08A in template set Warning: unaligning (T0308)N11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z08A)V30 Warning: unaligning (T0308)S12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z08A)V30 Warning: unaligning (T0308)Q57 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z08A)P86 Warning: unaligning (T0308)E65 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z08A)P86 T0308 1 :EVHVLCLGLD 1z08A 19 :SFKVVLLGEG T0308 13 :GKTTIINKLKPSNA 1z08A 31 :GKTSLVLRYCENKF T0308 27 :QSQNILPTIGFSIEKFKSSS 1z08A 46 :DKHITTLGASFLTKKLNIGG T0308 47 :LSFTVFDMSG 1z08A 68 :VNLAIWDTAG T0308 66 :HYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1z08A 87 :IYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLG T0308 105 :RRIPILFFANKMDLRDAVTSV 1z08A 123 :NEICLCIVGNKIDLEKERHVS T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1z08A 144 :IQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRM Number of specific fragments extracted= 7 number of extra gaps= 1 total=856 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kmqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kmqA expands to /projects/compbio/data/pdb/1kmq.pdb.gz 1kmqA:# T0308 read from 1kmqA/merged-good-all-a2m # 1kmqA read from 1kmqA/merged-good-all-a2m # adding 1kmqA to template set # found chain 1kmqA in template set Warning: unaligning (T0308)I31 because of BadResidue code BAD_PEPTIDE in next template residue (1kmqA)V35 Warning: unaligning (T0308)L32 because of BadResidue code BAD_PEPTIDE at template residue (1kmqA)V35 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1kmqA 6 :KKLVIVGDGACGKTCLLIVNS T0308 24 :SNAQSQN 1kmqA 27 :KDQFPEV T0308 33 :PTIG 1kmqA 36 :PTVF T0308 37 :FSIEKFKSSS 1kmqA 41 :NYVADIEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1kmqA 53 :VELALWDTAGLEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPE T0308 92 :ELDTLLNH 1kmqA 99 :WTPEVKHF T0308 104 :HRRIPILFFANKMDLRDAVTSVK 1kmqA 107 :CPNVPIILVGNKKDLRNDEHTRR T0308 127 :VSQLLCLENIKDKP 1kmqA 139 :VKPEEGRDMANRIG T0308 141 :WHICASDAIKGEGLQEGVDWLQD 1kmqA 154 :FGYMECSAKTKDGVREVFEMATR Number of specific fragments extracted= 9 number of extra gaps= 1 total=865 Number of alignments=145 # 1kmqA read from 1kmqA/merged-good-all-a2m # found chain 1kmqA in template set Warning: unaligning (T0308)I31 because of BadResidue code BAD_PEPTIDE in next template residue (1kmqA)V35 Warning: unaligning (T0308)L32 because of BadResidue code BAD_PEPTIDE at template residue (1kmqA)V35 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1kmqA 6 :KKLVIVGDGACGKTCLLIVNSKDQF T0308 28 :SQN 1kmqA 31 :PEV T0308 33 :PTI 1kmqA 36 :PTV T0308 36 :GFSIEKFKSSS 1kmqA 40 :ENYVADIEVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAK 1kmqA 53 :VELALWDTAGLEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIP T0308 91 :EELDTLLNHP 1kmqA 98 :KWTPEVKHFC T0308 105 :RRIPILFFANKMDLRDAVTSVK 1kmqA 108 :PNVPIILVGNKKDLRNDEHTRR T0308 127 :VSQLLCLENIKDKP 1kmqA 139 :VKPEEGRDMANRIG T0308 141 :WHICASDAIKGEGLQEGVDWLQDQ 1kmqA 154 :FGYMECSAKTKDGVREVFEMATRA Number of specific fragments extracted= 9 number of extra gaps= 1 total=874 Number of alignments=146 # 1kmqA read from 1kmqA/merged-good-all-a2m # found chain 1kmqA in template set Warning: unaligning (T0308)S28 because of BadResidue code BAD_PEPTIDE in next template residue (1kmqA)V35 Warning: unaligning (T0308)Q29 because of BadResidue code BAD_PEPTIDE at template residue (1kmqA)V35 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1kmqA 5 :RKKLVIVGDGACGKTCLLIVNSKDQF T0308 27 :Q 1kmqA 33 :V T0308 30 :NILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKE 1kmqA 36 :PTVFENYVADIEVDGKQVELALWDTAGLEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPE T0308 92 :ELDTLLNHPD 1kmqA 99 :WTPEVKHFCP T0308 106 :RIPILFFANKMDLRDAVTSV 1kmqA 109 :NVPIILVGNKKDLRNDEHTR T0308 129 :QLLCL 1kmqA 129 :RELAK T0308 134 :ENIKDKPW 1kmqA 146 :DMANRIGA T0308 142 :HICASDAIKGEGLQEGVDWLQD 1kmqA 155 :GYMECSAKTKDGVREVFEMATR Number of specific fragments extracted= 8 number of extra gaps= 1 total=882 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a5jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a5jA expands to /projects/compbio/data/pdb/2a5j.pdb.gz 2a5jA:# T0308 read from 2a5jA/merged-good-all-a2m # 2a5jA read from 2a5jA/merged-good-all-a2m # adding 2a5jA to template set # found chain 2a5jA in template set Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a5jA)I44 Warning: unaligning (T0308)I35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a5jA)I44 T0308 2 :VHVLCLGLDNSGKTTIINKLK 2a5jA 12 :FKYIIIGDTGVGKSCLLLQFT T0308 24 :SNAQS 2a5jA 33 :DKRFQ T0308 36 :G 2a5jA 45 :G T0308 37 :FSIEKFKSSS 2a5jA 48 :FGARMVNIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 2a5jA 60 :IKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQH T0308 103 :KHRRIPILFFANKMDLRDAV 2a5jA 113 :SSSNMVIMLIGNKSDLESRR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5jA 133 :DVKREEGEAFAREHGLIFMETSAKTACNVEEAFINTAKEI Number of specific fragments extracted= 7 number of extra gaps= 0 total=889 Number of alignments=148 # 2a5jA read from 2a5jA/merged-good-all-a2m # found chain 2a5jA in template set Warning: unaligning (T0308)Q27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a5jA)I44 Warning: unaligning (T0308)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a5jA)I44 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 2a5jA 12 :FKYIIIGDTGVGKSCLLLQFTDKRF T0308 34 :TIGFSIEKFKSSS 2a5jA 45 :GVEFGARMVNIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2a5jA 60 :IKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSS T0308 105 :RRIPILFFANKMDLRDAV 2a5jA 115 :SNMVIMLIGNKSDLESRR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVD 2a5jA 133 :DVKREEGEAFAREHGLIFMETSAKTACNVEEAFI T0308 160 :WLQDQ 2a5jA 171 :EIYRK Number of specific fragments extracted= 6 number of extra gaps= 0 total=895 Number of alignments=149 # 2a5jA read from 2a5jA/merged-good-all-a2m # found chain 2a5jA in template set Warning: unaligning (T0308)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a5jA)I44 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 2a5jA 11 :LFKYIIIGDTGVGKSCLLLQFTDKRF T0308 32 :LPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 2a5jA 45 :GVEFGARMVNIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSS T0308 105 :RRIPILFFANKMDLRDAVTSV 2a5jA 115 :SNMVIMLIGNKSDLESRRDVK T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 2a5jA 136 :REEGEAFAREHGLIFMETSAKTACNVEEAFINTAKEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=899 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zj6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zj6A expands to /projects/compbio/data/pdb/1zj6.pdb.gz 1zj6A:# T0308 read from 1zj6A/merged-good-all-a2m # 1zj6A read from 1zj6A/merged-good-all-a2m # adding 1zj6A to template set # found chain 1zj6A in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1zj6A)N51 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1zj6A)N51 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zj6A)R74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zj6A)R74 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNAQSQ 1zj6A 16 :EHKVIIVGLDNAGKTTILYQFSMNEVVHT T0308 32 :LPTIG 1zj6A 45 :SPTIG T0308 39 :IEKFKSSSLSFTVFDMS 1zj6A 52 :VEEIVINNTRFLMWDIG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDIKH 1zj6A 75 :SSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRK T0308 107 :IPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1zj6A 118 :AGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRL Number of specific fragments extracted= 5 number of extra gaps= 1 total=904 Number of alignments=151 # 1zj6A read from 1zj6A/merged-good-all-a2m # found chain 1zj6A in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1zj6A)N51 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1zj6A)N51 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zj6A)R74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zj6A)R74 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1zj6A 16 :EHKVIIVGLDNAGKTTILYQFSMNEV T0308 27 :QSQ 1zj6A 43 :HTS T0308 33 :PTIG 1zj6A 46 :PTIG T0308 39 :IEKFKSSSLSFTVFDMS 1zj6A 52 :VEEIVINNTRFLMWDIG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 1zj6A 75 :SSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDL T0308 105 :RRIPILFFANKMDLRDAV 1zj6A 116 :RKAGLLIFANKQDVKECM T0308 128 :SQLLCLENIK 1zj6A 134 :TVAEISQFLK T0308 138 :DKPWHICASDAIKGEGLQEGVDWLQDQI 1zj6A 149 :DHQWHIQACCALTGEGLCQGLEWMMSRL Number of specific fragments extracted= 8 number of extra gaps= 1 total=912 Number of alignments=152 # 1zj6A read from 1zj6A/merged-good-all-a2m # found chain 1zj6A in template set Warning: unaligning (T0308)F37 because of BadResidue code BAD_PEPTIDE in next template residue (1zj6A)N51 Warning: unaligning (T0308)S38 because of BadResidue code BAD_PEPTIDE at template residue (1zj6A)N51 Warning: unaligning (T0308)G56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zj6A)R74 Warning: unaligning (T0308)R61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zj6A)R74 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1zj6A 17 :HKVIIVGLDNAGKTTILYQFSMNEV T0308 30 :NILPTIG 1zj6A 43 :HTSPTIG T0308 39 :IEKFKSSSLSFTVFDMS 1zj6A 52 :VEEIVINNTRFLMWDIG T0308 62 :NLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1zj6A 75 :SSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHED T0308 104 :HRRIPILFFANKMDLRDAVTSVKVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1zj6A 115 :LRKAGLLIFANKQDVKECMTVAEISQFLKLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRL Number of specific fragments extracted= 5 number of extra gaps= 1 total=917 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i2mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1i2mA/merged-good-all-a2m # 1i2mA read from 1i2mA/merged-good-all-a2m # found chain 1i2mA in training set Warning: unaligning (T0308)K22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i2mA)K37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i2mA)K37 T0308 1 :EVHVLCLGLDNSGKTTIINKL 1i2mA 10 :QFKLVLVGDGGTGKTTFVKRH T0308 30 :NILPTIGFSIEKFKS 1i2mA 38 :KYVATLGVEVHPLVF T0308 45 :SS 1i2mA 56 :RG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1i2mA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRV T0308 105 :RRIPILFFANKMDLRDAVTSVKVS 1i2mA 113 :ENIPIVLCGNKVDIKDRKVKAKSI T0308 135 :NIKDKP 1i2mA 137 :VFHRKK T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1i2mA 144 :LQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 7 number of extra gaps= 0 total=924 Number of alignments=154 # 1i2mA read from 1i2mA/merged-good-all-a2m # found chain 1i2mA in training set Warning: unaligning (T0308)K22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i2mA)K37 Warning: unaligning (T0308)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i2mA)K37 T0308 2 :VHVLCLGLDNSGKTTIINKL 1i2mA 11 :FKLVLVGDGGTGKTTFVKRH T0308 30 :NILPTIGFSIEKFKS 1i2mA 38 :KYVATLGVEVHPLVF T0308 45 :SS 1i2mA 55 :NR T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHP 1i2mA 59 :IKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVC T0308 105 :RRIPILFFANKMDLRDAVTSVKVS 1i2mA 113 :ENIPIVLCGNKVDIKDRKVKAKSI T0308 135 :NIKDKP 1i2mA 137 :VFHRKK T0308 141 :WHICASDAIKGEGLQEGVDWLQDQI 1i2mA 144 :LQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 7 number of extra gaps= 0 total=931 Number of alignments=155 # 1i2mA read from 1i2mA/merged-good-all-a2m # found chain 1i2mA in training set Warning: unaligning (T0308)K22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i2mA)K37 T0308 1 :EVHVLCLGLDNSGKTTIINKL 1i2mA 10 :QFKLVLVGDGGTGKTTFVKRH T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1i2mA 39 :YVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE T0308 106 :RIPILFFANKMDLRDAVTSV 1i2mA 114 :NIPIVLCGNKVDIKDRKVKA T0308 133 :LENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1i2mA 136 :IVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=935 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r2qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0308 read from 1r2qA/merged-good-all-a2m # 1r2qA read from 1r2qA/merged-good-all-a2m # found chain 1r2qA in training set Warning: unaligning (T0308)K69 because of BadResidue code BAD_PEPTIDE in next template residue (1r2qA)G92 Warning: unaligning (T0308)E70 because of BadResidue code BAD_PEPTIDE at template residue (1r2qA)G92 T0308 2 :VHVLCLGLDNSGKTTIINKLK 1r2qA 21 :FKLVLLGESAVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 1r2qA 42 :KGQFHEFQESTIG T0308 37 :FSIEKFKSSS 1r2qA 57 :FLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYY 1r2qA 69 :VKFEIWDTAGQERYHSLAPMYY T0308 71 :GQAIIFVIDSSDRLRMVVAKEELDTLLNH 1r2qA 93 :AQAAIVVYDITNEESFARAKNWVKELQRQ T0308 103 :KHRRIPILFFANKMDLRDAV 1r2qA 122 :ASPNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r2qA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 7 number of extra gaps= 1 total=942 Number of alignments=157 # 1r2qA read from 1r2qA/merged-good-all-a2m # found chain 1r2qA in training set Warning: unaligning (T0308)K69 because of BadResidue code BAD_PEPTIDE in next template residue (1r2qA)G92 Warning: unaligning (T0308)E70 because of BadResidue code BAD_PEPTIDE at template residue (1r2qA)G92 T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1r2qA 21 :FKLVLLGESAVGKSSLVLRFVKGQF T0308 28 :SQNI 1r2qA 46 :HEFQ T0308 32 :LPTIGFSIEKFKSSS 1r2qA 52 :TIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYY 1r2qA 69 :VKFEIWDTAGQERYHSLAPMYY T0308 71 :GQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r2qA 93 :AQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAV 1r2qA 124 :PNIVIALSGNKADLANKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r2qA 142 :AVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 7 number of extra gaps= 1 total=949 Number of alignments=158 # 1r2qA read from 1r2qA/merged-good-all-a2m # found chain 1r2qA in training set Warning: unaligning (T0308)K69 because of BadResidue code BAD_PEPTIDE in next template residue (1r2qA)G92 Warning: unaligning (T0308)E70 because of BadResidue code BAD_PEPTIDE at template residue (1r2qA)G92 T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1r2qA 20 :QFKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYY 1r2qA 49 :QESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYY T0308 71 :GQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1r2qA 93 :AQAAIVVYDITNEESFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAVTSV 1r2qA 124 :PNIVIALSGNKADLANKRAVD T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1r2qA 145 :FQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=954 Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oivA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oivA expands to /projects/compbio/data/pdb/1oiv.pdb.gz 1oivA:# T0308 read from 1oivA/merged-good-all-a2m # 1oivA read from 1oivA/merged-good-all-a2m # adding 1oivA to template set # found chain 1oivA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1oivA 12 :FKVVLIGDSGVGKSNLLSRFT T0308 24 :SNAQSQNILPTIG 1oivA 33 :RNEFNLESKSTIG T0308 37 :FSIEKFKSSS 1oivA 48 :FATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1oivA 60 :IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH T0308 103 :KHRRIPILFFANKMDLRDAV 1oivA 113 :ADSNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oivA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 6 number of extra gaps= 0 total=960 Number of alignments=160 # 1oivA read from 1oivA/merged-good-all-a2m # found chain 1oivA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1oivA 12 :FKVVLIGDSGVGKSNLLSRFTRNEFNLESK T0308 32 :LPTIGFSIEKFKSSS 1oivA 43 :TIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oivA 60 :IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAV 1oivA 115 :SNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oivA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=965 Number of alignments=161 # 1oivA read from 1oivA/merged-good-all-a2m # found chain 1oivA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1oivA 11 :LFKVVLIGDSGVGKSNLLSRFTRNEF T0308 27 :QSQNILPTIGFSIEKFKSSS 1oivA 38 :LESKSTIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oivA 60 :IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAVTSV 1oivA 115 :SNIVIMLVGNKSDLRHLRAVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oivA 136 :TDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=970 Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 821p/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 821p expands to /projects/compbio/data/pdb/821p.pdb.gz 821p:Warning: there is no chain 821p will retry with 821pA # T0308 read from 821p/merged-good-all-a2m # 821p read from 821p/merged-good-all-a2m # adding 821p to template set # found chain 821p in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLK 821p 3 :EYKLVVVGAPGVGKSALTIQLI T0308 24 :SNAQSQNILPTIG 821p 25 :QNHFVDEYDPTIE T0308 37 :FSIEKFKSSS 821p 39 :SYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 821p 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRV T0308 102 :IKHRRIPILFFANKMDLRDAV 821p 104 :KDSDDVPMVLVGNKCDLAART T0308 127 :VSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 821p 125 :VESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=976 Number of alignments=163 # 821p read from 821p/merged-good-all-a2m # found chain 821p in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 821p 4 :YKLVVVGAPGVGKSALTIQLIQNHF T0308 28 :SQNILPTI 821p 29 :VDEYDPTI T0308 36 :GFSIEKFKSSS 821p 38 :DSYRKQVVIDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPDI 821p 51 :CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDS T0308 105 :RRIPILFFANKMDLRDA 821p 107 :DDVPMVLVGNKCDLAAR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 821p 124 :TVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 6 number of extra gaps= 0 total=982 Number of alignments=164 # 821p read from 821p/merged-good-all-a2m # found chain 821p in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 821p 3 :EYKLVVVGAPGVGKSALTIQLIQNHF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 821p 31 :EYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKD T0308 104 :HRRIPILFFANKMDLRDAVTS 821p 106 :SDDVPMVLVGNKCDLAARTVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 821p 127 :SRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREI Number of specific fragments extracted= 4 number of extra gaps= 0 total=986 Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1huqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1huqA expands to /projects/compbio/data/pdb/1huq.pdb.gz 1huqA:# T0308 read from 1huqA/merged-good-all-a2m # 1huqA read from 1huqA/merged-good-all-a2m # adding 1huqA to template set # found chain 1huqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1huqA 22 :FKLVLLGESAVGKSSLVLRFV T0308 24 :SNAQSQNILPTIG 1huqA 43 :KGQFHEYQESTIG T0308 37 :FSIEKFKSSS 1huqA 58 :FLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1huqA 70 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQ T0308 103 :KHRRIPILFFANKMDLRDAV 1huqA 123 :ASPNIVIALAGNKADLASKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1huqA 143 :AVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=992 Number of alignments=166 # 1huqA read from 1huqA/merged-good-all-a2m # found chain 1huqA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNA 1huqA 22 :FKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQN 1huqA 48 :EYQE T0308 32 :LPTIGFSIEKFKSSS 1huqA 53 :TIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1huqA 70 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAV 1huqA 125 :PNIVIALAGNKADLASKR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1huqA 143 :AVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=998 Number of alignments=167 # 1huqA read from 1huqA/merged-good-all-a2m # found chain 1huqA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1huqA 21 :QFKLVLLGESAVGKSSLVLRFVKGQF T0308 27 :QSQNILPTIGFSIEKFKSSS 1huqA 48 :EYQESTIGAAFLTQTVCLDD T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1huqA 70 :VKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQAS T0308 105 :RRIPILFFANKMDLRDAVTSV 1huqA 125 :PNIVIALAGNKADLASKRAVE T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1huqA 146 :FQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=1003 Number of alignments=168 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oixA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oixA expands to /projects/compbio/data/pdb/1oix.pdb.gz 1oixA:Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 464, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 466, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1oixA Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 1oixA # T0308 read from 1oixA/merged-good-all-a2m # 1oixA read from 1oixA/merged-good-all-a2m # adding 1oixA to template set # found chain 1oixA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLK 1oixA 12 :FKVVLIGDSGVGKSNLLSRFT T0308 24 :SNAQSQNILPTIG 1oixA 33 :RNEFNLESKSTIG T0308 37 :FSIEKFKSSS 1oixA 48 :FATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNH 1oixA 60 :IKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDH T0308 103 :KHRRIPILFFANKMDLRDAV 1oixA 113 :ADSNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oixA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 6 number of extra gaps= 0 total=1009 Number of alignments=169 # 1oixA read from 1oixA/merged-good-all-a2m # found chain 1oixA in template set T0308 2 :VHVLCLGLDNSGKTTIINKLKPSNAQSQNI 1oixA 12 :FKVVLIGDSGVGKSNLLSRFTRNEFNLESK T0308 32 :LPTIGFSIEKFKSSS 1oixA 43 :TIGVEFATRSIQVDG T0308 47 :LSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oixA 60 :IKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAV 1oixA 115 :SNIVIMLVGNKSDLRHLR T0308 126 :KVSQLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oixA 133 :AVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=1014 Number of alignments=170 # 1oixA read from 1oixA/merged-good-all-a2m # found chain 1oixA in template set T0308 1 :EVHVLCLGLDNSGKTTIINKLKPSNA 1oixA 11 :LFKVVLIGDSGVGKSNLLSRFTRNEF T0308 27 :QSQNILPTIGFSIEKFKSSSLSFTVFDMSGQGRYRNLWEHYYKEGQAIIFVIDSSDRLRMVVAKEELDTLLNHPD 1oixA 40 :SKSTIGVEFATRSIQVDGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHAD T0308 105 :RRIPILFFANKMDLRDAVTSV 1oixA 115 :SNIVIMLVGNKSDLRHLRAVP T0308 129 :QLLCLENIKDKPWHICASDAIKGEGLQEGVDWLQDQI 1oixA 136 :TDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=1018 Number of alignments=171 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0308//projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0308//projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)V51.CB) [> 3.4181 = 5.6969 < 7.4060] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)A148.CB) [> 2.8683 = 4.7806 < 6.2147] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)N114.CB) [> 3.9568 = 6.5947 < 8.5732] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)F112.CB) [> 4.3021 = 7.1701 < 9.3212] w=1.0000 to align # Constraint # added constraint: constraint((T0308)T16.CB, (T0308)A148.CB) [> 2.3463 = 3.9105 < 5.0836] w=1.0000 to align # Constraint # added constraint: constraint((T0308)G13.CA, (T0308)A148.CB) [> 3.4844 = 5.8074 < 7.5496] w=1.0000 to align # Constraint # added constraint: constraint((T0308)G13.CA, (T0308)N114.CB) [> 3.2230 = 5.3716 < 6.9831] w=1.0000 to align # Constraint # added constraint: constraint((T0308)G13.CA, (T0308)D79.CB) [> 4.2592 = 7.0987 < 9.2283] w=1.0000 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)E92.CB) [> 3.5254 = 5.8757 < 7.6385] w=1.0000 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)F76.CB) [> 3.6080 = 6.0133 < 7.8173] w=1.0000 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)F76.CB) [> 3.2066 = 5.3443 < 6.9476] w=1.0000 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)I75.CB) [> 4.2332 = 7.0553 < 9.1719] w=1.0000 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)I74.CB) [> 3.6844 = 6.1407 < 7.9829] w=1.0000 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I75.CB) [> 2.8509 = 4.7515 < 6.1769] w=1.0000 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)V51.CB) [> 3.8036 = 6.3394 < 8.2412] w=1.0000 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I18.CB) [> 3.8138 = 6.3564 < 8.2633] w=1.0000 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I17.CB) [> 4.1292 = 6.8820 < 8.9466] w=1.0000 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)I75.CB) [> 4.2904 = 7.1506 < 9.2958] w=1.0000 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)I74.CB) [> 3.0305 = 5.0508 < 6.5660] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)I75.CB) [> 3.8769 = 6.4615 < 8.3999] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)I74.CB) [> 4.3465 = 7.2442 < 9.4175] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)A73.CB) [> 2.9436 = 4.9060 < 6.3778] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)Q72.CB) [> 4.0912 = 6.8186 < 8.8642] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)G71.CA) [> 4.3021 = 7.1701 < 9.3212] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)T50.CB) [> 4.2182 = 7.0303 < 9.1394] w=1.0000 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)F49.CB) [> 3.3712 = 5.6186 < 7.3042] w=1.0000 to align # Constraint # added constraint: constraint((T0308)K115.CB, (T0308)A148.CB) [> 4.6002 = 7.6670 < 9.9670] w=1.0000 to align # Constraint # added constraint: constraint((T0308)N114.CB, (T0308)A148.CB) [> 3.6849 = 6.1415 < 7.9840] w=1.0000 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)I143.CB) [> 4.1337 = 6.8896 < 8.9564] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)I143.CB) [> 2.7614 = 4.6023 < 5.9830] w=1.0000 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)H142.CB) [> 2.9765 = 4.9608 < 6.4490] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I109.CB, (T0308)W141.CB) [> 2.8191 = 4.6985 < 6.1081] w=1.0000 to align # Constraint # added constraint: constraint((T0308)S81.CB, (T0308)K115.CB) [> 3.1679 = 5.2798 < 6.8638] w=1.0000 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)M116.CB) [> 3.4794 = 5.7990 < 7.5388] w=1.0000 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)K115.CB) [> 3.2020 = 5.3366 < 6.9376] w=1.0000 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)N114.CB) [> 3.9375 = 6.5626 < 8.5313] w=1.0000 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)A113.CB) [> 2.7905 = 4.6508 < 6.0460] w=1.0000 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)K115.CB) [> 3.1775 = 5.2958 < 6.8846] w=1.0000 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)N114.CB) [> 3.5310 = 5.8849 < 7.6504] w=1.0000 to align # Constraint # added constraint: constraint((T0308)K20.CB, (T0308)A148.CB) [> 3.0043 = 5.0072 < 6.5094] w=1.0000 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)P108.CB) [> 2.5514 = 4.2523 < 5.5280] w=1.0000 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)I109.CB) [> 4.3203 = 7.2004 < 9.3606] w=1.0000 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)L161.CB) [> 3.0102 = 5.0170 < 6.5221] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)I107.CB) [> 3.5956 = 5.9928 < 7.7906] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)I109.CB) [> 2.9941 = 4.9902 < 6.4872] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L110.CB) [> 4.3771 = 7.2952 < 9.4838] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I75.CB, (T0308)L110.CB) [> 3.0592 = 5.0987 < 6.6284] w=1.0000 to align # Constraint # added constraint: constraint((T0308)I75.CB, (T0308)F112.CB) [> 3.4952 = 5.8254 < 7.5730] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)L93.CB) [> 3.7521 = 6.2536 < 8.1296] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)I109.CB) [> 3.7355 = 6.2258 < 8.0936] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)L110.CB) [> 4.2567 = 7.0945 < 9.2229] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)F111.CB) [> 3.1478 = 5.2463 < 6.8202] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)F112.CB) [> 4.1649 = 6.9415 < 9.0239] w=1.0000 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)H142.CB) [> 4.1464 = 6.9106 < 8.9838] w=0.9939 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)L161.CB) [> 3.1821 = 5.3035 < 6.8946] w=0.9939 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)P108.CB) [> 4.3241 = 7.2069 < 9.3689] w=0.9904 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)T50.CB) [> 3.2540 = 5.4233 < 7.0502] w=0.9818 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)G71.CA) [> 2.6036 = 4.3393 < 5.6411] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L96.CB) [> 3.5675 = 5.9458 < 7.7295] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)G157.CA) [> 3.7418 = 6.2363 < 8.1072] w=0.9818 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)G157.CA) [> 4.2599 = 7.0998 < 9.2298] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)G71.CA) [> 3.5262 = 5.8770 < 7.6402] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)L154.CB) [> 3.7596 = 6.2659 < 8.1457] w=0.9818 to align # Constraint # added constraint: constraint((T0308)H142.CB, (T0308)W160.CB) [> 3.3856 = 5.6427 < 7.3355] w=0.9818 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)V77.CB) [> 3.8419 = 6.4032 < 8.3241] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)V77.CB) [> 4.2105 = 7.0176 < 9.1228] w=0.9818 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)V77.CB) [> 3.0319 = 5.0531 < 6.5690] w=0.9818 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)I78.CB) [> 4.1475 = 6.9125 < 8.9862] w=0.9818 to align # Constraint # added constraint: constraint((T0308)G13.CA, (T0308)V77.CB) [> 3.6389 = 6.0648 < 7.8842] w=0.9818 to align # Constraint # added constraint: constraint((T0308)K14.CB, (T0308)V77.CB) [> 3.1374 = 5.2291 < 6.7978] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)V77.CB) [> 3.9727 = 6.6211 < 8.6075] w=0.9818 to align # Constraint # added constraint: constraint((T0308)V77.CB, (T0308)F112.CB) [> 2.8560 = 4.7600 < 6.1880] w=0.9818 to align # Constraint # added constraint: constraint((T0308)V77.CB, (T0308)N114.CB) [> 3.2465 = 5.4109 < 7.0341] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)Y68.CB) [> 3.9562 = 6.5937 < 8.5718] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)W141.CB) [> 3.9425 = 6.5709 < 8.5422] w=0.9818 to align # Constraint # added constraint: constraint((T0308)K20.CB, (T0308)L154.CB) [> 3.2144 = 5.3574 < 6.9646] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)V88.CB) [> 3.2349 = 5.3915 < 7.0089] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)R85.CB) [> 2.7629 = 4.6048 < 5.9862] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)D79.CB) [> 4.2919 = 7.1532 < 9.2992] w=0.9818 to align # Constraint # added constraint: constraint((T0308)G13.CA, (T0308)K115.CB) [> 4.3839 = 7.3065 < 9.4985] w=0.9818 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)N114.CB) [> 3.5093 = 5.8488 < 7.6034] w=0.9818 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)D79.CB) [> 2.7001 = 4.5001 < 5.8502] w=0.9818 to align # Constraint # added constraint: constraint((T0308)N11.CB, (T0308)D79.CB) [> 4.0874 = 6.8123 < 8.8560] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)N114.CB) [> 4.0496 = 6.7493 < 8.7741] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)A113.CB) [> 3.4404 = 5.7340 < 7.4543] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)F112.CB) [> 4.3303 = 7.2171 < 9.3822] w=0.9818 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)A89.CB) [> 3.2502 = 5.4170 < 7.0421] w=0.9818 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)L154.CB) [> 3.5132 = 5.8554 < 7.6120] w=0.9722 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)A73.CB) [> 4.5096 = 7.5161 < 9.7709] w=0.9722 to align # Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)P108.CB) [> 4.1055 = 6.8425 < 8.8953] w=0.9722 to align # Constraint # added constraint: constraint((T0308)Y68.CB, (T0308)H99.CB) [> 3.0685 = 5.1141 < 6.6484] w=0.9697 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)W141.CB) [> 3.3499 = 5.5832 < 7.2582] w=0.9697 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)Q72.CB) [> 3.1200 = 5.1999 < 6.7599] w=0.9637 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)C144.CB) [> 3.9353 = 6.5588 < 8.5264] w=0.9637 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)C144.CB) [> 4.3278 = 7.2130 < 9.3768] w=0.9637 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)C144.CB) [> 3.2220 = 5.3699 < 6.9809] w=0.9637 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)C144.CB) [> 4.2440 = 7.0734 < 9.1954] w=0.9637 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)A145.CB) [> 2.7917 = 4.6528 < 6.0487] w=0.9637 to align # Constraint # added constraint: constraint((T0308)C144.CB, (T0308)G153.CA) [> 3.8276 = 6.3793 < 8.2931] w=0.9637 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)V77.CB) [> 2.7410 = 4.5683 < 5.9387] w=0.9637 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)I78.CB) [> 3.3895 = 5.6492 < 7.3439] w=0.9637 to align # Constraint # added constraint: constraint((T0308)K20.CB, (T0308)G151.CA) [> 3.4449 = 5.7415 < 7.4640] w=0.9637 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)W160.CB) [> 3.8395 = 6.3992 < 8.3190] w=0.9576 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)L110.CB) [> 4.1696 = 6.9494 < 9.0342] w=0.9541 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)M54.CB) [> 3.4959 = 5.8265 < 7.5745] w=0.9541 to align # Constraint # added constraint: constraint((T0308)C144.CB, (T0308)G157.CA) [> 2.9993 = 4.9988 < 6.4985] w=0.9455 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)E70.CB) [> 3.5023 = 5.8372 < 7.5883] w=0.9455 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)S146.CB) [> 3.1840 = 5.3067 < 6.8987] w=0.9455 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)S146.CB) [> 4.1746 = 6.9577 < 9.0450] w=0.9455 to align # Constraint # added constraint: constraint((T0308)N114.CB, (T0308)S146.CB) [> 3.1022 = 5.1703 < 6.7214] w=0.9455 to align # Constraint # added constraint: constraint((T0308)N114.CB, (T0308)D147.CB) [> 4.1443 = 6.9072 < 8.9793] w=0.9455 to align # Constraint # added constraint: constraint((T0308)K115.CB, (T0308)D147.CB) [> 3.8253 = 6.3755 < 8.2882] w=0.9455 to align # Constraint # added constraint: constraint((T0308)M116.CB, (T0308)D147.CB) [> 2.8241 = 4.7069 < 6.1189] w=0.9455 to align # Constraint # added constraint: constraint((T0308)D117.CB, (T0308)I149.CB) [> 3.3240 = 5.5400 < 7.2020] w=0.9455 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)F111.CB) [> 4.3945 = 7.3242 < 9.5214] w=0.9455 to align # Constraint # added constraint: constraint((T0308)M116.CB, (T0308)A145.CB) [> 2.7283 = 4.5471 < 5.9113] w=0.9455 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)I107.CB) [> 3.8410 = 6.4016 < 8.3221] w=0.9455 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)Y67.CB) [> 3.6424 = 6.0706 < 7.8918] w=0.9455 to align # Constraint # added constraint: constraint((T0308)C144.CB, (T0308)E156.CB) [> 3.7976 = 6.3293 < 8.2282] w=0.9455 to align # Constraint # added constraint: constraint((T0308)S81.CB, (T0308)L118.CB) [> 2.8484 = 4.7474 < 6.1716] w=0.9274 to align # Constraint # added constraint: constraint((T0308)M116.CB, (T0308)S146.CB) [> 3.5880 = 5.9800 < 7.7740] w=0.9274 to align # Constraint # added constraint: constraint((T0308)P108.CB, (T0308)L161.CB) [> 3.7834 = 6.3056 < 8.1973] w=0.9274 to align # Constraint # added constraint: constraint((T0308)T16.CB, (T0308)I149.CB) [> 4.2751 = 7.1252 < 9.2628] w=0.9274 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)A73.CB) [> 4.0384 = 6.7306 < 8.7498] w=0.9228 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)Q72.CB) [> 2.9578 = 4.9297 < 6.4086] w=0.9228 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)S48.CB) [> 4.3412 = 7.2354 < 9.4060] w=0.9228 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)L47.CB) [> 3.6502 = 6.0836 < 7.9086] w=0.9228 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)L161.CB) [> 3.9363 = 6.5605 < 8.5286] w=0.9228 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)L118.CB) [> 4.1525 = 6.9208 < 8.9971] w=0.9177 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)S146.CB) [> 4.1391 = 6.8985 < 8.9681] w=0.9107 to align # Constraint # added constraint: constraint((T0308)P108.CB, (T0308)Q164.CB) [> 2.7949 = 4.6582 < 6.0557] w=0.9094 to align # Constraint # added constraint: constraint((T0308)D117.CB, (T0308)K150.CB) [> 3.2029 = 5.3381 < 6.9395] w=0.9092 to align # Constraint # added constraint: constraint((T0308)D117.CB, (T0308)D147.CB) [> 2.5691 = 4.2819 < 5.5664] w=0.9092 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)I78.CB) [> 4.1873 = 6.9789 < 9.0726] w=0.9092 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)F52.CB) [> 4.0761 = 6.7935 < 8.8315] w=0.9092 to align # Constraint # added constraint: constraint((T0308)C144.CB, (T0308)W160.CB) [> 4.1842 = 6.9737 < 9.0658] w=0.9034 to align # Constraint # added constraint: constraint((T0308)S146.CB, (T0308)G157.CA) [> 4.2588 = 7.0980 < 9.2274] w=0.8996 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)L96.CB) [> 4.2006 = 7.0010 < 9.1013] w=0.8938 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)F52.CB) [> 2.9767 = 4.9612 < 6.4495] w=0.8910 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)A145.CB) [> 4.1048 = 6.8414 < 8.8938] w=0.8729 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)V51.CB) [> 2.9768 = 4.9614 < 6.4498] w=0.8729 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)F52.CB) [> 4.2277 = 7.0462 < 9.1600] w=0.8729 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)D53.CB) [> 3.1583 = 5.2638 < 6.8430] w=0.8729 to align # Constraint # added constraint: constraint((T0308)T15.CB, (T0308)D53.CB) [> 3.3823 = 5.6372 < 7.3284] w=0.8729 to align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)D53.CB) [> 3.0319 = 5.0532 < 6.5692] w=0.8729 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)I143.CB) [> 4.6399 = 7.7331 < 10.0530] w=0.8729 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)I143.CB) [> 4.5235 = 7.5391 < 9.8009] w=0.8729 to align # Constraint # added constraint: constraint((T0308)L133.CB, (T0308)I143.CB) [> 3.2900 = 5.4834 < 7.1284] w=0.8698 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)A89.CB) [> 3.5478 = 5.9130 < 7.6870] w=0.8562 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I74.CB) [> 4.6106 = 7.6844 < 9.9897] w=0.8550 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)F52.CB) [> 4.2551 = 7.0918 < 9.2193] w=0.8547 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)A73.CB) [> 4.6049 = 7.6749 < 9.9773] w=0.8365 to align # Constraint # added constraint: constraint((T0308)F52.CB, (T0308)Y67.CB) [> 3.5366 = 5.8943 < 7.6626] w=0.8365 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)M54.CB) [> 3.8072 = 6.3454 < 8.2490] w=0.8365 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)I136.CB) [> 3.0462 = 5.0770 < 6.6001] w=0.8301 to align # Constraint # added constraint: constraint((T0308)I109.CB, (T0308)K139.CB) [> 4.1139 = 6.8565 < 8.9134] w=0.8293 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)Q164.CB) [> 4.0674 = 6.7790 < 8.8127] w=0.8289 to align # Constraint # added constraint: constraint((T0308)L47.CB, (T0308)Q162.CB) [> 3.5243 = 5.8739 < 7.6361] w=0.8184 to align # Constraint # added constraint: constraint((T0308)I39.CB, (T0308)V51.CB) [> 4.2206 = 7.0343 < 9.1446] w=0.8115 to align # Constraint # added constraint: constraint((T0308)I39.CB, (T0308)T50.CB) [> 3.3448 = 5.5747 < 7.2471] w=0.8115 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)D82.CB) [> 4.4728 = 7.4547 < 9.6912] w=0.8103 to align # Constraint # added constraint: constraint((T0308)M54.CB, (T0308)Y67.CB) [> 3.8199 = 6.3665 < 8.2764] w=0.8088 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)T50.CB) [> 4.2744 = 7.1240 < 9.2612] w=0.8017 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)F49.CB) [> 3.2477 = 5.4129 < 7.0367] w=0.8017 to align # Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)I165.CB) [> 3.3109 = 5.5182 < 7.1737] w=0.8015 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)G56.CA) [> 3.0841 = 5.1401 < 6.6821] w=0.8002 to align # Constraint # added constraint: constraint((T0308)E40.CB, (T0308)F49.CB) [> 3.3971 = 5.6618 < 7.3604] w=0.7864 to align # Constraint # added constraint: constraint((T0308)E40.CB, (T0308)V51.CB) [> 3.6911 = 6.1519 < 7.9974] w=0.7775 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)M54.CB) [> 4.0107 = 6.6845 < 8.6898] w=0.7724 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)I165.CB) [> 3.3043 = 5.5071 < 7.1592] w=0.7712 to align # Constraint # added constraint: constraint((T0308)C132.CB, (T0308)I143.CB) [> 3.5508 = 5.9180 < 7.6934] w=0.7701 to align # Constraint # added constraint: constraint((T0308)P108.CB, (T0308)I165.CB) [> 3.2977 = 5.4962 < 7.1450] w=0.7657 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)V51.CB) [> 4.6487 = 7.7479 < 10.0723] w=0.7545 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)L96.CB) [> 4.4771 = 7.4618 < 9.7004] w=0.7543 to align # Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)I107.CB) [> 3.8935 = 6.4892 < 8.4360] w=0.7543 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)V51.CB) [> 4.4056 = 7.3427 < 9.5455] w=0.7543 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)F52.CB) [> 3.2689 = 5.4482 < 7.0826] w=0.7538 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)C132.CB) [> 3.0112 = 5.0186 < 6.5242] w=0.7487 to align # Constraint # added constraint: constraint((T0308)M86.CB, (T0308)C132.CB) [> 4.2397 = 7.0662 < 9.1861] w=0.7487 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)A145.CB) [> 4.4923 = 7.4871 < 9.7332] w=0.7457 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)M54.CB) [> 4.0964 = 6.8273 < 8.8755] w=0.7376 to align # Constraint # added constraint: constraint((T0308)G71.CA, (T0308)I107.CB) [> 3.5706 = 5.9510 < 7.7362] w=0.7361 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)I75.CB) [> 4.4893 = 7.4822 < 9.7269] w=0.7195 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)V51.CB) [> 4.0331 = 6.7218 < 8.7383] w=0.7138 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)I165.CB) [> 3.4097 = 5.6828 < 7.3876] w=0.7112 to align # Constraint # added constraint: constraint((T0308)F49.CB, (T0308)V158.CB) [> 4.1198 = 6.8664 < 8.9263] w=0.7109 to align # Constraint # added constraint: constraint((T0308)A89.CB, (T0308)F111.CB) [> 4.0895 = 6.8158 < 8.8606] w=0.7109 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)E92.CB) [> 3.1568 = 5.2614 < 6.8398] w=0.7109 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)R85.CB) [> 4.2673 = 7.1122 < 9.2459] w=0.7109 to align # Constraint # added constraint: constraint((T0308)L93.CB, (T0308)I109.CB) [> 4.2787 = 7.1311 < 9.2705] w=0.7109 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)C132.CB) [> 4.0410 = 6.7350 < 8.7555] w=0.7013 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)Q155.CB) [> 4.0860 = 6.8100 < 8.8530] w=0.7013 to align # Constraint # added constraint: constraint((T0308)I39.CB, (T0308)S48.CB) [> 3.5324 = 5.8873 < 7.6535] w=0.6956 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)T50.CB) [> 3.5298 = 5.8830 < 7.6479] w=0.6956 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)L84.CB) [> 4.2827 = 7.1378 < 9.2792] w=0.6928 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)A113.CB) [> 4.5688 = 7.6147 < 9.8991] w=0.6928 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)R85.CB) [> 3.0512 = 5.0853 < 6.6108] w=0.6928 to align # Constraint # added constraint: constraint((T0308)I75.CB, (T0308)I109.CB) [> 4.6139 = 7.6899 < 9.9969] w=0.6928 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)V88.CB) [> 4.3384 = 7.2306 < 9.3998] w=0.6746 to align # Constraint # added constraint: constraint((T0308)L96.CB, (T0308)I109.CB) [> 4.0373 = 6.7288 < 8.7475] w=0.6731 to align # Constraint # added constraint: constraint((T0308)S38.CB, (T0308)D53.CB) [> 3.8613 = 6.4354 < 8.3661] w=0.6690 to align # Constraint # added constraint: constraint((T0308)I109.CB, (T0308)H142.CB) [> 4.3821 = 7.3036 < 9.4946] w=0.6668 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)S55.CB) [> 4.3389 = 7.2315 < 9.4010] w=0.6665 to align # Constraint # added constraint: constraint((T0308)P33.CB, (T0308)S55.CB) [> 3.9337 = 6.5561 < 8.5230] w=0.6639 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)D53.CB) [> 4.1336 = 6.8894 < 8.9562] w=0.6630 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)C132.CB) [> 4.4717 = 7.4529 < 9.6888] w=0.6622 to align # Constraint # added constraint: constraint((T0308)M86.CB, (T0308)V127.CB) [> 3.3220 = 5.5367 < 7.1976] w=0.6606 to align # Constraint # added constraint: constraint((T0308)I39.CB, (T0308)F49.CB) [> 4.1493 = 6.9156 < 8.9902] w=0.6605 to align # Constraint # added constraint: constraint((T0308)N19.CB, (T0308)A148.CB) [> 4.5112 = 7.5187 < 9.7743] w=0.6592 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)Q162.CB) [> 3.8098 = 6.3496 < 8.2545] w=0.6589 to align # Constraint # added constraint: constraint((T0308)L93.CB, (T0308)K139.CB) [> 3.6334 = 6.0556 < 7.8723] w=0.6583 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)K115.CB) [> 4.6286 = 7.7143 < 10.0286] w=0.6564 to align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)S38.CB) [> 3.6047 = 6.0079 < 7.8102] w=0.6480 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)V127.CB) [> 4.0512 = 6.7520 < 8.7775] w=0.6305 to align # Constraint # added constraint: constraint((T0308)M86.CB, (T0308)A113.CB) [> 4.5816 = 7.6360 < 9.9268] w=0.6201 to align # Constraint # added constraint: constraint((T0308)S44.CB, (T0308)Q162.CB) [> 3.6357 = 6.0596 < 7.8774] w=0.6177 to align # Constraint # added constraint: constraint((T0308)T34.CB, (T0308)S55.CB) [> 3.0665 = 5.1108 < 6.6440] w=0.6146 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)G56.CA) [> 3.4952 = 5.8253 < 7.5729] w=0.6090 to align # Constraint # added constraint: constraint((T0308)H142.CB, (T0308)G157.CA) [> 4.4141 = 7.3568 < 9.5638] w=0.6041 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)C132.CB) [> 4.4691 = 7.4484 < 9.6830] w=0.6038 to align # Constraint # added constraint: constraint((T0308)I75.CB, (T0308)G157.CA) [> 4.4710 = 7.4517 < 9.6872] w=0.6022 to align # Constraint # added constraint: constraint((T0308)L96.CB, (T0308)I107.CB) [> 3.8770 = 6.4617 < 8.4002] w=0.6020 to align # Constraint # added constraint: constraint((T0308)N114.CB, (T0308)A145.CB) [> 4.5724 = 7.6207 < 9.9069] w=0.5923 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)G56.CA) [> 3.6643 = 6.1072 < 7.9394] w=0.5908 to align # Constraint # added constraint: constraint((T0308)M86.CB, (T0308)L131.CB) [> 4.4557 = 7.4263 < 9.6541] w=0.5905 to align # Constraint # added constraint: constraint((T0308)M86.CB, (T0308)N135.CB) [> 4.2239 = 7.0399 < 9.1518] w=0.5805 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)S55.CB) [> 3.6415 = 6.0692 < 7.8900] w=0.5600 to align # Constraint # added constraint: constraint((T0308)C132.CB, (T0308)A145.CB) [> 4.4010 = 7.3350 < 9.5355] w=0.5572 to align # Constraint # added constraint: constraint((T0308)T16.CB, (T0308)N114.CB) [> 4.6668 = 7.7780 < 10.1114] w=0.5379 to align # Constraint # added constraint: constraint((T0308)K14.CB, (T0308)G56.CA) [> 4.3987 = 7.3311 < 9.5304] w=0.5366 to align # Constraint # added constraint: constraint((T0308)M54.CB, (T0308)W64.CB) [> 3.5358 = 5.8930 < 7.6609] w=0.5366 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)Q57.CB) [> 2.7962 = 4.6603 < 6.0584] w=0.5363 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)G56.CA) [> 4.4790 = 7.4651 < 9.7046] w=0.5231 to align # Constraint # added constraint: constraint((T0308)I109.CB, (T0308)P140.CB) [> 4.3728 = 7.2879 < 9.4743] w=0.5189 to align # Constraint # added constraint: constraint((T0308)T34.CB, (T0308)D53.CB) [> 3.4771 = 5.7952 < 7.5338] w=0.5056 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)V77.CB) [> 4.7040 = 7.8401 < 10.1921] w=0.5030 to align # Constraint # added constraint: constraint((T0308)G36.CA, (T0308)F52.CB) [> 4.1620 = 6.9366 < 9.0176] w=0.4992 to align # Constraint # added constraint: constraint((T0308)R83.CB, (T0308)V127.CB) [> 3.6655 = 6.1092 < 7.9420] w=0.4913 to align # Constraint # added constraint: constraint((T0308)K90.CB, (T0308)N135.CB) [> 4.2403 = 7.0672 < 9.1874] w=0.4877 to align # Constraint # added constraint: constraint((T0308)F42.CB, (T0308)D159.CB) [> 4.0028 = 6.6714 < 8.6728] w=0.4844 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)E40.CB) [> 3.9339 = 6.5565 < 8.5234] w=0.4839 to align # Constraint # added constraint: constraint((T0308)T15.CB, (T0308)T34.CB) [> 3.6904 = 6.1507 < 7.9959] w=0.4813 to align # Constraint # added constraint: constraint((T0308)K14.CB, (T0308)I75.CB) [> 4.6672 = 7.7787 < 10.1123] w=0.4680 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)A89.CB) [> 3.7704 = 6.2840 < 8.1692] w=0.4676 to align # Constraint # added constraint: constraint((T0308)K69.CB, (T0308)H99.CB) [> 3.8407 = 6.4012 < 8.3215] w=0.4609 to align # Constraint # added constraint: constraint((T0308)N11.CB, (T0308)R85.CB) [> 4.6436 = 7.7393 < 10.0611] w=0.4394 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)W141.CB) [> 4.5188 = 7.5313 < 9.7907] w=0.4349 to align # Constraint # added constraint: constraint((T0308)E1.CB, (T0308)S48.CB) [> 3.0432 = 5.0720 < 6.5936] w=0.4338 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)Q164.CB) [> 4.2130 = 7.0216 < 9.1281] w=0.4273 to align # Constraint # added constraint: constraint((T0308)E40.CB, (T0308)V158.CB) [> 4.4254 = 7.3757 < 9.5884] w=0.4189 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)W64.CB) [> 4.0664 = 6.7773 < 8.8105] w=0.4178 to align # Constraint # added constraint: constraint((T0308)I75.CB, (T0308)V158.CB) [> 4.4804 = 7.4674 < 9.7076] w=0.4110 to align # Constraint # added constraint: constraint((T0308)I75.CB, (T0308)F111.CB) [> 4.6467 = 7.7445 < 10.0679] w=0.4107 to align # Constraint # added constraint: constraint((T0308)M54.CB, (T0308)L63.CB) [> 4.2441 = 7.0734 < 9.1955] w=0.4092 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)D53.CB) [> 4.1440 = 6.9066 < 8.9786] w=0.4070 to align # Constraint # added constraint: constraint((T0308)Y68.CB, (T0308)T95.CB) [> 4.1777 = 6.9629 < 9.0518] w=0.4004 to align # Constraint # added constraint: constraint((T0308)T15.CB, (T0308)I31.CB) [> 3.1887 = 5.3146 < 6.9089] w=0.3843 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)G71.CA) [> 4.6207 = 7.7011 < 10.0114] w=0.3805 to align # Constraint # added constraint: constraint((T0308)P108.CB, (T0308)W141.CB) [> 4.3144 = 7.1907 < 9.3479] w=0.3799 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)E92.CB) [> 4.3320 = 7.2199 < 9.3859] w=0.3799 to align # Constraint # added constraint: constraint((T0308)T34.CB, (T0308)M54.CB) [> 4.2774 = 7.1290 < 9.2677] w=0.3786 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)L161.CB) [> 4.5550 = 7.5916 < 9.8691] w=0.3740 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)P33.CB) [> 3.9422 = 6.5703 < 8.5414] w=0.3686 to align # Constraint # added constraint: constraint((T0308)E1.CB, (T0308)T50.CB) [> 3.7508 = 6.2514 < 8.1268] w=0.3672 to align # Constraint # added constraint: constraint((T0308)T15.CB, (T0308)L32.CB) [> 4.0773 = 6.7955 < 8.8341] w=0.3641 to align # Constraint # added constraint: constraint((T0308)E1.CB, (T0308)L47.CB) [> 4.4209 = 7.3681 < 9.5786] w=0.3613 to align # Constraint # added constraint: constraint((T0308)V77.CB, (T0308)A113.CB) [> 4.7220 = 7.8701 < 10.2311] w=0.3498 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)F52.CB) [> 3.3401 = 5.5668 < 7.2368] w=0.3465 to align # Constraint # added constraint: constraint((T0308)S146.CB, (T0308)E156.CB) [> 4.5805 = 7.6342 < 9.9245] w=0.3461 to align # Constraint # added constraint: constraint((T0308)L97.CB, (T0308)I107.CB) [> 4.2761 = 7.1269 < 9.2650] w=0.3426 to align # Constraint # added constraint: constraint((T0308)T34.CB, (T0308)G56.CA) [> 4.1926 = 6.9877 < 9.0840] w=0.3417 to align # Constraint # added constraint: constraint((T0308)E40.CB, (T0308)T50.CB) [> 4.5054 = 7.5090 < 9.7617] w=0.3394 to align # Constraint # added constraint: constraint((T0308)V77.CB, (T0308)F111.CB) [> 4.6961 = 7.8269 < 10.1749] w=0.3287 to align # Constraint # added constraint: constraint((T0308)L97.CB, (T0308)I109.CB) [> 4.3735 = 7.2892 < 9.4759] w=0.3272 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)Y60.CB) [> 4.1169 = 6.8615 < 8.9199] w=0.3185 to align # Constraint # added constraint: constraint((T0308)L32.CB, (T0308)S55.CB) [> 3.2128 = 5.3547 < 6.9611] w=0.3163 to align # Constraint # added constraint: constraint((T0308)K41.CB, (T0308)T50.CB) [> 3.1071 = 5.1785 < 6.7321] w=0.3044 to align # Constraint # added constraint: constraint((T0308)I39.CB, (T0308)F52.CB) [> 2.9598 = 4.9330 < 6.4129] w=0.3044 to align # Constraint # added constraint: constraint((T0308)K14.CB, (T0308)T34.CB) [> 4.3410 = 7.2350 < 9.4055] w=0.2961 to align # Constraint # added constraint: constraint((T0308)T16.CB, (T0308)I31.CB) [> 3.6536 = 6.0894 < 7.9162] w=0.2902 to align # Constraint # added constraint: constraint((T0308)P108.CB, (T0308)H142.CB) [> 4.4812 = 7.4686 < 9.7092] w=0.2897 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)F49.CB) [> 4.6075 = 7.6791 < 9.9829] w=0.2891 to align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)E40.CB) [> 3.6038 = 6.0064 < 7.8083] w=0.2834 to align # Constraint # added constraint: constraint((T0308)E1.CB, (T0308)F49.CB) [> 4.5410 = 7.5684 < 9.8389] w=0.2787 to align # Constraint # added constraint: constraint((T0308)Y68.CB, (T0308)I107.CB) [> 4.6374 = 7.7289 < 10.0476] w=0.2742 to align # Constraint # added constraint: constraint((T0308)K22.CB, (T0308)I39.CB) [> 4.3255 = 7.2092 < 9.3720] w=0.2736 to align # Constraint # added constraint: constraint((T0308)K41.CB, (T0308)V51.CB) [> 4.4419 = 7.4032 < 9.6242] w=0.2681 to align # Constraint # added constraint: constraint((T0308)L93.CB, (T0308)F111.CB) [> 4.5042 = 7.5070 < 9.7591] w=0.2543 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)F49.CB) [> 4.5653 = 7.6088 < 9.8915] w=0.2506 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)R119.CB) [> 4.2189 = 7.0315 < 9.1410] w=0.2319 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)F42.CB) [> 3.3631 = 5.6052 < 7.2867] w=0.2317 to align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)F42.CB) [> 4.0763 = 6.7938 < 8.8320] w=0.2317 to align # Constraint # added constraint: constraint((T0308)N11.CB, (T0308)P33.CB) [> 4.4635 = 7.4391 < 9.6708] w=0.2212 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)F76.CB) [> 4.7281 = 7.8802 < 10.2442] w=0.2179 to align # Constraint # added constraint: constraint((T0308)G71.CA, (T0308)H104.CB) [> 4.1581 = 6.9302 < 9.0092] w=0.2120 to align # Constraint # added constraint: constraint((T0308)F52.CB, (T0308)G71.CA) [> 4.5048 = 7.5079 < 9.7603] w=0.2094 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)I165.CB) [> 4.5605 = 7.6008 < 9.8810] w=0.2037 to align # Constraint # added constraint: constraint((T0308)T34.CB, (T0308)Y60.CB) [> 3.9015 = 6.5026 < 8.4533] w=0.2004 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)W64.CB) [> 4.5875 = 7.6458 < 9.9395] w=0.1983 to align # Constraint # added constraint: constraint((T0308)I39.CB, (T0308)D53.CB) [> 4.3736 = 7.2894 < 9.4762] w=0.1954 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)E92.CB) [> 4.6214 = 7.7023 < 10.0130] w=0.1940 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)L96.CB) [> 4.4066 = 7.3444 < 9.5477] w=0.1912 to align # Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)R106.CB) [> 4.4960 = 7.4933 < 9.7413] w=0.1895 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)F49.CB) [> 4.1173 = 6.8621 < 8.9208] w=0.1885 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)S48.CB) [> 3.8097 = 6.3494 < 8.2543] w=0.1885 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)V51.CB) [> 3.8861 = 6.4768 < 8.4198] w=0.1885 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)T50.CB) [> 3.6308 = 6.0513 < 7.8667] w=0.1885 to align # Constraint # added constraint: constraint((T0308)L47.CB, (T0308)I165.CB) [> 4.2926 = 7.1543 < 9.3006] w=0.1829 to align # Constraint # added constraint: constraint((T0308)S38.CB, (T0308)S48.CB) [> 4.5110 = 7.5183 < 9.7738] w=0.1825 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)A148.CB) [> 4.6192 = 7.6986 < 10.0082] w=0.1816 to align # Constraint # added constraint: constraint((T0308)S55.CB, (T0308)W64.CB) [> 3.8720 = 6.4533 < 8.3893] w=0.1816 to align # Constraint # added constraint: constraint((T0308)Q129.CB, (T0308)I143.CB) [> 4.0268 = 6.7112 < 8.7246] w=0.1816 to align # Constraint # added constraint: constraint((T0308)S128.CB, (T0308)I143.CB) [> 3.1735 = 5.2892 < 6.8760] w=0.1815 to align # Constraint # added constraint: constraint((T0308)F112.CB, (T0308)L154.CB) [> 4.3942 = 7.3237 < 9.5209] w=0.1801 to align # Constraint # added constraint: constraint((T0308)F111.CB, (T0308)L133.CB) [> 4.2926 = 7.1544 < 9.3007] w=0.1756 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)Q57.CB) [> 4.4524 = 7.4207 < 9.6469] w=0.1755 to align # Constraint # added constraint: constraint((T0308)V127.CB, (T0308)I143.CB) [> 3.8827 = 6.4711 < 8.4125] w=0.1751 to align # Constraint # added constraint: constraint((T0308)N11.CB, (T0308)I31.CB) [> 4.1406 = 6.9010 < 8.9713] w=0.1699 to align # Constraint # added constraint: constraint((T0308)T34.CB, (T0308)L63.CB) [> 3.4755 = 5.7924 < 7.5302] w=0.1641 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)L63.CB) [> 3.9969 = 6.6616 < 8.6601] w=0.1641 to align # Constraint # added constraint: constraint((T0308)R83.CB, (T0308)S124.CB) [> 3.4774 = 5.7956 < 7.5343] w=0.1631 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)L93.CB) [> 4.7293 = 7.8822 < 10.2468] w=0.1619 to align # Constraint # added constraint: constraint((T0308)S44.CB, (T0308)V158.CB) [> 3.6694 = 6.1156 < 7.9503] w=0.1591 to align # Constraint # added constraint: constraint((T0308)E40.CB, (T0308)D53.CB) [> 4.4924 = 7.4874 < 9.7336] w=0.1591 to align # Constraint # added constraint: constraint((T0308)P33.CB, (T0308)M54.CB) [> 3.5462 = 5.9103 < 7.6834] w=0.1560 to align # Constraint # added constraint: constraint((T0308)S81.CB, (T0308)R119.CB) [> 4.4017 = 7.3362 < 9.5370] w=0.1559 to align # Constraint # added constraint: constraint((T0308)I35.CB, (T0308)Y67.CB) [> 3.6549 = 6.0915 < 7.9189] w=0.1552 to align # Constraint # added constraint: constraint((T0308)P33.CB, (T0308)Y60.CB) [> 4.1095 = 6.8492 < 8.9040] w=0.1518 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)S124.CB) [> 4.2567 = 7.0945 < 9.2228] w=0.1510 to align # Constraint # added constraint: constraint((T0308)K90.CB, (T0308)I136.CB) [> 3.1509 = 5.2515 < 6.8270] w=0.1498 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)Y68.CB) [> 4.1778 = 6.9629 < 9.0518] w=0.1469 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)A89.CB) [> 4.6453 = 7.7422 < 10.0648] w=0.1453 to align # Constraint # added constraint: constraint((T0308)I78.CB, (T0308)I136.CB) [> 4.4189 = 7.3648 < 9.5742] w=0.1438 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)V127.CB) [> 4.7090 = 7.8484 < 10.2029] w=0.1396 to align # Constraint # added constraint: constraint((T0308)S124.CB, (T0308)C144.CB) [> 4.4501 = 7.4169 < 9.6419] w=0.1392 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)T15.CB) [> 4.7122 = 7.8537 < 10.2098] w=0.1271 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)S48.CB) [> 3.1182 = 5.1970 < 6.7561] w=0.1271 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)S48.CB) [> 4.2228 = 7.0379 < 9.1493] w=0.1271 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)F49.CB) [> 3.5529 = 5.9216 < 7.6981] w=0.1271 to align # Constraint # added constraint: constraint((T0308)C6.CB, (T0308)T50.CB) [> 4.2665 = 7.1108 < 9.2441] w=0.1271 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)F52.CB) [> 3.7710 = 6.2849 < 8.1704] w=0.1271 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)D53.CB) [> 3.8953 = 6.4921 < 8.4398] w=0.1271 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)D53.CB) [> 3.9925 = 6.6542 < 8.6504] w=0.1271 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)M54.CB) [> 3.5251 = 5.8752 < 7.6377] w=0.1271 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)D53.CB) [> 2.7081 = 4.5135 < 5.8676] w=0.1271 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)L118.CB) [> 4.6367 = 7.7279 < 10.0462] w=0.1271 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)D53.CB) [> 4.5102 = 7.5170 < 9.7722] w=0.1271 to align # Constraint # added constraint: constraint((T0308)L21.CB, (T0308)S44.CB) [> 4.1516 = 6.9193 < 8.9950] w=0.1256 to align # Constraint # added constraint: constraint((T0308)L131.CB, (T0308)I143.CB) [> 4.5057 = 7.5095 < 9.7624] w=0.1214 to align # Constraint # added constraint: constraint((T0308)G13.CA, (T0308)I31.CB) [> 4.6618 = 7.7697 < 10.1007] w=0.1102 to align # Constraint # added constraint: constraint((T0308)L9.CB, (T0308)S55.CB) [> 3.2581 = 5.4301 < 7.0592] w=0.1090 to align # Constraint # added constraint: constraint((T0308)G8.CA, (T0308)S55.CB) [> 4.4207 = 7.3678 < 9.5782] w=0.1090 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)V51.CB) [> 4.3681 = 7.2802 < 9.4642] w=0.1090 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)D53.CB) [> 4.6000 = 7.6666 < 9.9666] w=0.1090 to align # Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)H104.CB) [> 4.4368 = 7.3947 < 9.6131] w=0.1035 to align # Constraint # added constraint: constraint((T0308)L32.CB, (T0308)Y60.CB) [> 3.7738 = 6.2896 < 8.1765] w=0.1028 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)R59.CB) [> 2.7502 = 4.5836 < 5.9587] w=0.1004 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)Y67.CB) [> 4.4023 = 7.3371 < 9.5383] w=0.0908 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L93.CB) [> 4.5563 = 7.5938 < 9.8720] w=0.0908 to align # Constraint # added constraint: constraint((T0308)F49.CB, (T0308)A73.CB) [> 4.7101 = 7.8502 < 10.2052] w=0.0823 to align # Constraint # added constraint: constraint((T0308)T15.CB, (T0308)G36.CA) [> 4.1394 = 6.8990 < 8.9687] w=0.0793 to align # Constraint # added constraint: constraint((T0308)E1.CB, (T0308)S46.CB) [> 3.0216 = 5.0360 < 6.5468] w=0.0787 to align # Constraint # added constraint: constraint((T0308)H3.CB, (T0308)L47.CB) [> 4.6054 = 7.6757 < 9.9784] w=0.0726 to align # Constraint # added constraint: constraint((T0308)S24.CB, (T0308)K43.CB) [> 3.5833 = 5.9722 < 7.7639] w=0.0726 to align # Constraint # added constraint: constraint((T0308)I17.CB, (T0308)G151.CA) [> 4.7145 = 7.8574 < 10.2147] w=0.0726 to align # Constraint # added constraint: constraint((T0308)L118.CB, (T0308)D147.CB) [> 4.4676 = 7.4460 < 9.6797] w=0.0726 to align # Constraint # added constraint: constraint((T0308)S45.CB, (T0308)V158.CB) [> 4.4462 = 7.4104 < 9.6335] w=0.0711 to align # Constraint # added constraint: constraint((T0308)V4.CB, (T0308)F42.CB) [> 4.6109 = 7.6849 < 9.9904] w=0.0711 to align # Constraint # added constraint: constraint((T0308)K115.CB, (T0308)S146.CB) [> 4.6651 = 7.7752 < 10.1078] w=0.0705 to align # Constraint # added constraint: constraint((T0308)Q129.CB, (T0308)C144.CB) [> 4.4522 = 7.4203 < 9.6464] w=0.0605 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)L32.CB) [> 4.4952 = 7.4920 < 9.7396] w=0.0551 to align # Constraint # added constraint: constraint((T0308)F52.CB, (T0308)E70.CB) [> 4.7402 = 7.9003 < 10.2704] w=0.0545 to align # Constraint # added constraint: constraint((T0308)L5.CB, (T0308)E70.CB) [> 4.6967 = 7.8278 < 10.1762] w=0.0545 to align # Constraint # added constraint: constraint((T0308)V77.CB, (T0308)S146.CB) [> 4.7409 = 7.9015 < 10.2720] w=0.0545 to align # Constraint # added constraint: constraint((T0308)C144.CB, (T0308)L154.CB) [> 4.3702 = 7.2837 < 9.4689] w=0.0530 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)S128.CB) [> 4.5555 = 7.5925 < 9.8702] w=0.0488 to align # Constraint # added constraint: constraint((T0308)G71.CA, (T0308)R106.CB) [> 4.2006 = 7.0010 < 9.1012] w=0.0484 to align # Constraint # added constraint: constraint((T0308)I31.CB, (T0308)K41.CB) [> 3.9193 = 6.5321 < 8.4918] w=0.0424 to align # Constraint # added constraint: constraint((T0308)P33.CB, (T0308)H66.CB) [> 4.6023 = 7.6705 < 9.9717] w=0.0401 to align # Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)L161.CB) [> 4.5121 = 7.5201 < 9.7761] w=0.0396 to align # Constraint # added constraint: constraint((T0308)F76.CB, (T0308)K139.CB) [> 4.6374 = 7.7290 < 10.0477] w=0.0363 to align # Constraint # added constraint: constraint((T0308)L118.CB, (T0308)I149.CB) [> 4.0384 = 6.7306 < 8.7498] w=0.0363 to align # Constraint # added constraint: constraint((T0308)L7.CB, (T0308)S55.CB) [> 3.6121 = 6.0201 < 7.8261] w=0.0363 to align # Constraint # added constraint: constraint((T0308)K22.CB, (T0308)K43.CB) [> 3.8085 = 6.3476 < 8.2519] w=0.0363 to align # Constraint # added constraint: constraint((T0308)K22.CB, (T0308)K41.CB) [> 4.4890 = 7.4817 < 9.7262] w=0.0363 to align # Constraint # added constraint: constraint((T0308)D10.CB, (T0308)M54.CB) [> 4.6172 = 7.6953 < 10.0039] w=0.0363 to align # Constraint # added constraint: constraint((T0308)S12.CB, (T0308)F112.CB) [> 4.7073 = 7.8455 < 10.1991] w=0.0363 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)W64.CB) [> 4.4001 = 7.3335 < 9.5335] w=0.0363 to align # Constraint # added constraint: constraint((T0308)F37.CB, (T0308)Y60.CB) [> 3.7526 = 6.2544 < 8.1307] w=0.0363 to align # Constraint # added constraint: constraint((T0308)S81.CB, (T0308)M116.CB) [> 3.7699 = 6.2832 < 8.1681] w=0.0348 to align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)F37.CB) [> 4.7103 = 7.8505 < 10.2057] w=0.0303 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)F42.CB) [> 4.0645 = 6.7742 < 8.8065] w=0.0303 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)S124.CB) [> 4.6907 = 7.8178 < 10.1632] w=0.0303 to align # Constraint # added constraint: constraint((T0308)S80.CB, (T0308)V125.CB) [> 3.6882 = 6.1470 < 7.9911] w=0.0303 to align # Constraint # added constraint: constraint((T0308)A113.CB, (T0308)V125.CB) [> 4.4176 = 7.3626 < 9.5714] w=0.0295 to align # Constraint # added constraint: constraint((T0308)S128.CB, (T0308)A145.CB) [> 4.0690 = 6.7817 < 8.8162] w=0.0242 to align # Constraint # added constraint: constraint((T0308)E70.CB, (T0308)R106.CB) [> 4.0515 = 6.7524 < 8.7781] w=0.0242 to align # Constraint # added constraint: constraint((T0308)A73.CB, (T0308)W141.CB) [> 4.6834 = 7.8056 < 10.1473] w=0.0182 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)S44.CB) [> 3.7549 = 6.2581 < 8.1355] w=0.0182 to align # Constraint # added constraint: constraint((T0308)N11.CB, (T0308)M116.CB) [> 4.1846 = 6.9744 < 9.0667] w=0.0182 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)M116.CB) [> 2.7341 = 4.5568 < 5.9239] w=0.0182 to align # Constraint # added constraint: constraint((T0308)D79.CB, (T0308)D117.CB) [> 4.5306 = 7.5510 < 9.8163] w=0.0182 to align # Constraint # added constraint: constraint((T0308)K115.CB, (T0308)A145.CB) [> 4.2518 = 7.0863 < 9.2122] w=0.0182 to align # Constraint # added constraint: constraint((T0308)L110.CB, (T0308)I136.CB) [> 4.6818 = 7.8030 < 10.1439] w=0.0182 to align # Constraint # added constraint: constraint((T0308)S38.CB, (T0308)M54.CB) [> 4.7934 = 7.9891 < 10.3858] w=0.0182 to align # Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L97.CB) [> 4.2446 = 7.0744 < 9.1967] w=0.0182 to align # Constraint # added constraint: constraint((T0308)M54.CB, (T0308)E65.CB) [> 4.6673 = 7.7789 < 10.1125] w=0.0182 to align # Constraint # added constraint: constraint((T0308)I18.CB, (T0308)S44.CB) [> 4.5034 = 7.5057 < 9.7573] w=0.0182 to align # Constraint # added constraint: constraint((T0308)V2.CB, (T0308)E70.CB) [> 3.7777 = 6.2961 < 8.1849] w=0.0182 to align # Constraint # added constraint: constraint((T0308)L131.CB, (T0308)A145.CB) [> 4.6952 = 7.8254 < 10.1730] w=0.0182 to align # Constraint # added constraint: constraint((T0308)T16.CB, (T0308)N30.CB) [> 4.4685 = 7.4476 < 9.6818] w=0.0172 to align # Constraint # added constraint: constraint((T0308)I109.CB, (T0308)L133.CB) [> 4.7059 = 7.8432 < 10.1961] w=0.0121 to align # Constraint # added constraint: constraint((T0308)L32.CB, (T0308)K43.CB) [> 4.6115 = 7.6859 < 9.9916] w=0.0121 to align # Constraint # added constraint: constraint((T0308)T16.CB, (T0308)P33.CB) [> 3.0721 = 5.1202 < 6.6563] w=0.0061 to align # Constraint # added constraint: constraint((T0308)V125.CB, (T0308)I143.CB) [> 4.7276 = 7.8794 < 10.2432] w=0.0053 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0308/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0308/decoys/ # ReadConformPDB reading from PDB file chimera-9-4.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr308.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 195, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 197, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 201, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 203, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 57 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 21 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 82, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 84, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 86, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 143, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 145, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 149, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 151, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 432, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 498, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 500, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 23, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 25, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 29, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 279, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 281, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 283, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 285, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 639, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0308 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.5375 model score -0.5390 model score -0.2142 model score -0.2142 model score -0.2152 model score -0.2208 model score -0.1543 model score -0.2526 model score -0.2522 model score -0.2025 model score -0.2600 model score -0.2490 model score -0.2030 model score -0.2172 model score -0.2308 model score -0.2071 model score -0.2129 model score -0.3106 model score -0.1344 model score 0.6575 model score 1.4928 model score -0.1228 model score 1.4101 model score 1.2807 model score 1.1776 model score 1.3116 model score 1.3898 model score -0.5669 model score -0.5199 model score -0.6455 model score -0.0291 model score -0.6774 model score -0.7023 model score -0.2468 model score -0.2818 model score -0.2232 model score -0.2475 model score -0.2546 model score -0.2516 model score -0.2661 model score -0.2891 model score -0.5155 model score -0.3217 model score -0.2497 model score 1.2741 model score 1.2739 model score 1.2731 model score 1.2747 model score 1.2732 model score -0.2634 model score -0.2580 model score -0.2475 model score -0.2164 model score -0.2795 model score -0.2866 model score -0.2818 model score -0.2546 model score -0.2555 model score -0.2580 model score -0.5404 model score -0.5115 model score 0.3420 model score 1.0898 model score 0.2439 model score 1.2739 model score 1.2713 model score 1.2773 model score 1.2717 model score 1.2758 model score 1.2713 model score 1.2739 model score 1.2758 model score 1.2810 model score 1.2717 model score 2.3035 model score 2.6218 model score 2.3575 model score 2.5840 model score 2.3083 model score -0.4380 model score 0.4561 model score -0.0272 model score -0.1853 model score 1.7402 model score 1.2712 model score 1.2715 model score 1.2770 model score 1.2752 model score 1.2811 model score -0.2425 model score -0.2654 model score -0.2741 model score -0.2555 model score -0.2818 model score -0.5178 model score -0.5315 model score -0.5583 model score -0.5495 model score -0.2972 model score -0.3099 model score -0.5651 model score -0.5707 model score -0.2851 model score -0.2121 model score -0.4930 model score -0.2375 model score -0.2807 model score -0.1177 model score -0.4438 model score -0.1989 model score -0.4818 model score -0.2004 model score -0.4596 model score -0.3610 model score -0.2797 model score -0.3928 model score -0.5134 model score -0.3427 model score -0.4589 model score -0.5399 model score -0.5402 model score -0.5413 model score -0.5396 model score -0.5414 model score -0.5326 model score -0.5399 model score -0.5437 model score -0.5263 model score -0.5216 model score -0.5402 model score -0.5503 model score -0.5403 model score -0.5208 model score -0.5452 model score -0.2902 model score -0.2444 model score -0.3159 model score -0.3159 model score -0.3159 model score -0.3159 model score -0.3106 model score -0.5402 model score -0.2972 model score -0.2972 model score -0.5503 model score -0.3173 model score -0.3220 model score -0.2767 model score -0.2778 model score -0.5334 model score -0.2796 model score -0.2641 model score -0.2060 model score -0.2393 model score -0.2183 model score -0.3242 model score -0.2962 model score -0.2262 model score -0.2589 model score -0.2470 model score -0.2808 model score -0.2934 model score -0.3267 model score -0.2928 model score -0.2871 model score -0.2621 model score -0.2874 model score -0.0645 model score -0.5490 model score -0.2640 model score 1.2712 model score 1.2739 model score 1.2771 model score 1.2762 model score 1.2713 model score 1.2771 model score 1.2714 model score 1.2765 model score 1.2779 model score 1.2780 model score -0.5460 model score -0.3099 model score -0.3068 model score -0.5153 model score -0.2047 model score -0.4589 model score -0.3220 model score -0.2553 model score -0.2793 model score -0.2822 model score -0.4589 model score -0.3220 model score -0.2531 model score -0.2832 model score -0.2588 model score -0.4589 model score -0.3220 model score -0.2553 model score -0.2776 model score -0.2782 model score 1.2717 model score 1.2712 model score 1.2765 model score 1.2715 model score 1.2770 model score -0.4792 model score 1.2717 model score 1.2712 model score 1.2765 model score 1.2715 model score 1.2770 model score -0.5538 model score -0.5115 model score -0.4896 model score -0.2845 model score -0.3877 model score -0.3416 model score -0.3066 model score 1.2716 model score 1.2771 model score 1.2717 model score 1.2717 model score 1.2732 model score 1.2717 model score 1.2745 model score 1.2713 model score 1.2752 model score 1.2755 model score -0.5449 model score -0.5432 model score -0.5514 model score -0.5402 model score -0.5481 model score 2.2307 model score 1.9924 model score 2.1997 model score 1.8254 model score -0.2926 model score -0.2793 model score -0.3011 model score -0.3196 model score -0.2776 model score -0.5016 model score 0.0933 model score -0.4901 model score -0.3101 model score -0.4107 model score -0.5760 model score -0.2359 model score -0.2610 USE_META, weight: 0.9554 cost: -0.5375 min: -0.7023 max: 2.6218 USE_META, weight: 0.9558 cost: -0.5390 min: -0.7023 max: 2.6218 USE_META, weight: 0.8678 cost: -0.2142 min: -0.7023 max: 2.6218 USE_META, weight: 0.8678 cost: -0.2142 min: -0.7023 max: 2.6218 USE_META, weight: 0.8681 cost: -0.2152 min: -0.7023 max: 2.6218 USE_META, weight: 0.8696 cost: -0.2208 min: -0.7023 max: 2.6218 USE_META, weight: 0.8516 cost: -0.1543 min: -0.7023 max: 2.6218 USE_META, weight: 0.8782 cost: -0.2526 min: -0.7023 max: 2.6218 USE_META, weight: 0.8781 cost: -0.2522 min: -0.7023 max: 2.6218 USE_META, weight: 0.8647 cost: -0.2025 min: -0.7023 max: 2.6218 USE_META, weight: 0.8802 cost: -0.2600 min: -0.7023 max: 2.6218 USE_META, weight: 0.8773 cost: -0.2490 min: -0.7023 max: 2.6218 USE_META, weight: 0.8648 cost: -0.2030 min: -0.7023 max: 2.6218 USE_META, weight: 0.8687 cost: -0.2172 min: -0.7023 max: 2.6218 USE_META, weight: 0.8723 cost: -0.2308 min: -0.7023 max: 2.6218 USE_META, weight: 0.8659 cost: -0.2071 min: -0.7023 max: 2.6218 USE_META, weight: 0.8675 cost: -0.2129 min: -0.7023 max: 2.6218 USE_META, weight: 0.8939 cost: -0.3106 min: -0.7023 max: 2.6218 USE_META, weight: 0.8462 cost: -0.1344 min: 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USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.7932 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.7932 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.7932 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9473 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9473 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9473 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, 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eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9938 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9938 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9938 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.6044 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.6044 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.6044 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, 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max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9123 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9123 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.9123 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 Number of contacts in models: 250 Number of contacts in alignments: 171 NUMB_ALIGNS: 171 Adding 4044 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -264.6156, CN propb: -264.6156 weights: 0.4430 constraints: 513 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 513 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 513 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 3531 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 3531 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 4044 # command: