# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0347 numbered 1 through 205 Created new target T0347 from T0347.a2m # command:CPU_time= 6.257 sec, elapsed time= 6.465 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk1A/T0347-1vk1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1vk1A/T0347-1vk1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk1A read from 1vk1A/T0347-1vk1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vk1A in training set Warning: unaligning (T0347)L17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)P28 Warning: unaligning (T0347)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)P28 Warning: unaligning (T0347)D97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)V113 Warning: unaligning (T0347)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)V113 Warning: unaligning (T0347)A142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)A134 Warning: unaligning (T0347)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)A134 Warning: unaligning (T0347)M145 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)G137 Warning: unaligning (T0347)G147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)G137 T0347 3 :HIYEPRLSRIAIDK 1vk1A 12 :PVKKVEYVFIELDK # choosing archetypes in rotamer library T0347 20 :TQIAV 1vk1A 29 :HEQLV T0347 26 :FREVELKRKEWRETR 1vk1A 34 :QRELEDFIESVTGSG T0347 50 :NHIVPVVAGPK 1vk1A 51 :WKPMLLAKIPG T0347 61 :DRAYLIDHHHLVLALSKEGVEHVLTSEV 1vk1A 63 :DEYLIVDGHHRWAGLQKLGAKRAPSVIL T0347 90 :KFS 1vk1A 98 :KVY T0347 95 :GK 1vk1A 109 :DV T0347 100 :WSVMDHRNLIYPFDAQ 1vk1A 114 :IERLKAEGLEVIEDEK T0347 140 :AG 1vk1A 130 :AE T0347 148 :GY 1vk1A 138 :EI Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk1A/T0347-1vk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1vk1A/T0347-1vk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk1A read from 1vk1A/T0347-1vk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vk1A in training set Warning: unaligning (T0347)L17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)P28 Warning: unaligning (T0347)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)P28 Warning: unaligning (T0347)D97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)V113 Warning: unaligning (T0347)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)V113 Warning: unaligning (T0347)A142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)A134 Warning: unaligning (T0347)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)A134 Warning: unaligning (T0347)M145 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)G137 Warning: unaligning (T0347)G147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)G137 Warning: unaligning (T0347)E158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)K160 Warning: unaligning (T0347)F159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)K160 Warning: unaligning (T0347)R171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)E173 T0347 5 :YEPRLSRIAIDK 1vk1A 14 :KKVEYVFIELDK T0347 20 :TQIAV 1vk1A 29 :HEQLV T0347 26 :FREVELKRKEWRETR 1vk1A 34 :QRELEDFIESVTGSG T0347 50 :NHIVPVVAGPK 1vk1A 51 :WKPMLLAKIPG T0347 61 :DRAYLIDHHHLVLALSKEGVEHVLTSEV 1vk1A 63 :DEYLIVDGHHRWAGLQKLGAKRAPSVIL T0347 95 :GK 1vk1A 109 :DV T0347 100 :WSVMDHRNLIYPFDAQ 1vk1A 114 :IERLKAEGLEVIEDEK T0347 140 :AG 1vk1A 130 :AE T0347 148 :GY 1vk1A 138 :EI T0347 150 :AKV 1vk1A 146 :EKS T0347 157 :S 1vk1A 157 :E T0347 161 :WADFLRRRID 1vk1A 161 :VSKVLDEMDQ Number of specific fragments extracted= 12 number of extra gaps= 1 total=22 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk1A/T0347-1vk1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1vk1A/T0347-1vk1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk1A read from 1vk1A/T0347-1vk1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vk1A in training set Warning: unaligning (T0347)L17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)P28 Warning: unaligning (T0347)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)P28 Warning: unaligning (T0347)D97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)V113 Warning: unaligning (T0347)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)V113 Warning: unaligning (T0347)A142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)A134 Warning: unaligning (T0347)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)A134 Warning: unaligning (T0347)M145 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)G137 Warning: unaligning (T0347)G147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)G137 Warning: unaligning (T0347)E158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)K160 Warning: unaligning (T0347)F159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk1A)K160 Warning: unaligning (T0347)R171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk1A)E173 T0347 5 :YEPRLSRIAIDK 1vk1A 14 :KKVEYVFIELDK T0347 20 :TQI 1vk1A 29 :HEQ T0347 24 :VGFREVELKRKEWRETR 1vk1A 32 :LVQRELEDFIESVTGSG T0347 50 :NHIVPVVAGPK 1vk1A 51 :WKPMLLAKIPG T0347 61 :DRAYLIDHHHLVLALSKEGVEHVLTSEV 1vk1A 63 :DEYLIVDGHHRWAGLQKLGAKRAPSVIL T0347 89 :AKFSHL 1vk1A 97 :VKVYTW T0347 95 :GK 1vk1A 109 :DV T0347 100 :WSVMDHRNLIYPFDAQ 1vk1A 114 :IERLKAEGLEVIEDEK T0347 140 :AG 1vk1A 130 :AE T0347 148 :GYA 1vk1A 138 :EIA T0347 151 :K 1vk1A 147 :K T0347 152 :VIIPFS 1vk1A 152 :PGGLEE T0347 161 :WADFLRRRID 1vk1A 161 :VSKVLDEMDQ Number of specific fragments extracted= 13 number of extra gaps= 1 total=35 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xb4A/T0347-1xb4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xb4A expands to /projects/compbio/data/pdb/1xb4.pdb.gz 1xb4A:# T0347 read from 1xb4A/T0347-1xb4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xb4A read from 1xb4A/T0347-1xb4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xb4A to template set # found chain 1xb4A in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)K73 Warning: unaligning (T0347)S86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)K73 Warning: unaligning (T0347)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)T116 Warning: unaligning (T0347)G122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)T116 T0347 31 :LKRKEWRETRKKDGDDFLGNHIVPV 1xb4A 21 :LTRRQQISTWIDIISQYCKTKKIWY T0347 57 :AGPKDRA 1xb4A 46 :MSVDGTV T0347 87 :EVAKFSHLG 1xb4A 74 :NLFNNEDIQ T0347 96 :KDEFWSVMDHRNLIYPFDAQGLR 1xb4A 90 :IDEIWSQMTKEGKCLPIDQSGRR T0347 123 :DIP 1xb4A 117 :TTT T0347 174 :LSDSFDDALAEAMKLAKSREAR 1xb4A 124 :LWKSLDSWASLILQWFEDSGKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=41 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xb4A/T0347-1xb4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1xb4A/T0347-1xb4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xb4A read from 1xb4A/T0347-1xb4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xb4A in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)K73 Warning: unaligning (T0347)S86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)K73 Warning: unaligning (T0347)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)T116 Warning: unaligning (T0347)G122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)T116 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVV 1xb4A 22 :TRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKDRA 1xb4A 47 :SVDGTV T0347 87 :EVAKFSHLGK 1xb4A 74 :NLFNNEDIQR T0347 97 :DEFWSVMDHRNLIYPFDAQGLR 1xb4A 91 :DEIWSQMTKEGKCLPIDQSGRR T0347 123 :D 1xb4A 117 :T T0347 174 :LSDSFDDALAEAMKLAKSR 1xb4A 124 :LWKSLDSWASLILQWFEDS T0347 199 :GWCG 1xb4A 143 :GKLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=48 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xb4A/T0347-1xb4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1xb4A/T0347-1xb4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xb4A read from 1xb4A/T0347-1xb4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xb4A in template set Warning: unaligning (T0347)H68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)K73 Warning: unaligning (T0347)S86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)K73 Warning: unaligning (T0347)R119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xb4A)T116 Warning: unaligning (T0347)G122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xb4A)T116 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVV 1xb4A 22 :TRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKDRA 1xb4A 47 :SVDGTV T0347 87 :EVAKFSHL 1xb4A 74 :NLFNNEDI T0347 95 :GK 1xb4A 86 :SQ T0347 97 :DEFWSVMDHRNLIYPFDAQGLR 1xb4A 91 :DEIWSQMTKEGKCLPIDQSGRR T0347 152 :VII 1xb4A 117 :TTT T0347 174 :LSDSFDDALAEAMKLAKS 1xb4A 124 :LWKSLDSWASLILQWFED Number of specific fragments extracted= 7 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xw3A/T0347-1xw3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xw3A expands to /projects/compbio/data/pdb/1xw3.pdb.gz 1xw3A:Skipped atom 133, because occupancy 0.5 <= existing 0.500 in 1xw3A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 1xw3A Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1xw3A # T0347 read from 1xw3A/T0347-1xw3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xw3A read from 1xw3A/T0347-1xw3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xw3A to template set # found chain 1xw3A in template set T0347 1 :MTHIYEPRLSRIAIDKL 1xw3A 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRET 1xw3A 51 :RPLPSVLDPAKVQSLVDTIRED T0347 45 :DDFLGNHIVPVVAGPKDRAYLID 1xw3A 73 :PDSVPPIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVAK 1xw3A 98 :GCHRYAAYQQLQRETIPAKLVQS T0347 95 :GKDEFWSVM 1xw3A 121 :TLSDLRVYL Number of specific fragments extracted= 5 number of extra gaps= 0 total=60 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xw3A/T0347-1xw3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1xw3A/T0347-1xw3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xw3A read from 1xw3A/T0347-1xw3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xw3A in template set T0347 1 :MTHIYEPRLSRIAIDKL 1xw3A 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETRKK 1xw3A 51 :RPLPSVLDPAKVQSLVDTIREDPDS T0347 48 :LGNHIVPVVAGPKDRAYLID 1xw3A 76 :VPPIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1xw3A 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVM 1xw3A 120 :STLSDLRVYL Number of specific fragments extracted= 5 number of extra gaps= 0 total=65 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xw3A/T0347-1xw3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1xw3A/T0347-1xw3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xw3A read from 1xw3A/T0347-1xw3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xw3A in template set T0347 1 :MTHIYEPRLSRIAIDKL 1xw3A 33 :IHSGRIAAVHNVPLSVL T0347 23 :AVGFREVELKRKEWRETRKK 1xw3A 56 :VLDPAKVQSLVDTIREDPDS T0347 53 :VPVVAGPKDRAYLID 1xw3A 81 :VLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVAK 1xw3A 98 :GCHRYAAYQQLQRETIPAKLVQS T0347 95 :GKDEFWSVM 1xw3A 121 :TLSDLRVYL T0347 121 :SGDIP 1xw3A 130 :GASTP Number of specific fragments extracted= 6 number of extra gaps= 0 total=71 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzsA/T0347-1yzsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yzsA expands to /projects/compbio/data/pdb/1yzs.pdb.gz 1yzsA:# T0347 read from 1yzsA/T0347-1yzsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzsA read from 1yzsA/T0347-1yzsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yzsA to template set # found chain 1yzsA in template set T0347 1 :MTHIYEPRLSRIAIDKL 1yzsA 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETR 1yzsA 51 :RPLPSVLDPAKVQSLVDTIREDP T0347 46 :DFLGNHIVPVVAGPKDRAYLID 1yzsA 74 :DSVPPIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1yzsA 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVMDHR 1yzsA 120 :STLSDLRVYLGAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=76 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzsA/T0347-1yzsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1yzsA/T0347-1yzsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzsA read from 1yzsA/T0347-1yzsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzsA in template set T0347 1 :MTHIYEPRLSRIAIDKL 1yzsA 33 :IHSGRIAAVHNVPLSVL T0347 18 :RPTQIAVGFREVELKRKEWRETRKK 1yzsA 51 :RPLPSVLDPAKVQSLVDTIREDPDS T0347 44 :G 1yzsA 77 :P T0347 50 :NHIVPVVAGPKDRAYLID 1yzsA 78 :PIDVLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1yzsA 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVMDHR 1yzsA 120 :STLSDLRVYLGAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzsA/T0347-1yzsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1yzsA/T0347-1yzsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzsA read from 1yzsA/T0347-1yzsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzsA in template set T0347 1 :MTHIYEPRLSRIAIDKL 1yzsA 33 :IHSGRIAAVHNVPLSVL T0347 23 :AVGFREVELKRKEWRETRKK 1yzsA 56 :VLDPAKVQSLVDTIREDPDS T0347 53 :VPVVAGPKDRAYLID 1yzsA 81 :VLWIKGAQGGDYFYS T0347 68 :HHHLVLALSKEGVEHVLTSEVA 1yzsA 98 :GCHRYAAYQQLQRETIPAKLVQ T0347 94 :LGKDEFWSVMDHR 1yzsA 120 :STLSDLRVYLGAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=87 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u5tC/T0347-1u5tC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u5tC expands to /projects/compbio/data/pdb/1u5t.pdb.gz 1u5tC:# T0347 read from 1u5tC/T0347-1u5tC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u5tC read from 1u5tC/T0347-1u5tC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u5tC to template set # found chain 1u5tC in template set Warning: unaligning (T0347)R62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u5tC)S72 Warning: unaligning (T0347)H93 because of BadResidue code BAD_PEPTIDE in next template residue (1u5tC)Q82 Warning: unaligning (T0347)L94 because of BadResidue code BAD_PEPTIDE at template residue (1u5tC)Q82 T0347 31 :LKRKEWRETRKKDGDDFLGNHIVPVV 1u5tC 21 :LTRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKD 1u5tC 47 :SVDG T0347 89 :AKFS 1u5tC 77 :NNED T0347 95 :G 1u5tC 83 :R T0347 97 :DEFWSVMDHRNLIYPFDAQGLRRQSGDI 1u5tC 91 :DEIWSQMTKEGKCLPIDQSGRRSSNTTT T0347 131 :LEDDPFRSLAGALR 1u5tC 123 :ILWKSLDSWASLIL T0347 145 :MAGGYAKVII 1u5tC 141 :DSGKLNQVIT Number of specific fragments extracted= 7 number of extra gaps= 1 total=94 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u5tC/T0347-1u5tC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1u5tC/T0347-1u5tC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u5tC read from 1u5tC/T0347-1u5tC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u5tC in template set Warning: unaligning (T0347)R62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u5tC)S72 Warning: unaligning (T0347)K90 because of BadResidue code BAD_PEPTIDE in next template residue (1u5tC)Q82 Warning: unaligning (T0347)F91 because of BadResidue code BAD_PEPTIDE at template residue (1u5tC)Q82 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVV 1u5tC 22 :TRRQQISTWIDIISQYCKTKKIWYM T0347 58 :GPKD 1u5tC 47 :SVDG T0347 84 :LTSEVA 1u5tC 75 :LFNNED T0347 92 :SHLGK 1u5tC 83 :RSVSQ T0347 97 :DEFWSVMDHRNLIYPFDAQGLRRQSGD 1u5tC 91 :DEIWSQMTKEGKCLPIDQSGRRSSNTT T0347 133 :DDPFRSLAGALR 1u5tC 125 :WKSLDSWASLIL T0347 145 :MAGGYAKVI 1u5tC 141 :DSGKLNQVI Number of specific fragments extracted= 7 number of extra gaps= 1 total=101 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u5tC/T0347-1u5tC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1u5tC/T0347-1u5tC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u5tC read from 1u5tC/T0347-1u5tC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u5tC in template set Warning: unaligning (T0347)R62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u5tC)S72 T0347 32 :KRKEWRETRKKDGDDFLGNHIVPVVAG 1u5tC 22 :TRRQQISTWIDIISQYCKTKKIWYMSV T0347 60 :KD 1u5tC 49 :DG T0347 92 :SHLGK 1u5tC 83 :RSVSQ T0347 97 :DEFWSVMDHRNLIYPFDAQGLRRQSGDI 1u5tC 91 :DEIWSQMTKEGKCLPIDQSGRRSSNTTT T0347 175 :SD 1u5tC 119 :TR T0347 177 :SFDDALAEAMKLAK 1u5tC 127 :SLDSWASLILQWFE Number of specific fragments extracted= 6 number of extra gaps= 0 total=107 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gs5A/T0347-1gs5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gs5A expands to /projects/compbio/data/pdb/1gs5.pdb.gz 1gs5A:Skipped atom 7, because occupancy 0.400 <= existing 0.400 in 1gs5A Skipped atom 9, because occupancy 0.400 <= existing 0.400 in 1gs5A Skipped atom 11, because occupancy 0.400 <= existing 0.400 in 1gs5A Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1364, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1573, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1575, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1577, because occupancy 0.500 <= existing 0.500 in 1gs5A Skipped atom 1579, because occupancy 0.500 <= existing 0.500 in 1gs5A # T0347 read from 1gs5A/T0347-1gs5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gs5A read from 1gs5A/T0347-1gs5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gs5A to template set # found chain 1gs5A in template set T0347 8 :RLSRIA 1gs5A 111 :KVTQLD T0347 15 :DKLRPTQIAVG 1gs5A 117 :EELGHVGLAQP T0347 39 :TRKKDGDDFLGNHIVPVV 1gs5A 128 :GSPKLINSLLENGYLPVV T0347 57 :AGPKDRAYLIDHHHLVLALSKE 1gs5A 150 :VTDEGQLMNVNADQAATALAAT T0347 79 :G 1gs5A 173 :G T0347 83 :VLTSEVAKFSH 1gs5A 174 :ADLILLSDVSG T0347 111 :PFDAQGLRRQ 1gs5A 185 :ILDGKGQRIA T0347 137 :RSLAGALRMAGGYAKV 1gs5A 198 :AAKAEQLIEQGIITDG T0347 156 :FSEFGWADFLRRRIDR 1gs5A 215 :IVKVNAALDAARTLGR Number of specific fragments extracted= 9 number of extra gaps= 0 total=116 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gs5A/T0347-1gs5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1gs5A/T0347-1gs5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gs5A read from 1gs5A/T0347-1gs5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gs5A in template set T0347 8 :RLSRIA 1gs5A 111 :KVTQLD T0347 15 :DKLRPTQIA 1gs5A 117 :EELGHVGLA T0347 39 :TRKKDGDDFLGNHIVPVV 1gs5A 128 :GSPKLINSLLENGYLPVV T0347 57 :AGPKDRAYLIDHHHLVLALSKE 1gs5A 150 :VTDEGQLMNVNADQAATALAAT T0347 79 :GVEHVLTSE 1gs5A 173 :GADLILLSD T0347 108 :LIYPFDAQGLRR 1gs5A 182 :VSGILDGKGQRI T0347 137 :RSLAGALRMAGGYAKV 1gs5A 198 :AAKAEQLIEQGIITDG T0347 156 :FSEFGWADFLRRRID 1gs5A 215 :IVKVNAALDAARTLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=124 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gs5A/T0347-1gs5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1gs5A/T0347-1gs5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gs5A read from 1gs5A/T0347-1gs5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gs5A in template set T0347 40 :RKKDGDDFLGNHIVPVV 1gs5A 129 :SPKLINSLLENGYLPVV T0347 57 :AGPKDRAYLIDHHHLVLALSKE 1gs5A 150 :VTDEGQLMNVNADQAATALAAT T0347 79 :GV 1gs5A 173 :GA T0347 84 :LTSEVAKFS 1gs5A 175 :DLILLSDVS T0347 110 :YPFDAQGLRRQ 1gs5A 184 :GILDGKGQRIA T0347 137 :RSLAGALRMAGGYAK 1gs5A 198 :AAKAEQLIEQGIITD T0347 157 :SEFGWADFLRRR 1gs5A 216 :VKVNAALDAART Number of specific fragments extracted= 7 number of extra gaps= 0 total=131 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5zA/T0347-1z5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z5zA expands to /projects/compbio/data/pdb/1z5z.pdb.gz 1z5zA:# T0347 read from 1z5zA/T0347-1z5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z5zA read from 1z5zA/T0347-1z5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z5zA to template set # found chain 1z5zA in template set T0347 17 :LRPTQIAVGFREVELKRKEWRETRKKDGDDFL 1z5zA 672 :LTPEQAAMYKAEVENLFNNIDSVTGIKRKGMI T0347 49 :GNHIVPVVAGP 1z5zA 746 :EGDKIAIFTQF T0347 68 :HHHLVLALSKEGVE 1z5zA 759 :MGKIIRNIIEKELN T0347 82 :HVLT 1z5zA 774 :EVPF T0347 87 :E 1z5zA 778 :L T0347 91 :FSHLGKDE 1z5zA 779 :YGELSKKE T0347 99 :FWSVMDHRNLIYP 1z5zA 790 :IISKFQNNPSVKF T0347 112 :FDAQGLRRQSGD 1z5zA 807 :VKAGGFGINLTS Number of specific fragments extracted= 8 number of extra gaps= 0 total=139 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5zA/T0347-1z5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1z5zA/T0347-1z5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z5zA read from 1z5zA/T0347-1z5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z5zA in template set T0347 10 :SRIA 1z5zA 668 :VYCN T0347 17 :LRPTQIAVGFREVELKRKEWRETRKKDGDDFL 1z5zA 672 :LTPEQAAMYKAEVENLFNNIDSVTGIKRKGMI T0347 49 :GNHIVPVVAGP 1z5zA 746 :EGDKIAIFTQF T0347 68 :HHHLVLALSKEGVEHVLTSEVAKFSHLGKDEFWSVMDHRNLIYP 1z5zA 759 :MGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKF T0347 112 :FDAQGLRRQSGDI 1z5zA 807 :VKAGGFGINLTSA Number of specific fragments extracted= 5 number of extra gaps= 0 total=144 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5zA/T0347-1z5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1z5zA/T0347-1z5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z5zA read from 1z5zA/T0347-1z5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z5zA in template set T0347 9 :LSRIA 1z5zA 667 :NVYCN T0347 17 :LRPTQIAVGFREVELKRKEWRETRKKDGDDFLGN 1z5zA 672 :LTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILS T0347 59 :PKDRAYLIDHH 1z5zA 746 :EGDKIAIFTQF T0347 71 :LVLALS 1z5zA 762 :IIRNII T0347 77 :KEGVEHVLTS 1z5zA 770 :ELNTEVPFLY T0347 92 :SHLGKDE 1z5zA 780 :GELSKKE T0347 99 :FWSVMDHRN 1z5zA 790 :IISKFQNNP T0347 108 :LIYPFDAQGLRRQSG 1z5zA 803 :IVLSVKAGGFGINLT Number of specific fragments extracted= 8 number of extra gaps= 0 total=152 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3dA/T0347-1p3dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p3dA expands to /projects/compbio/data/pdb/1p3d.pdb.gz 1p3dA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 1p3dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1p3dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1p3dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 1974, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 1p3dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 3486, because occupancy 0.500 <= existing 0.500 in 1p3dA Skipped atom 3488, because occupancy 0.500 <= existing 0.500 in 1p3dA # T0347 read from 1p3dA/T0347-1p3dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p3dA read from 1p3dA/T0347-1p3dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p3dA to template set # found chain 1p3dA in template set T0347 5 :YEPRLSRIAID 1p3dA 276 :PNNERINVLLN T0347 23 :AVGFREVELK 1p3dA 287 :VPGKHNALNA T0347 38 :ETRKKDGDDFL 1p3dA 307 :GIANEAILEAL T0347 58 :GPKDRAYLID 1p3dA 335 :RPNGKVRLVD T0347 68 :HHH 1p3dA 347 :GHH T0347 71 :LVLALSKEGVEHVLTSEV 1p3dA 356 :TIKAAREGWGDKRIVMIF T0347 96 :KDEFWSVMDHRNL 1p3dA 385 :FDDFVQVLSQVDA T0347 109 :IYPFDAQGLRR 1p3dA 401 :LDVYAAGEAPI T0347 132 :EDDPFRSLAGALRMAGGYAKVII 1p3dA 412 :VGADSKSLCRSIRNLGKVDPILV T0347 156 :FSEFGWADFLRRRIDRD 1p3dA 435 :SDTSQLGDVLDQIIQDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=162 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3dA/T0347-1p3dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1p3dA/T0347-1p3dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p3dA read from 1p3dA/T0347-1p3dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p3dA in template set T0347 5 :YEPRLSRIAID 1p3dA 276 :PNNERINVLLN T0347 24 :VGFREVELK 1p3dA 288 :PGKHNALNA T0347 38 :ETRKKDGDDFL 1p3dA 307 :GIANEAILEAL T0347 56 :VAGPKDRAYLID 1p3dA 333 :FIRPNGKVRLVD T0347 68 :HHH 1p3dA 347 :GHH T0347 72 :VLALSKEGVEHVLTSEV 1p3dA 357 :IKAAREGWGDKRIVMIF T0347 97 :DEFWSVMDHRNLI 1p3dA 386 :DDFVQVLSQVDAL T0347 110 :YPFDAQGLRR 1p3dA 402 :DVYAAGEAPI T0347 132 :EDDPFRSLAGALRMAGGY 1p3dA 412 :VGADSKSLCRSIRNLGKV T0347 151 :KVIIPFSEFGWADFLRRRIDRD 1p3dA 430 :DPILVSDTSQLGDVLDQIIQDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=172 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3dA/T0347-1p3dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1p3dA/T0347-1p3dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p3dA read from 1p3dA/T0347-1p3dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p3dA in template set T0347 40 :RKKDGDDFLGNHIV 1p3dA 309 :ANEAILEALADFQG T0347 60 :KDRAYLIDHHHLVLALSKE 1p3dA 366 :DKRIVMIFQPHRYSRTRDL T0347 96 :KDEFWSVMDHRNLIY 1p3dA 385 :FDDFVQVLSQVDALI T0347 111 :PFDAQGLR 1p3dA 403 :VYAAGEAP T0347 131 :LEDDPFRSLAGALRMAGGYAK 1p3dA 411 :IVGADSKSLCRSIRNLGKVDP T0347 152 :V 1p3dA 436 :D T0347 158 :EFGWADFLRRRIDRD 1p3dA 437 :TSQLGDVLDQIIQDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6t1/T0347-1t6t1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t6t1 expands to /projects/compbio/data/pdb/1t6t.pdb.gz 1t6t1:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0347 read from 1t6t1/T0347-1t6t1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6t1 read from 1t6t1/T0347-1t6t1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t6t1 to template set # found chain 1t6t1 in template set T0347 31 :LKRKEWR 1t6t1 10 :EWIKELK T0347 46 :DFLGNHI 1t6t1 17 :KASREAV T0347 55 :VVA 1t6t1 24 :ILV T0347 67 :DHHHLVLALSKEGVEHVL 1t6t1 27 :EGKNDKKALSKFSIKNVI T0347 90 :KFSHLGKDEFWSVMDHRN 1t6t1 45 :DLSGKRYADVVDMLEGKW T0347 109 :IYPFDAQ 1t6t1 66 :ILLFDLD T0347 136 :FRSLAGALRMAGGY 1t6t1 79 :NQKMKELLSSQGFL T0347 157 :SEFGWADFLRRRIDRDLLS 1t6t1 93 :VDENFRNFLKKWNIIHIEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=187 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6t1/T0347-1t6t1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1t6t1/T0347-1t6t1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6t1 read from 1t6t1/T0347-1t6t1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6t1 in template set T0347 31 :LKRKEWRE 1t6t1 10 :EWIKELKK T0347 47 :FLGNH 1t6t1 18 :ASREA T0347 54 :PVVAGP 1t6t1 23 :VILVEG T0347 69 :HHLVLALSKEGVEHVLT 1t6t1 29 :KNDKKALSKFSIKNVID T0347 91 :FSHLGKDEFWSVMDHRN 1t6t1 46 :LSGKRYADVVDMLEGKW T0347 108 :LIYPFDAQGLR 1t6t1 67 :LLFDLDTHGER T0347 135 :PFRSLAGALRMAGG 1t6t1 78 :INQKMKELLSSQGF T0347 156 :FSEFGWADFLRRRIDRDL 1t6t1 92 :LVDENFRNFLKKWNIIHI Number of specific fragments extracted= 8 number of extra gaps= 0 total=195 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6t1/T0347-1t6t1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1t6t1/T0347-1t6t1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6t1 read from 1t6t1/T0347-1t6t1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6t1 in template set T0347 43 :DGDDFLGNH 1t6t1 10 :EWIKELKKA T0347 59 :PKDRAYLIDHHHLVLALSKEGVEHVL 1t6t1 19 :SREAVILVEGKNDKKALSKFSIKNVI T0347 90 :KFSHLGKDEFWSVMDHRN 1t6t1 45 :DLSGKRYADVVDMLEGKW T0347 109 :IYPFDAQ 1t6t1 66 :ILLFDLD T0347 135 :PFRSLAGALRMAGGY 1t6t1 78 :INQKMKELLSSQGFL T0347 157 :SEFGWADFLRRRIDRDL 1t6t1 93 :VDENFRNFLKKWNIIHI Number of specific fragments extracted= 6 number of extra gaps= 0 total=201 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wd5A/T0347-1wd5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wd5A expands to /projects/compbio/data/pdb/1wd5.pdb.gz 1wd5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0347 read from 1wd5A/T0347-1wd5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wd5A read from 1wd5A/T0347-1wd5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wd5A to template set # found chain 1wd5A in template set T0347 28 :EVELKRKEWRETRKKDGDDFLGNHIVP 1wd5A 90 :YLEREAARQRDVLRKRAERYRRVRPKA T0347 57 :AGPKDRAYLIDH 1wd5A 117 :ARKGRDVVLVDD T0347 70 :HLVLALSKEGVEHVLTSEV 1wd5A 138 :AALSVVFQEGPRRVVVAVP T0347 96 :KDEFWSVMDHRNLIYPFD 1wd5A 159 :SPEAVERLKARAEVVALS T0347 124 :IPKNIHDLE 1wd5A 177 :VPQDFAAVG Number of specific fragments extracted= 5 number of extra gaps= 0 total=206 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wd5A/T0347-1wd5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1wd5A/T0347-1wd5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wd5A read from 1wd5A/T0347-1wd5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wd5A in template set T0347 28 :EVELKRKEWRETRKKDGDDFLGNHIVP 1wd5A 90 :YLEREAARQRDVLRKRAERYRRVRPKA T0347 58 :GPKDRAYLIDH 1wd5A 118 :RKGRDVVLVDD T0347 69 :HHLVLALSKEGVEHVLTSEV 1wd5A 137 :EAALSVVFQEGPRRVVVAVP T0347 96 :KDEFWSVMDHRNLIYPFDAQGLRRQSGDIPKNIHDLEDDPFRSLA 1wd5A 159 :SPEAVERLKARAEVVALSVPQDFAAVGAYYLDFGEVTDEDVEAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=210 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wd5A/T0347-1wd5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0347 read from 1wd5A/T0347-1wd5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wd5A read from 1wd5A/T0347-1wd5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wd5A in template set T0347 27 :REVELKRKEWRETRKKDGDDFLGNHIVP 1wd5A 89 :SYLEREAARQRDVLRKRAERYRRVRPKA T0347 57 :AGPKDRAYLIDHH 1wd5A 117 :ARKGRDVVLVDDG T0347 70 :HLVLALSKEGVEHVLTSEV 1wd5A 138 :AALSVVFQEGPRRVVVAVP T0347 96 :KDEFWSVMDHRNLIYPF 1wd5A 159 :SPEAVERLKARAEVVAL T0347 113 :DAQ 1wd5A 178 :PQD T0347 118 :RRQSGDIPKNIHDLED 1wd5A 181 :FAAVGAYYLDFGEVTD Number of specific fragments extracted= 6 number of extra gaps= 0 total=216 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 12.285 sec, elapsed time= 13.180 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 20910 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.334 sec, elapsed time= 13.235 sec. # command:Reading probabilities from T0347.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.185 Optimizing... Probability sum: -389.831, CN propb: -389.831 weights: 0.284 constraints: 360 # command:CPU_time= 23.703 sec, elapsed time= 24.674 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 360 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 360 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 771 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 771 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 18175 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 18175 # command:CPU_time= 24.051 sec, elapsed time= 25.266 sec. # command: