# command:# Seed set to 1274902455 # 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 # 493441 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 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # 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:CPU_time= 23.119 sec, elapsed time= 26.936 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1963 20 (100.000%) # n-terminus 2 1934 333 (83.250%) # middle 1 483679 20 (100.000%) # middle 2 477517 400 (100.000%) # middle 3 471578 7988 (99.850%) # middle 4 465793 120683 (75.427%) # c-terminus 1 1917 20 (100.000%) # c-terminus 2 1889 372 (93.000%) # ss-bonds 1052 # command:CPU_time= 36.474 sec, elapsed time= 44.175 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0550 numbered 1 through 339 Created new target T0550 from T0550.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.477 sec, elapsed time= 44.219 sec. # command:# Prefix for input files set to # command:# reading script from file T0550.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3flpA/T0550-3flpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3flpA expands to /projects/compbio/data/pdb/3flp.pdb.gz 3flpA:# T0550 read from 3flpA/T0550-3flpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3flpA read from 3flpA/T0550-3flpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3flpA to template set # found chain 3flpA in template set T0550 76 :DRDIHIA 3flpA 6 :DVKISFP # choosing archetypes in rotamer library T0550 97 :SLYRPELWY 3flpA 13 :GTQNPKFPH T0550 137 :QDIDMLEKWVLPLTIVD 3flpA 26 :QTLPAVRQLTVCQRIKP T0550 183 :SYTASSMKVYTYINGKPDTNARTTDKRTGYV 3flpA 43 :FHRNTGYIFSCATSNQDNQFITSMYVKSDGT T0550 239 :KINVHFKEDGTLDMKQD 3flpA 75 :NLGLQVNASSNKYISCP T0550 263 :FELIGTPTYSSTSVMDA 3flpA 92 :IEIELGQWYHVCHVWSG T0550 280 :TRPYLERRYVQIMFEY 3flpA 113 :MAVYANGSPCGTMENV T0550 296 :DFQ 3flpA 133 :QIS T0550 299 :DFTYGGSG 3flpA 137 :GGTVVIGQ T0550 308 :EVIPIKYRVAGSMTLLRNINTQIPDEDQQI 3flpA 151 :GGFEEQESWSGELSDLQVWDEALTTHQVST Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_705874180.pdb -s /var/tmp/to_scwrl_705874180.seq -o /var/tmp/from_scwrl_705874180.pdb > /var/tmp/scwrl_705874180.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_705874180.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ms9A/T0550-1ms9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0550 read from 1ms9A/T0550-1ms9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ms9A read from 1ms9A/T0550-1ms9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ms9A in training set Warning: unaligning (T0550)V119 because of BadResidue code BAD_PEPTIDE in next template residue (1ms9A)V184 Warning: unaligning (T0550)H120 because of BadResidue code BAD_PEPTIDE at template residue (1ms9A)V184 T0550 25 :EDEQYEQYVSFKAPIASGSDGVTTIYVRYKDN 1ms9A 73 :DGETWETQIAIKNSRASSVSRVVDPTVIVKGN T0550 58 :KVT 1ms9A 105 :KLY T0550 61 :YQLPIIV 1ms9A 134 :AVGEVTK T0550 71 :TVNSQDRDIHIAV 1ms9A 141 :STAGGKITASIKW T0550 97 :S 1ms9A 154 :G T0550 99 :Y 1ms9A 155 :S T0550 105 :YTEMEED 1ms9A 156 :PVSLKEF T0550 115 :FPET 1ms9A 163 :FPAE T0550 121 :IPAG 1ms9A 185 :ASNG T0550 144 :KWVLPLTIVDDGS 1ms9A 189 :NLVYPVQVTNKKK T0550 157 :YAYQSHPRKNY 1ms9A 207 :IFYSEDEGKTW T0550 168 :AKALLKVVPFNNYSGSYTASSMKVY 1ms9A 420 :VGFLSHSATKTEWEDAYRCVNASTA T0550 193 :TYING 1ms9A 447 :ERVPN T0550 198 :KPDTNARTTDKRTGYVVDNNSIFFYAGLINE 1ms9A 478 :ANHAFTLVASVTIHEVPKGASPLLGASLDSS T0550 235 :RKKYKINVHFKEDGTLDMKQDDPSNEMEFELIGTPTYSSTSVMDA 1ms9A 509 :GGKKLLGLSYDKRHQWQPIYGSTPVTPTGSWEMGKRYHVVLTMAN T0550 280 :TRPYLERRYV 1ms9A 556 :GSVYIDGEPL T0550 290 :QIMFEYDFQDFT 1ms9A 571 :TVVPDERTPDIS T0550 302 :YGGSGTEVIPIKYRVAGSMTLLRNINTQIPDEDQQ 1ms9A 584 :FYVGGYKRSGMPTDSRVTVNNVLLYNRQLNAEEIR Number of specific fragments extracted= 18 number of extra gaps= 1 total=28 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_1791373467.pdb -s /var/tmp/to_scwrl_1791373467.seq -o /var/tmp/from_scwrl_1791373467.pdb > /var/tmp/scwrl_1791373467.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1791373467.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ginA/T0550-3ginA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3ginA expands to /projects/compbio/data/pdb/3gin.pdb.gz 3ginA:# T0550 read from 3ginA/T0550-3ginA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ginA read from 3ginA/T0550-3ginA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ginA to template set # found chain 3ginA in template set Warning: unaligning (T0550)G45 because first residue in template chain is (3ginA)P370 Warning: unaligning (T0550)S97 because of BadResidue code BAD_PEPTIDE in next template residue (3ginA)G414 Warning: unaligning (T0550)L98 because of BadResidue code BAD_PEPTIDE at template residue (3ginA)G414 Warning: unaligning (T0550)Y159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3ginA)A482 Warning: unaligning (T0550)P176 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3ginA)A482 Warning: unaligning (T0550)S187 because of BadResidue code BAD_PEPTIDE in next template residue (3ginA)T491 Warning: unaligning (T0550)S188 because of BadResidue code BAD_PEPTIDE at template residue (3ginA)T491 Warning: unaligning (T0550)G197 because of BadResidue code BAD_PEPTIDE in next template residue (3ginA)H501 Warning: unaligning (T0550)K198 because of BadResidue code BAD_PEPTIDE at template residue (3ginA)H501 T0550 46 :VTTIYV 3ginA 371 :VSKIFF T0550 54 :KDN 3ginA 377 :EQG T0550 57 :GKVTYQLPIIVSGST 3ginA 386 :NCGTVALTIIRRGGD T0550 73 :NSQDRDIHIAV 3ginA 401 :LTNTVFVDFRT T0550 99 :Y 3ginA 415 :T T0550 105 :YTE 3ginA 416 :ANA T0550 110 :EDKYEFP 3ginA 419 :GSDYEFT T0550 117 :ETVHIPAGSCVELLNIDF 3ginA 427 :GTVVFKPGETQKEIRVGI T0550 135 :NLQDIDMLEKWVLPLT 3ginA 446 :DDDIFEEDKNFLVHLS T0550 156 :SYA 3ginA 462 :NVK T0550 177 :FNN 3ginA 483 :LAC T0550 183 :SYTA 3ginA 486 :LGSP T0550 189 :MKVYTYIN 3ginA 492 :ATVTIFDD Number of specific fragments extracted= 13 number of extra gaps= 3 total=41 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_270436370.pdb -s /var/tmp/to_scwrl_270436370.seq -o /var/tmp/from_scwrl_270436370.pdb > /var/tmp/scwrl_270436370.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_270436370.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dpkA/T0550-2dpkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dpkA expands to /projects/compbio/data/pdb/2dpk.pdb.gz 2dpkA:# T0550 read from 2dpkA/T0550-2dpkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dpkA read from 2dpkA/T0550-2dpkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dpkA to template set # found chain 2dpkA in template set Warning: unaligning (T0550)G42 because first residue in template chain is (2dpkA)H367 Warning: unaligning (T0550)S161 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2dpkA)E468 Warning: unaligning (T0550)H162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dpkA)E468 Warning: unaligning (T0550)N178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dpkA)S481 Warning: unaligning (T0550)N179 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dpkA)A482 Warning: unaligning (T0550)Y180 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dpkA)L483 Warning: unaligning (T0550)P199 because last residue in template chain is (2dpkA)A502 T0550 43 :SDGVTTIYV 2dpkA 368 :GIPVSKIFF T0550 54 :KDN 2dpkA 377 :EQG T0550 57 :GKVTYQLPIIVSGST 2dpkA 386 :NCGTVALTIIRRGGD T0550 73 :NSQDRDIHIAV 2dpkA 401 :LTNTVFVDFRT T0550 84 :DK 2dpkA 413 :DG T0550 97 :SLY 2dpkA 415 :TAN T0550 107 :E 2dpkA 418 :A T0550 110 :EDKYEFP 2dpkA 419 :GSDYEFT T0550 117 :ETVHIPAGSCVELLNIDF 2dpkA 427 :GTVVFKPGETQKEIRVGI T0550 135 :NLQDIDMLEKWVLPLT 2dpkA 446 :DDDIFEEDENFLVHLS T0550 156 :SYAYQ 2dpkA 462 :NVKVS T0550 181 :SGSYTASSMKVYTYINGK 2dpkA 484 :ACLGSPSTATVTIFDDDH Number of specific fragments extracted= 12 number of extra gaps= 1 total=53 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_1851193759.pdb -s /var/tmp/to_scwrl_1851193759.seq -o /var/tmp/from_scwrl_1851193759.pdb > /var/tmp/scwrl_1851193759.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1851193759.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ebnA/T0550-2ebnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ebnA expands to /projects/compbio/data/pdb/2ebn.pdb.gz 2ebnA:# T0550 read from 2ebnA/T0550-2ebnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ebnA read from 2ebnA/T0550-2ebnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ebnA to template set # found chain 2ebnA in template set Warning: unaligning (T0550)W145 because of BadResidue code BAD_PEPTIDE in next template residue (2ebnA)S46 Warning: unaligning (T0550)V146 because of BadResidue code BAD_PEPTIDE at template residue (2ebnA)S46 T0550 147 :LPLTIVDDGS 2ebnA 47 :ANINYDAAND T0550 158 :AYQSHPRKNY 2ebnA 57 :KVFVSNNPNV T0550 168 :AKALLKVVPFNNYSGSYT 2ebnA 170 :VYVYSRTSSFPTAVDGVN T0550 186 :ASSMKVYTYINGKPDT 2ebnA 189 :GSYVDYAIHDYGGSYD T0550 303 :GGSGTEVIPI 2ebnA 205 :LATNYPGLAK T0550 317 :AGSMTLLRNIN 2ebnA 215 :SGMVMSSQEFN T0550 328 :TQIPDEDQQI 2ebnA 228 :RYATAQALRN Number of specific fragments extracted= 7 number of extra gaps= 1 total=60 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_430224505.pdb -s /var/tmp/to_scwrl_430224505.seq -o /var/tmp/from_scwrl_430224505.pdb > /var/tmp/scwrl_430224505.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_430224505.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h6fA/T0550-1h6fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0550 read from 1h6fA/T0550-1h6fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h6fA read from 1h6fA/T0550-1h6fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h6fA in training set T0550 80 :HIAV 1h6fA 104 :KVHL T0550 84 :DKDTLKTLNIE 1h6fA 109 :AKELWDQFHKR T0550 97 :SLY 1h6fA 120 :GTE T0550 119 :VHIPAGSCVE 1h6fA 123 :MVITKSGRRM T0550 129 :LLNIDF 1h6fA 135 :PFKVRC T0550 137 :QDIDMLEKWVLPLTIVDDGSYAYQSHPRKNY 1h6fA 141 :SGLDKKAKYILLMDIIAADDCRYKFHNSRWM T0550 168 :AKALLKVVPFNNYSGSYTASSMKVYT 1h6fA 228 :YQPRFHIVRANDILKLPYSTFRTYLF T0550 215 :DNNSIFFYAGLINEDMDKDMRKKY 1h6fA 254 :PETEFIAVTAYQNDKITQLKIDNN Number of specific fragments extracted= 8 number of extra gaps= 0 total=68 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_859359495.pdb -s /var/tmp/to_scwrl_859359495.seq -o /var/tmp/from_scwrl_859359495.pdb > /var/tmp/scwrl_859359495.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_859359495.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2v73A/T0550-2v73A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2v73A expands to /projects/compbio/data/pdb/2v73.pdb.gz 2v73A:# T0550 read from 2v73A/T0550-2v73A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v73A read from 2v73A/T0550-2v73A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2v73A to template set # found chain 2v73A in template set Warning: unaligning (T0550)G197 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v73A)N61 Warning: unaligning (T0550)K198 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v73A)N61 Warning: unaligning (T0550)P199 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v73A)K62 Warning: unaligning (T0550)Q254 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v73A)Q83 Warning: unaligning (T0550)D255 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v73A)Q83 T0550 126 :CVELLNID 2v73A 10 :NYGNLKIT T0550 134 :FNL 2v73A 23 :VNI T0550 137 :QDIDM 2v73A 27 :GDLEK T0550 142 :LEKWVLPLTIVDD 2v73A 35 :LEEGTIVTRFNMN T0550 185 :TASSMKVYTYIN 2v73A 48 :DTSIQSLIGLSD T0550 200 :DTNARTTDKRTG 2v73A 63 :ANNYFSLYVSGG T0550 239 :KINVHFK 2v73A 75 :KVGYELR T0550 256 :DPSNEMEFELIGT 2v73A 84 :EGNGDFNVHHSAD T0550 269 :PTYSSTSVMDA 2v73A 102 :GINTLALKIEK T0550 280 :TRPYLERRYVQIMFEYD 2v73A 116 :AKIFLNGSLVKTVSDPN T0550 297 :FQDFTYGGSGTEVIPIK 2v73A 136 :LNAINLNSGFIGKTDRA T0550 314 :YRVAGSMTLLRNINTQIPDEDQQI 2v73A 158 :YLFRGNIDFMNIYDKPVSDNYLLR Number of specific fragments extracted= 12 number of extra gaps= 2 total=80 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_270498279.pdb -s /var/tmp/to_scwrl_270498279.seq -o /var/tmp/from_scwrl_270498279.pdb > /var/tmp/scwrl_270498279.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_270498279.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ffzA/T0550-3ffzA-t04-local-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3ffzA expands to /projects/compbio/data/pdb/3ffz.pdb.gz 3ffzA:# T0550 read from 3ffzA/T0550-3ffzA-t04-local-adpstyle1.a2m # 3ffzA read from 3ffzA/T0550-3ffzA-t04-local-adpstyle1.a2m # adding 3ffzA to template set # found chain 3ffzA in template set Warning: unaligning (T0550)D200 because of BadResidue code BAD_PEPTIDE in next template residue (3ffzA)N914 Warning: unaligning (T0550)T201 because of BadResidue code BAD_PEPTIDE at template residue (3ffzA)N914 T0550 156 :SYAYQSHPRKNY 3ffzA 8 :NYNDPVNDRTIL T0550 168 :AKALLKVVPFNNY 3ffzA 872 :ININGDVYKYPTN T0550 181 :SGSYTASSMKVYTYING 3ffzA 888 :FGIYNDKLSEVNISQND T0550 198 :KP 3ffzA 911 :KY T0550 202 :NARTTDKRTGYVVD 3ffzA 915 :FSISFWVRIPNYDN T0550 216 :NNSIFFYAGLINEDMD 3ffzA 934 :NNEYTIINCMRDNNSG T0550 232 :KDMRKKYKINVHFKED 3ffzA 951 :KVSLNHNEIIWTLQDN T0550 248 :GTLDMKQDDPSNEMEFELIGTPTYSSTSVMDA 3ffzA 968 :GINQKLAFNYGNANGISDYINKWIFVTITNDR T0550 280 :TRPYLERRYVQIMFEYDFQDFTYGGSGTE 3ffzA 1003 :SKLYINGNLIDQKSILNLGNIHVSDNILF T0550 309 :VIPIKYRVAGSMTLLRNINTQIPDEDQQIEW 3ffzA 1033 :IVNCSYTRYIGIRYFNIFDKELDETEIQTLY Number of specific fragments extracted= 10 number of extra gaps= 1 total=90 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_250757175.pdb -s /var/tmp/to_scwrl_250757175.seq -o /var/tmp/from_scwrl_250757175.pdb > /var/tmp/scwrl_250757175.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_250757175.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sacA/T0550-1sacA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sacA expands to /projects/compbio/data/pdb/1sac.pdb.gz 1sacA:# T0550 read from 1sacA/T0550-1sacA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sacA read from 1sacA/T0550-1sacA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sacA to template set # found chain 1sacA in template set Warning: unaligning (T0550)H120 because of BadResidue code BAD_PEPTIDE in next template residue (1sacA)F11 Warning: unaligning (T0550)I121 because of BadResidue code BAD_PEPTIDE at template residue (1sacA)F11 T0550 115 :FPETV 1sacA 4 :LSGKV T0550 122 :PAGSCVELLNIDFNLQ 1sacA 12 :PRESVTDHVNLITPLE T0550 140 :DMLEKWVLPLTIVD 1sacA 28 :KPLQNFTLCFRAYS T0550 183 :SYTASSMKVYTYINGK 1sacA 42 :DLSRAYSLFSYNTQGR T0550 215 :DNNSIFFY 1sacA 58 :DNELLVYK T0550 235 :RKKYKINVHFKE 1sacA 66 :ERVGEYSLYIGR T0550 248 :GTLDMKQDDPSN 1sacA 78 :HKVTSKVIEKFP T0550 269 :PTYSSTSVMDA 1sacA 90 :APVHICVSWES T0550 280 :TRPYLERRYV 1sacA 105 :AEFWINGTPL T0550 290 :QIMFEYDFQD 1sacA 118 :GLRQGYFVEA T0550 300 :FTYGGSGTEVIPIKYRVAGSMTLLRNINTQIPDEDQQI 1sacA 134 :GQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILS Number of specific fragments extracted= 11 number of extra gaps= 1 total=101 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_697191624.pdb -s /var/tmp/to_scwrl_697191624.seq -o /var/tmp/from_scwrl_697191624.pdb > /var/tmp/scwrl_697191624.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_697191624.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2w08A/T0550-2w08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2w08A expands to /projects/compbio/data/pdb/2w08.pdb.gz 2w08A:Skipped atom 927, because occupancy 0.47 <= existing 0.530 in 2w08A Skipped atom 928, because occupancy 0.470 <= existing 0.530 in 2w08A Skipped atom 929, because occupancy 0.470 <= existing 0.530 in 2w08A Skipped atom 930, because occupancy 0.470 <= existing 0.530 in 2w08A Skipped atom 931, because occupancy 0.470 <= existing 0.530 in 2w08A Skipped atom 932, because occupancy 0.470 <= existing 0.530 in 2w08A Skipped atom 933, because occupancy 0.470 <= existing 0.530 in 2w08A Skipped atom 1388, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1389, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1390, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1391, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1392, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1393, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1394, because occupancy 0.420 <= existing 0.580 in 2w08A Skipped atom 1395, because occupancy 0.420 <= existing 0.580 in 2w08A # T0550 read from 2w08A/T0550-2w08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w08A read from 2w08A/T0550-2w08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2w08A to template set # found chain 2w08A in template set T0550 114 :EFPE 2w08A 3 :DLSG T0550 118 :TVHIPAGSCVELLNIDFNLQ 2w08A 8 :VFVFPRESVTDHVNLITPLE T0550 140 :DMLEKWVLPLTIVD 2w08A 28 :KPLQNFTLCFRAYS T0550 183 :SYTASSMKVYTYING 2w08A 42 :DLSRAYSLFSYNTQG T0550 214 :VDNNSIFFY 2w08A 57 :RDNELLVYK T0550 235 :RKKYKINVHFKE 2w08A 66 :ERVGEYSLYIGR T0550 248 :GTLDMKQDDP 2w08A 78 :HKVTSKVIEK T0550 267 :GTPTYSSTSVMDA 2w08A 88 :FPAPVHICVSWES T0550 280 :TRPYLERRYV 2w08A 105 :AEFWINGTPL T0550 290 :QIMFEYDFQD 2w08A 118 :GLRQGYFVEA T0550 300 :FTYGGSGTEVIPIKYRVAGSMTLLRNINTQIPDEDQQI 2w08A 134 :GQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILS Number of specific fragments extracted= 11 number of extra gaps= 0 total=112 # request to SCWRL produces command: ulimit -t 306 ; scwrl4 -t -i /var/tmp/to_scwrl_2012925446.pdb -s /var/tmp/to_scwrl_2012925446.seq -o /var/tmp/from_scwrl_2012925446.pdb > /var/tmp/scwrl_2012925446.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2012925446.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 0.686 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 12730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 12730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 12730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 12730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 12730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.621 rmsd (weighted)= 21.075 (unweighted)= 58.022 superimposing iter= 1 total_weight= 4221.377 rmsd (weighted)= 9.553 (unweighted)= 61.569 superimposing iter= 2 total_weight= 2359.252 rmsd (weighted)= 6.137 (unweighted)= 64.626 superimposing iter= 3 total_weight= 2028.946 rmsd (weighted)= 4.178 (unweighted)= 67.342 superimposing iter= 4 total_weight= 2373.995 rmsd (weighted)= 2.680 (unweighted)= 68.670 superimposing iter= 5 total_weight= 2082.568 rmsd (weighted)= 1.918 (unweighted)= 69.099 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.160 rmsd (weighted)= 10.822 (unweighted)= 62.730 superimposing iter= 1 total_weight= 974.617 rmsd (weighted)= 5.765 (unweighted)= 61.926 superimposing iter= 2 total_weight= 434.716 rmsd (weighted)= 4.752 (unweighted)= 61.600 superimposing iter= 3 total_weight= 362.223 rmsd (weighted)= 4.302 (unweighted)= 61.347 superimposing iter= 4 total_weight= 336.899 rmsd (weighted)= 4.037 (unweighted)= 61.150 superimposing iter= 5 total_weight= 322.218 rmsd (weighted)= 3.872 (unweighted)= 61.016 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.177 rmsd (weighted)= 11.665 (unweighted)= 69.326 superimposing iter= 1 total_weight= 1107.026 rmsd (weighted)= 5.984 (unweighted)= 69.791 superimposing iter= 2 total_weight= 496.257 rmsd (weighted)= 4.835 (unweighted)= 69.762 superimposing iter= 3 total_weight= 362.163 rmsd (weighted)= 4.584 (unweighted)= 69.712 superimposing iter= 4 total_weight= 341.502 rmsd (weighted)= 4.479 (unweighted)= 69.652 superimposing iter= 5 total_weight= 332.958 rmsd (weighted)= 4.431 (unweighted)= 69.587 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.234 rmsd (weighted)= 14.579 (unweighted)= 96.550 superimposing iter= 1 total_weight= 963.906 rmsd (weighted)= 9.439 (unweighted)= 95.264 superimposing iter= 2 total_weight= 504.874 rmsd (weighted)= 8.522 (unweighted)= 94.840 superimposing iter= 3 total_weight= 468.819 rmsd (weighted)= 8.012 (unweighted)= 94.682 superimposing iter= 4 total_weight= 453.679 rmsd (weighted)= 7.685 (unweighted)= 94.622 superimposing iter= 5 total_weight= 435.975 rmsd (weighted)= 7.529 (unweighted)= 94.602 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.149 rmsd (weighted)= 11.340 (unweighted)= 101.220 superimposing iter= 1 total_weight= 768.392 rmsd (weighted)= 6.253 (unweighted)= 102.917 superimposing iter= 2 total_weight= 474.219 rmsd (weighted)= 4.619 (unweighted)= 103.853 superimposing iter= 3 total_weight= 359.431 rmsd (weighted)= 3.973 (unweighted)= 104.467 superimposing iter= 4 total_weight= 309.823 rmsd (weighted)= 3.703 (unweighted)= 104.890 superimposing iter= 5 total_weight= 289.693 rmsd (weighted)= 3.576 (unweighted)= 105.231 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.537 rmsd (weighted)= 6.777 (unweighted)= 86.204 superimposing iter= 1 total_weight= 4707.082 rmsd (weighted)= 2.614 (unweighted)= 85.641 superimposing iter= 2 total_weight= 2617.477 rmsd (weighted)= 1.548 (unweighted)= 85.454 superimposing iter= 3 total_weight= 1477.490 rmsd (weighted)= 1.254 (unweighted)= 85.362 superimposing iter= 4 total_weight= 1120.275 rmsd (weighted)= 1.173 (unweighted)= 85.309 superimposing iter= 5 total_weight= 1022.471 rmsd (weighted)= 1.149 (unweighted)= 85.281 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.526 rmsd (weighted)= 8.060 (unweighted)= 140.723 superimposing iter= 1 total_weight= 3970.220 rmsd (weighted)= 3.555 (unweighted)= 141.799 superimposing iter= 2 total_weight= 2298.761 rmsd (weighted)= 2.194 (unweighted)= 142.155 superimposing iter= 3 total_weight= 1656.888 rmsd (weighted)= 1.634 (unweighted)= 142.250 superimposing iter= 4 total_weight= 1337.010 rmsd (weighted)= 1.367 (unweighted)= 142.282 superimposing iter= 5 total_weight= 1169.924 rmsd (weighted)= 1.227 (unweighted)= 142.307 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.507 rmsd (weighted)= 4.419 (unweighted)= 93.921 superimposing iter= 1 total_weight= 5660.592 rmsd (weighted)= 1.451 (unweighted)= 93.768 superimposing iter= 2 total_weight= 2163.616 rmsd (weighted)= 0.937 (unweighted)= 93.679 superimposing iter= 3 total_weight= 1143.210 rmsd (weighted)= 0.842 (unweighted)= 93.616 superimposing iter= 4 total_weight= 996.270 rmsd (weighted)= 0.813 (unweighted)= 93.582 superimposing iter= 5 total_weight= 961.968 rmsd (weighted)= 0.798 (unweighted)= 93.563 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.509 rmsd (weighted)= 4.419 (unweighted)= 78.470 superimposing iter= 1 total_weight= 5593.333 rmsd (weighted)= 1.453 (unweighted)= 78.608 superimposing iter= 2 total_weight= 2298.462 rmsd (weighted)= 0.909 (unweighted)= 78.615 superimposing iter= 3 total_weight= 1203.571 rmsd (weighted)= 0.798 (unweighted)= 78.620 superimposing iter= 4 total_weight= 1021.152 rmsd (weighted)= 0.761 (unweighted)= 78.637 superimposing iter= 5 total_weight= 975.109 rmsd (weighted)= 0.743 (unweighted)= 78.658 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 0.686 rmsd (weighted)= 6.011 (unweighted)= 54.159 superimposing iter= 1 total_weight= 4468.838 rmsd (weighted)= 2.892 (unweighted)= 54.924 superimposing iter= 2 total_weight= 2476.433 rmsd (weighted)= 1.992 (unweighted)= 55.155 superimposing iter= 3 total_weight= 1825.243 rmsd (weighted)= 1.627 (unweighted)= 55.219 superimposing iter= 4 total_weight= 1656.976 rmsd (weighted)= 1.399 (unweighted)= 55.264 superimposing iter= 5 total_weight= 1685.884 rmsd (weighted)= 1.190 (unweighted)= 55.301 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.137 rmsd (weighted)= 21.405 (unweighted)= 38.700 superimposing iter= 1 total_weight= 5167.628 rmsd (weighted)= 11.970 (unweighted)= 38.890 superimposing iter= 2 total_weight= 4069.724 rmsd (weighted)= 7.826 (unweighted)= 39.661 superimposing iter= 3 total_weight= 3993.356 rmsd (weighted)= 5.202 (unweighted)= 40.315 superimposing iter= 4 total_weight= 5000.102 rmsd (weighted)= 3.089 (unweighted)= 40.640 superimposing iter= 5 total_weight= 4187.361 rmsd (weighted)= 2.044 (unweighted)= 40.676 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.431 rmsd (weighted)= 10.403 (unweighted)= 46.298 superimposing iter= 1 total_weight= 1599.563 rmsd (weighted)= 7.231 (unweighted)= 46.261 superimposing iter= 2 total_weight= 957.754 rmsd (weighted)= 6.550 (unweighted)= 46.247 superimposing iter= 3 total_weight= 855.288 rmsd (weighted)= 6.287 (unweighted)= 46.231 superimposing iter= 4 total_weight= 819.682 rmsd (weighted)= 6.167 (unweighted)= 46.215 superimposing iter= 5 total_weight= 804.120 rmsd (weighted)= 6.107 (unweighted)= 46.201 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.466 rmsd (weighted)= 12.116 (unweighted)= 52.178 superimposing iter= 1 total_weight= 2135.162 rmsd (weighted)= 7.523 (unweighted)= 52.073 superimposing iter= 2 total_weight= 1070.841 rmsd (weighted)= 6.676 (unweighted)= 52.005 superimposing iter= 3 total_weight= 913.864 rmsd (weighted)= 6.424 (unweighted)= 51.992 superimposing iter= 4 total_weight= 873.864 rmsd (weighted)= 6.324 (unweighted)= 52.001 superimposing iter= 5 total_weight= 859.542 rmsd (weighted)= 6.279 (unweighted)= 52.015 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.358 rmsd (weighted)= 13.479 (unweighted)= 64.744 superimposing iter= 1 total_weight= 1878.176 rmsd (weighted)= 7.570 (unweighted)= 64.631 superimposing iter= 2 total_weight= 883.247 rmsd (weighted)= 6.399 (unweighted)= 64.497 superimposing iter= 3 total_weight= 730.138 rmsd (weighted)= 5.986 (unweighted)= 64.398 superimposing iter= 4 total_weight= 681.672 rmsd (weighted)= 5.805 (unweighted)= 64.317 superimposing iter= 5 total_weight= 665.452 rmsd (weighted)= 5.700 (unweighted)= 64.240 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.503 rmsd (weighted)= 15.822 (unweighted)= 81.429 superimposing iter= 1 total_weight= 2435.397 rmsd (weighted)= 9.303 (unweighted)= 80.995 superimposing iter= 2 total_weight= 1397.958 rmsd (weighted)= 7.381 (unweighted)= 80.476 superimposing iter= 3 total_weight= 1251.508 rmsd (weighted)= 6.261 (unweighted)= 80.069 superimposing iter= 4 total_weight= 1148.196 rmsd (weighted)= 5.564 (unweighted)= 79.747 superimposing iter= 5 total_weight= 1121.491 rmsd (weighted)= 5.009 (unweighted)= 79.452 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.623 rmsd (weighted)= 8.049 (unweighted)= 54.360 superimposing iter= 1 total_weight= 4493.940 rmsd (weighted)= 3.637 (unweighted)= 54.416 superimposing iter= 2 total_weight= 2406.781 rmsd (weighted)= 2.395 (unweighted)= 54.440 superimposing iter= 3 total_weight= 1771.804 rmsd (weighted)= 1.882 (unweighted)= 54.468 superimposing iter= 4 total_weight= 1454.097 rmsd (weighted)= 1.646 (unweighted)= 54.498 superimposing iter= 5 total_weight= 1312.523 rmsd (weighted)= 1.520 (unweighted)= 54.529 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.804 rmsd (weighted)= 13.409 (unweighted)= 107.681 superimposing iter= 1 total_weight= 6634.265 rmsd (weighted)= 5.508 (unweighted)= 107.919 superimposing iter= 2 total_weight= 3198.669 rmsd (weighted)= 3.624 (unweighted)= 108.070 superimposing iter= 3 total_weight= 2089.897 rmsd (weighted)= 3.011 (unweighted)= 108.288 superimposing iter= 4 total_weight= 1879.963 rmsd (weighted)= 2.638 (unweighted)= 108.490 superimposing iter= 5 total_weight= 1981.304 rmsd (weighted)= 2.247 (unweighted)= 108.631 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.670 rmsd (weighted)= 5.722 (unweighted)= 69.662 superimposing iter= 1 total_weight= 4877.041 rmsd (weighted)= 2.636 (unweighted)= 69.674 superimposing iter= 2 total_weight= 2452.201 rmsd (weighted)= 1.810 (unweighted)= 69.788 superimposing iter= 3 total_weight= 1753.759 rmsd (weighted)= 1.486 (unweighted)= 69.862 superimposing iter= 4 total_weight= 1481.000 rmsd (weighted)= 1.334 (unweighted)= 69.900 superimposing iter= 5 total_weight= 1342.250 rmsd (weighted)= 1.259 (unweighted)= 69.919 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.682 rmsd (weighted)= 5.638 (unweighted)= 62.197 superimposing iter= 1 total_weight= 4969.564 rmsd (weighted)= 2.602 (unweighted)= 62.322 superimposing iter= 2 total_weight= 2473.208 rmsd (weighted)= 1.799 (unweighted)= 62.425 superimposing iter= 3 total_weight= 1749.744 rmsd (weighted)= 1.491 (unweighted)= 62.479 superimposing iter= 4 total_weight= 1482.935 rmsd (weighted)= 1.344 (unweighted)= 62.502 superimposing iter= 5 total_weight= 1365.874 rmsd (weighted)= 1.264 (unweighted)= 62.509 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 0.686 rmsd (weighted)= 6.571 (unweighted)= 54.975 superimposing iter= 1 total_weight= 4238.225 rmsd (weighted)= 3.341 (unweighted)= 55.816 superimposing iter= 2 total_weight= 2111.505 rmsd (weighted)= 2.487 (unweighted)= 56.277 superimposing iter= 3 total_weight= 1782.662 rmsd (weighted)= 2.052 (unweighted)= 56.506 superimposing iter= 4 total_weight= 1612.912 rmsd (weighted)= 1.793 (unweighted)= 56.606 superimposing iter= 5 total_weight= 1578.109 rmsd (weighted)= 1.584 (unweighted)= 56.650 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.137 rmsd (weighted)= 19.863 (unweighted)= 38.706 superimposing iter= 1 total_weight= 5355.091 rmsd (weighted)= 10.935 (unweighted)= 38.986 superimposing iter= 2 total_weight= 3938.355 rmsd (weighted)= 7.310 (unweighted)= 39.622 superimposing iter= 3 total_weight= 4043.495 rmsd (weighted)= 4.854 (unweighted)= 40.123 superimposing iter= 4 total_weight= 4754.059 rmsd (weighted)= 2.969 (unweighted)= 40.338 superimposing iter= 5 total_weight= 3964.022 rmsd (weighted)= 2.021 (unweighted)= 40.347 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.431 rmsd (weighted)= 10.984 (unweighted)= 47.294 superimposing iter= 1 total_weight= 1777.164 rmsd (weighted)= 7.208 (unweighted)= 46.947 superimposing iter= 2 total_weight= 1027.186 rmsd (weighted)= 6.270 (unweighted)= 46.668 superimposing iter= 3 total_weight= 902.925 rmsd (weighted)= 5.834 (unweighted)= 46.476 superimposing iter= 4 total_weight= 845.362 rmsd (weighted)= 5.619 (unweighted)= 46.337 superimposing iter= 5 total_weight= 823.892 rmsd (weighted)= 5.488 (unweighted)= 46.237 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.466 rmsd (weighted)= 12.562 (unweighted)= 53.205 superimposing iter= 1 total_weight= 2282.931 rmsd (weighted)= 7.516 (unweighted)= 53.034 superimposing iter= 2 total_weight= 1121.710 rmsd (weighted)= 6.492 (unweighted)= 52.939 superimposing iter= 3 total_weight= 960.985 rmsd (weighted)= 6.072 (unweighted)= 52.910 superimposing iter= 4 total_weight= 906.434 rmsd (weighted)= 5.857 (unweighted)= 52.900 superimposing iter= 5 total_weight= 882.790 rmsd (weighted)= 5.729 (unweighted)= 52.895 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.358 rmsd (weighted)= 13.119 (unweighted)= 64.133 superimposing iter= 1 total_weight= 1943.030 rmsd (weighted)= 7.290 (unweighted)= 64.294 superimposing iter= 2 total_weight= 895.309 rmsd (weighted)= 6.108 (unweighted)= 64.406 superimposing iter= 3 total_weight= 719.860 rmsd (weighted)= 5.737 (unweighted)= 64.485 superimposing iter= 4 total_weight= 674.897 rmsd (weighted)= 5.579 (unweighted)= 64.533 superimposing iter= 5 total_weight= 660.988 rmsd (weighted)= 5.490 (unweighted)= 64.558 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.503 rmsd (weighted)= 16.039 (unweighted)= 81.960 superimposing iter= 1 total_weight= 2567.860 rmsd (weighted)= 9.106 (unweighted)= 81.620 superimposing iter= 2 total_weight= 1469.883 rmsd (weighted)= 7.048 (unweighted)= 81.206 superimposing iter= 3 total_weight= 1133.087 rmsd (weighted)= 6.303 (unweighted)= 80.943 superimposing iter= 4 total_weight= 1015.258 rmsd (weighted)= 5.971 (unweighted)= 80.739 superimposing iter= 5 total_weight= 983.771 rmsd (weighted)= 5.749 (unweighted)= 80.554 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.623 rmsd (weighted)= 8.190 (unweighted)= 54.040 superimposing iter= 1 total_weight= 3879.019 rmsd (weighted)= 4.024 (unweighted)= 54.012 superimposing iter= 2 total_weight= 2217.532 rmsd (weighted)= 2.764 (unweighted)= 54.027 superimposing iter= 3 total_weight= 1752.988 rmsd (weighted)= 2.182 (unweighted)= 54.057 superimposing iter= 4 total_weight= 1463.788 rmsd (weighted)= 1.907 (unweighted)= 54.087 superimposing iter= 5 total_weight= 1296.762 rmsd (weighted)= 1.777 (unweighted)= 54.121 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.804 rmsd (weighted)= 12.656 (unweighted)= 106.446 superimposing iter= 1 total_weight= 6521.356 rmsd (weighted)= 5.329 (unweighted)= 106.623 superimposing iter= 2 total_weight= 2933.056 rmsd (weighted)= 3.681 (unweighted)= 106.677 superimposing iter= 3 total_weight= 1956.530 rmsd (weighted)= 3.165 (unweighted)= 106.833 superimposing iter= 4 total_weight= 1780.602 rmsd (weighted)= 2.860 (unweighted)= 106.968 superimposing iter= 5 total_weight= 1859.978 rmsd (weighted)= 2.523 (unweighted)= 107.041 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.670 rmsd (weighted)= 5.911 (unweighted)= 69.621 superimposing iter= 1 total_weight= 4435.005 rmsd (weighted)= 2.866 (unweighted)= 69.747 superimposing iter= 2 total_weight= 2446.717 rmsd (weighted)= 1.966 (unweighted)= 69.875 superimposing iter= 3 total_weight= 1789.662 rmsd (weighted)= 1.604 (unweighted)= 69.968 superimposing iter= 4 total_weight= 1520.342 rmsd (weighted)= 1.428 (unweighted)= 70.029 superimposing iter= 5 total_weight= 1379.358 rmsd (weighted)= 1.338 (unweighted)= 70.071 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.682 rmsd (weighted)= 5.817 (unweighted)= 62.429 superimposing iter= 1 total_weight= 4361.002 rmsd (weighted)= 2.860 (unweighted)= 62.786 superimposing iter= 2 total_weight= 2453.130 rmsd (weighted)= 1.974 (unweighted)= 63.009 superimposing iter= 3 total_weight= 1839.851 rmsd (weighted)= 1.600 (unweighted)= 63.145 superimposing iter= 4 total_weight= 1564.454 rmsd (weighted)= 1.411 (unweighted)= 63.232 superimposing iter= 5 total_weight= 1423.991 rmsd (weighted)= 1.305 (unweighted)= 63.280 superimposing iter= 0 total_weight= 0.686 rmsd (weighted)= 6.805 (unweighted)= 55.342 superimposing iter= 1 total_weight= 4131.861 rmsd (weighted)= 3.521 (unweighted)= 56.210 superimposing iter= 2 total_weight= 2067.600 rmsd (weighted)= 2.642 (unweighted)= 56.731 superimposing iter= 3 total_weight= 1800.613 rmsd (weighted)= 2.157 (unweighted)= 57.024 superimposing iter= 4 total_weight= 1629.408 rmsd (weighted)= 1.873 (unweighted)= 57.157 superimposing iter= 5 total_weight= 1538.996 rmsd (weighted)= 1.677 (unweighted)= 57.230 superimposing iter= 0 total_weight= 1.137 rmsd (weighted)= 19.375 (unweighted)= 38.866 superimposing iter= 1 total_weight= 5413.075 rmsd (weighted)= 10.595 (unweighted)= 39.194 superimposing iter= 2 total_weight= 3990.848 rmsd (weighted)= 7.018 (unweighted)= 39.827 superimposing iter= 3 total_weight= 4283.010 rmsd (weighted)= 4.524 (unweighted)= 40.278 superimposing iter= 4 total_weight= 4606.670 rmsd (weighted)= 2.815 (unweighted)= 40.422 superimposing iter= 5 total_weight= 3852.873 rmsd (weighted)= 1.948 (unweighted)= 40.411 superimposing iter= 0 total_weight= 0.431 rmsd (weighted)= 10.911 (unweighted)= 47.327 superimposing iter= 1 total_weight= 1818.118 rmsd (weighted)= 7.058 (unweighted)= 47.037 superimposing iter= 2 total_weight= 1080.736 rmsd (weighted)= 5.974 (unweighted)= 46.802 superimposing iter= 3 total_weight= 964.615 rmsd (weighted)= 5.367 (unweighted)= 46.622 superimposing iter= 4 total_weight= 921.386 rmsd (weighted)= 4.939 (unweighted)= 46.459 superimposing iter= 5 total_weight= 897.920 rmsd (weighted)= 4.601 (unweighted)= 46.338 superimposing iter= 0 total_weight= 0.466 rmsd (weighted)= 12.414 (unweighted)= 53.187 superimposing iter= 1 total_weight= 2317.724 rmsd (weighted)= 7.376 (unweighted)= 53.098 superimposing iter= 2 total_weight= 1131.571 rmsd (weighted)= 6.344 (unweighted)= 53.056 superimposing iter= 3 total_weight= 994.279 rmsd (weighted)= 5.832 (unweighted)= 53.057 superimposing iter= 4 total_weight= 950.051 rmsd (weighted)= 5.488 (unweighted)= 53.061 superimposing iter= 5 total_weight= 921.160 rmsd (weighted)= 5.245 (unweighted)= 53.068 superimposing iter= 0 total_weight= 0.358 rmsd (weighted)= 12.999 (unweighted)= 63.992 superimposing iter= 1 total_weight= 1850.004 rmsd (weighted)= 7.441 (unweighted)= 64.301 superimposing iter= 2 total_weight= 871.443 rmsd (weighted)= 6.318 (unweighted)= 64.537 superimposing iter= 3 total_weight= 726.800 rmsd (weighted)= 5.901 (unweighted)= 64.715 superimposing iter= 4 total_weight= 683.955 rmsd (weighted)= 5.698 (unweighted)= 64.834 superimposing iter= 5 total_weight= 667.407 rmsd (weighted)= 5.581 (unweighted)= 64.911 superimposing iter= 0 total_weight= 0.503 rmsd (weighted)= 16.119 (unweighted)= 82.616 superimposing iter= 1 total_weight= 2685.352 rmsd (weighted)= 8.884 (unweighted)= 82.359 superimposing iter= 2 total_weight= 1661.998 rmsd (weighted)= 6.415 (unweighted)= 81.762 superimposing iter= 3 total_weight= 1372.932 rmsd (weighted)= 5.180 (unweighted)= 81.303 superimposing iter= 4 total_weight= 1302.064 rmsd (weighted)= 4.295 (unweighted)= 80.932 superimposing iter= 5 total_weight= 1194.946 rmsd (weighted)= 3.696 (unweighted)= 80.708 superimposing iter= 0 total_weight= 0.623 rmsd (weighted)= 8.243 (unweighted)= 53.770 superimposing iter= 1 total_weight= 3731.625 rmsd (weighted)= 4.170 (unweighted)= 53.724 superimposing iter= 2 total_weight= 2128.822 rmsd (weighted)= 2.919 (unweighted)= 53.723 superimposing iter= 3 total_weight= 1773.756 rmsd (weighted)= 2.283 (unweighted)= 53.762 superimposing iter= 4 total_weight= 1503.983 rmsd (weighted)= 1.964 (unweighted)= 53.796 superimposing iter= 5 total_weight= 1322.243 rmsd (weighted)= 1.810 (unweighted)= 53.830 superimposing iter= 0 total_weight= 0.804 rmsd (weighted)= 12.347 (unweighted)= 106.355 superimposing iter= 1 total_weight= 6471.628 rmsd (weighted)= 5.231 (unweighted)= 106.479 superimposing iter= 2 total_weight= 2958.785 rmsd (weighted)= 3.599 (unweighted)= 106.481 superimposing iter= 3 total_weight= 1972.866 rmsd (weighted)= 3.082 (unweighted)= 106.595 superimposing iter= 4 total_weight= 1808.797 rmsd (weighted)= 2.761 (unweighted)= 106.673 superimposing iter= 5 total_weight= 1880.550 rmsd (weighted)= 2.421 (unweighted)= 106.690 superimposing iter= 0 total_weight= 0.670 rmsd (weighted)= 5.993 (unweighted)= 69.469 superimposing iter= 1 total_weight= 4226.797 rmsd (weighted)= 2.978 (unweighted)= 69.607 superimposing iter= 2 total_weight= 2399.713 rmsd (weighted)= 2.055 (unweighted)= 69.712 superimposing iter= 3 total_weight= 1801.264 rmsd (weighted)= 1.671 (unweighted)= 69.784 superimposing iter= 4 total_weight= 1502.030 rmsd (weighted)= 1.498 (unweighted)= 69.836 superimposing iter= 5 total_weight= 1359.147 rmsd (weighted)= 1.415 (unweighted)= 69.873 superimposing iter= 0 total_weight= 0.682 rmsd (weighted)= 5.900 (unweighted)= 62.277 superimposing iter= 1 total_weight= 4120.658 rmsd (weighted)= 2.985 (unweighted)= 62.681 superimposing iter= 2 total_weight= 2409.860 rmsd (weighted)= 2.072 (unweighted)= 62.919 superimposing iter= 3 total_weight= 1859.266 rmsd (weighted)= 1.670 (unweighted)= 63.050 superimposing iter= 4 total_weight= 1559.444 rmsd (weighted)= 1.479 (unweighted)= 63.133 superimposing iter= 5 total_weight= 1428.165 rmsd (weighted)= 1.369 (unweighted)= 63.190 # command:# Printing sheets for alignments to T0550.undertaker-align.sheets # command: