# command:# Seed set to 1213557698 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 26.232 sec, elapsed time= 26.333 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0448 numbered 1 through 232 Created new target T0448 from T0448.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.546 sec, elapsed time= 36.881 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1957 20 (100.000%) # n-terminus 2 1932 333 (83.250%) # middle 1 481122 20 (100.000%) # middle 2 474896 400 (100.000%) # middle 3 468898 7988 (99.850%) # middle 4 463038 120397 (75.248%) # c-terminus 1 1914 20 (100.000%) # c-terminus 2 1887 372 (93.000%) # ss-bonds 1042 # command:CPU_time= 46.381 sec, elapsed time= 46.728 sec. # command:# Prefix for input files set to # command:# reading script from file T0448.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bzwA/T0448-3bzwA-t2k-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 3bzwA expands to /projects/compbio/data/pdb/3bzw.pdb.gz 3bzwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0448 read from 3bzwA/T0448-3bzwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bzwA read from 3bzwA/T0448-3bzwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bzwA to template set # found chain 3bzwA in template set Warning: unaligning (T0448)I14 because first residue in template chain is (3bzwA)C38 Warning: unaligning (T0448)H227 because last residue in template chain is (3bzwA)F285 T0448 15 :SNGHVSFKRPAWLGDSITANNGLATV 3bzwA 39 :IQHPWQGKKVGYIGDSITDPNCYGDN # choosing archetypes in rotamer library T0448 41 :HYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGD 3bzwA 66 :KKYWDFLKEWLGITPFVYGISGRQWDDVPRQAEKLKKEHGGEVDAILVFMGTNDYNSSVPIGEWFT T0448 107 :CDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSF 3bzwA 157 :MTQDTYRGRINIGITQLKKLFPDKQIVLLTPLHRSLANFGDK T0448 149 :SAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYS 3bzwA 204 :ESYQNGCGEYIDAYVQAIKEAGNIWGIPVIDFNAVTGMNPMVEEQLIYFY T0448 199 :VDTLHPNNAGHRVIARKLQSFLDSHFLE 3bzwA 257 :YDRLHPDTKGQERMARTLMYQLLALPVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1207540352.pdb -s /var/tmp/to_scwrl_1207540352.seq -o /var/tmp/from_scwrl_1207540352.pdb > /var/tmp/scwrl_1207540352.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1207540352.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ivnA/T0448-1ivnA-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 1ivnA expands to /projects/compbio/data/pdb/1ivn.pdb.gz 1ivnA:# T0448 read from 1ivnA/T0448-1ivnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ivnA read from 1ivnA/T0448-1ivnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ivnA to template set # found chain 1ivnA in template set Warning: unaligning (T0448)F21 because first residue in template chain is (1ivnA)A1 Warning: unaligning (T0448)W50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ivnA)S33 Warning: unaligning (T0448)D51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ivnA)S33 Warning: unaligning (T0448)L225 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ivnA)H180 Warning: unaligning (T0448)E226 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ivnA)H180 T0448 22 :KRPAWLGDSITANNGLA 1ivnA 2 :DTLLILGDSLSAGYRMS T0448 39 :TVHYHDILAAD 1ivnA 20 :SAAWPALLNDK T0448 52 :VERSDNLGISGSTIGSRYDAMAVRYQAI 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQH T0448 82 :DADFIAVFGGVNDYGRD 1ivnA 62 :QPRWVLVELGGNDGLRG T0448 107 :CDMTTFYGALMMLLTGLQTN 1ivnA 79 :FQPQQTEQTLRQILQDVKAA T0448 129 :TVPKLFISA 1ivnA 99 :NAEPLLMQI T0448 139 :HIGSDFGGSF 1ivnA 108 :RLPANYGRRY T0448 159 :QSDYEAAIAQMTADYGVPHLSLY 1ivnA 118 :NEAFSAIYPKLAKEFDVPLLPFF T0448 182 :RDAGM 1ivnA 142 :EEVYL T0448 193 :QAAIYSVDTLHPNNAGHRVIARKLQSFLDSHF 1ivnA 147 :KPQWMQDDGIHPNRDAQPFIADWMAKQLQPLV Number of specific fragments extracted= 10 number of extra gaps= 1 total=15 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_559705406.pdb -s /var/tmp/to_scwrl_559705406.seq -o /var/tmp/from_scwrl_559705406.pdb > /var/tmp/scwrl_559705406.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_559705406.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hsjA/T0448-2hsjA-t2k-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 2hsjA expands to /projects/compbio/data/pdb/2hsj.pdb.gz 2hsjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2, because occupancy 0.5 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1364, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2hsjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1557, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1559, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1563, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1565, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1567, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1569, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1571, because occupancy 0.500 <= existing 0.500 in 2hsjA Skipped atom 1573, because occupancy 0.500 <= existing 0.500 in 2hsjA # T0448 read from 2hsjA/T0448-2hsjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hsjA read from 2hsjA/T0448-2hsjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hsjA to template set # found chain 2hsjA in template set T0448 6 :VKGGLAMAISNGHVSFKRPAWLGDSITANNGLATVHY 2hsjA 16 :KIQTKYRHLNHISVVEPNILFIGDSIVEYYPLQELFG T0448 51 :DVERSDNLGISGSTIGSRYDA 2hsjA 53 :TSKTIVNRGIRGYQTGLLLEN T0448 74 :VRYQAIPEDADFIAVFGGVNDYGRD 2hsjA 74 :LDAHLYGGAVDKIFLLIGTNDIGKD T0448 107 :CDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYR 2hsjA 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEYQQAVYIRSNEKI T0448 160 :SDYEAAIAQMTADYG 2hsjA 151 :QNWNQAYQELASAYM T0448 175 :VPHLSLYRDAGM 2hsjA 167 :VEFVPVFDCLTD T0448 189 :AIPAQAAIYSVDTLHPNNAGHRVIARKLQSFL 2hsjA 179 :QAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL Number of specific fragments extracted= 7 number of extra gaps= 0 total=22 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1266781690.pdb -s /var/tmp/to_scwrl_1266781690.seq -o /var/tmp/from_scwrl_1266781690.pdb > /var/tmp/scwrl_1266781690.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1266781690.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjgA/T0448-1vjgA-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 1vjgA expands to /projects/compbio/data/pdb/1vjg.pdb.gz 1vjgA:Skipped atom 37, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 39, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 41, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 43, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 418, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 422, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1vjgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0448 read from 1vjgA/T0448-1vjgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjgA read from 1vjgA/T0448-1vjgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjgA to template set # found chain 1vjgA in template set Warning: unaligning (T0448)S20 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0448)F21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0448)W127 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0448)P128 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0448 22 :K 1vjgA 7 :T T0448 23 :RPAWLGDSITANNGLA 1vjgA 10 :RICFVGDSFVNGTGDP T0448 39 :TVHYHDILAADW 1vjgA 27 :CLGWTGRVCVNA T0448 51 :DVE 1vjgA 44 :DVT T0448 55 :SDNLGISGSTIGSRYDAMAVRYQAIPE 1vjgA 47 :YYNLGIRRDTSSDIAKRWLQEVSLRLH T0448 82 :DADFIAVFGGVNDYGRD 1vjgA 76 :YNSLVVFSFGLNDTTLE T0448 102 :GQYGDCDMTTFYGALMMLLTGLQTN 1vjgA 93 :NGKPRVSIAETIKNTREILTQAKKL T0448 132 :KLFISAIHIGSDFGGSFSAV 1vjgA 120 :VLMISPAPYIEQQDPGRRRR T0448 159 :QSDYEAAIAQMTADYGVPHLSLYRDAGMTFAI 1vjgA 140 :TIDLSQQLALVCQDLDVPYLDVFPLLEKPSVW T0448 193 :QAAIYSVDTLHPNNAGHRVIARKLQ 1vjgA 172 :LHEAKANDGVHPQAGGYTEFARIVE T0448 218 :SFLDS 1vjgA 199 :DAWLN Number of specific fragments extracted= 11 number of extra gaps= 1 total=33 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1489948127.pdb -s /var/tmp/to_scwrl_1489948127.seq -o /var/tmp/from_scwrl_1489948127.pdb > /var/tmp/scwrl_1489948127.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1489948127.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2q0sA/T0448-2q0sA-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 2q0sA expands to /projects/compbio/data/pdb/2q0s.pdb.gz 2q0sA:Bad short name: C1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Bad short name: N1 for alphabet: pdb_atoms Bad short name: CA1 for alphabet: pdb_atoms Bad short name: CB2 for alphabet: pdb_atoms Bad short name: CG3 for alphabet: pdb_atoms Bad short name: CD4 for alphabet: pdb_atoms Bad short name: CG5 for alphabet: pdb_atoms Bad short name: CD6 for alphabet: pdb_atoms # T0448 read from 2q0sA/T0448-2q0sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2q0sA read from 2q0sA/T0448-2q0sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2q0sA to template set # found chain 2q0sA in template set Warning: unaligning (T0448)F21 because first residue in template chain is (2q0sA)A2 Warning: unaligning (T0448)D29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2q0sA)L12 Warning: unaligning (T0448)I31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2q0sA)L12 Warning: unaligning (T0448)G66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2q0sA)L68 Warning: unaligning (T0448)A194 because of BadResidue code BAD_PEPTIDE in next template residue (2q0sA)S187 Warning: unaligning (T0448)A195 because of BadResidue code BAD_PEPTIDE at template residue (2q0sA)S187 T0448 22 :KRPAWLG 2q0sA 3 :KRILCFG T0448 32 :TANNGLATV 2q0sA 13 :TWGWVPVED T0448 41 :HYHDILAADW 2q0sA 33 :RWTGVLAQQL T0448 51 :DVE 2q0sA 45 :DFE T0448 55 :SDNLGISGSTI 2q0sA 48 :VIEEGLSARTT T0448 67 :SRYDAMAVRYQAIP 2q0sA 69 :NGASYLPSCLATHL T0448 82 :DADFIAVFGGVNDYGRD 2q0sA 83 :PLDLVIIMLGTNDTKAY T0448 105 :GDCDMTTFYGALMMLLTGLQTN 2q0sA 100 :FRRTPLDIALGMSVLVTQVLTS T0448 127 :WPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYR 2q0sA 129 :YPAPKVLVVSPPPLAPMPHPWFQLIFEGGEQKTTELARVYSALASFMKVPFFDAGS T0448 193 :Q 2q0sA 185 :V T0448 196 :IYSVDTLHPNNAGHRVIARKLQSFLDSH 2q0sA 188 :TDGVDGIHFTEANNRDLGVALAEQVRSL Number of specific fragments extracted= 11 number of extra gaps= 2 total=44 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1398810451.pdb -s /var/tmp/to_scwrl_1398810451.seq -o /var/tmp/from_scwrl_1398810451.pdb > /var/tmp/scwrl_1398810451.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1398810451.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vptA/T0448-2vptA-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 2vptA expands to /projects/compbio/data/pdb/2vpt.pdb.gz 2vptA:Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2vptA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 230, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1594, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1596, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1598, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 2vptA Skipped atom 1600, because occupancy 0.500 <= existing 0.500 in 2vptA # T0448 read from 2vptA/T0448-2vptA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vptA read from 2vptA/T0448-2vptA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2vptA to template set # found chain 2vptA in template set Warning: unaligning (T0448)K22 because first residue in template chain is (2vptA)K34 Warning: unaligning (T0448)D106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2vptA)L132 Warning: unaligning (T0448)C107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2vptA)L132 Warning: unaligning (T0448)I135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2vptA)D157 Warning: unaligning (T0448)S136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2vptA)D157 Warning: unaligning (T0448)H229 because last residue in template chain is (2vptA)G234 T0448 23 :RPAWLGDSITANNGLATV 2vptA 37 :KIMPVGDSCTEGMGGGEM T0448 41 :HYHDILAADW 2vptA 56 :SYRTELYRLL T0448 51 :DVERSDNLGISGSTIGSRYDAMAVRYQAI 2vptA 84 :SLPDKDHEGHSGWTIPQIASNINNWLNTH T0448 82 :DADFIAVFGGVNDYGRD 2vptA 113 :NPDVVFLWIGGNDLLLN T0448 105 :G 2vptA 130 :G T0448 108 :DM 2vptA 133 :NA T0448 114 :GALMMLLTGLQTNWPTVPKLF 2vptA 135 :TGLSNLIDQIFTVKPNVTLFV T0448 137 :AIHIGSDFG 2vptA 158 :YYPWPEAIK T0448 157 :YRQSDYEAAIAQMTADY 2vptA 167 :QYNAVIPGIVQQKANAG T0448 174 :GVPHLSLY 2vptA 185 :KVYFVKLS T0448 187 :TFAIP 2vptA 193 :EIQFD T0448 193 :QAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHH 2vptA 198 :RNTDISWDGLHLSEIGYKKIANIWYKYTIDILRALA Number of specific fragments extracted= 12 number of extra gaps= 2 total=56 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1323949599.pdb -s /var/tmp/to_scwrl_1323949599.seq -o /var/tmp/from_scwrl_1323949599.pdb > /var/tmp/scwrl_1323949599.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1323949599.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2o14A/T0448-2o14A-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 2o14A expands to /projects/compbio/data/pdb/2o14.pdb.gz 2o14A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0448 read from 2o14A/T0448-2o14A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o14A read from 2o14A/T0448-2o14A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2o14A to template set # found chain 2o14A in template set T0448 15 :SNGHVSFKRPAWLGDSITANNGLA 2o14A 156 :SDQPVTNRTIYVGGDSTVCNYYPL T0448 40 :V 2o14A 181 :S T0448 41 :HYHDILAADW 2o14A 186 :GWGQMLPHYI T0448 51 :DVE 2o14A 199 :TFQ T0448 55 :SDNLGISGSTIGSRYD 2o14A 202 :VRNMASGGQIARGFRN T0448 71 :AMAVRYQAIP 2o14A 220 :QLEAILKYIK T0448 82 :DADFIAVFGGVNDYGRD 2o14A 230 :PGDYFMLQLGINDTNPK T0448 105 :GDCDMTTFYGALMMLLTGLQTN 2o14A 247 :HKESEAEFKEVMRDMIRQVKAK T0448 129 :TVPKLFISAIHIGSDFGGSFSAVTNGLG 2o14A 269 :GADVILSTPQGRATDFTSEGIHSSVNRW T0448 162 :YEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAA 2o14A 297 :YRASILALAEEEKTYLIDLNVLSSAYFTSIGPER T0448 196 :IYSVDTLHPNNAGHRVIARKLQSFLDSH 2o14A 335 :YMDGDTLHPNRAGADALARLAVQELKRQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=67 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1491224597.pdb -s /var/tmp/to_scwrl_1491224597.seq -o /var/tmp/from_scwrl_1491224597.pdb > /var/tmp/scwrl_1491224597.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1491224597.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es9A/T0448-1es9A-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 # T0448 read from 1es9A/T0448-1es9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1es9A read from 1es9A/T0448-1es9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1es9A in training set Warning: unaligning (T0448)A47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0448)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1es9A)Q54 Warning: unaligning (T0448)D49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)C55 Warning: unaligning (T0448)W50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)E56 Warning: unaligning (T0448)V74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0448)M186 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0448)T187 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 Warning: unaligning (T0448)F224 because last residue in template chain is (1es9A)L216 T0448 5 :IVKGGLAMAISNGHV 1es9A 26 :LHHRFVADSKDKEPE T0448 24 :PAWLGDSITAN 1es9A 41 :VVFIGDSLVQL T0448 46 :L 1es9A 52 :M T0448 51 :DVE 1es9A 64 :PLH T0448 55 :SDNLGISGSTIGSRYDAMA 1es9A 67 :ALNFGIGGDSTQHVLWRLE T0448 75 :RYQAI 1es9A 88 :ELEHI T0448 82 :DADFIAVFGGVND 1es9A 93 :RPKIVVVWVGTNN T0448 105 :GDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSA 1es9A 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNPLREK T0448 159 :QSDYEAAIAQMTADY 1es9A 152 :NRRVNELVRAALAGH T0448 174 :GVPHLSLYRDAG 1es9A 168 :RAHFLDADPGFV T0448 188 :FAIP 1es9A 182 :DGTI T0448 194 :AAIYSVDTLHPNNAGHRVIARKLQSFLDSH 1es9A 186 :SHHDMYDYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 12 number of extra gaps= 3 total=79 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1119196814.pdb -s /var/tmp/to_scwrl_1119196814.seq -o /var/tmp/from_scwrl_1119196814.pdb > /var/tmp/scwrl_1119196814.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1119196814.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k7cA/T0448-1k7cA-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 # T0448 read from 1k7cA/T0448-1k7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k7cA read from 1k7cA/T0448-1k7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k7cA in training set Warning: unaligning (T0448)H139 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0448)I140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0448 23 :RPAWLGDSITANNGLA 1k7cA 2 :TVYLAGDSTMAKNGGG T0448 40 :V 1k7cA 19 :G T0448 41 :HYHDILAADWDVE 1k7cA 22 :GWGEYLASYLSAT T0448 55 :SDNLGISGSTIGSRYD 1k7cA 35 :VVNDAVAGRSARSYTR T0448 71 :AMAVRYQAIP 1k7cA 53 :RFENIADVVT T0448 82 :DADFIAVFGGVNDYGRDQPLGQYGDCD 1k7cA 63 :AGDYVIVEFGHNDGGSLSTDNGRTDCS T0448 112 :FYGALMMLLTGLQTN 1k7cA 110 :FPAYLENAAKLFTAK T0448 129 :TVPKLFISAI 1k7cA 125 :GAKVILSSQT T0448 141 :GSDFGGSFSAV 1k7cA 137 :NPWETGTFVNS T0448 159 :QSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPA 1k7cA 148 :PTRFVEYAELAAEVAGVEYVDHWSYVDSIYETLG T0448 193 :QAAIYSVDTLHPNNAGHRVIARKLQSFLDSH 1k7cA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAVVCT T0448 224 :FLEHHHHHH 1k7cA 219 :LKSVLTTTS Number of specific fragments extracted= 12 number of extra gaps= 1 total=91 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_112096447.pdb -s /var/tmp/to_scwrl_112096447.seq -o /var/tmp/from_scwrl_112096447.pdb > /var/tmp/scwrl_112096447.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_112096447.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2q0qA/T0448-2q0qA-t04-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2q0qA expands to /projects/compbio/data/pdb/2q0q.pdb.gz 2q0qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0448 read from 2q0qA/T0448-2q0qA-t04-global-adpstyle1.a2m # 2q0qA read from 2q0qA/T0448-2q0qA-t04-global-adpstyle1.a2m # adding 2q0qA to template set # found chain 2q0qA in template set Warning: unaligning (T0448)F21 because first residue in template chain is (2q0qA)A2 Warning: unaligning (T0448)G66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2q0qA)L68 Warning: unaligning (T0448)F224 because last residue in template chain is (2q0qA)L216 T0448 22 :KRPAWLGDSITANNGLA 2q0qA 3 :KRILCFGDSLTWGWVPV T0448 39 :TV 2q0qA 21 :DG T0448 41 :HYHDILAADW 2q0qA 33 :RWTGVLAQQL T0448 51 :DVE 2q0qA 45 :DFE T0448 55 :SDNLGISGSTI 2q0qA 48 :VIEEGLSARTT T0448 67 :SRYDAMAVRYQAIP 2q0qA 69 :NGASYLPSCLATHL T0448 82 :DADFIAVFGGVNDYGRD 2q0qA 83 :PLDLVIIMLGTNDTKAY T0448 105 :GDCDMTTFYGALMMLLTGLQTN 2q0qA 100 :FRRTPLDIALGMSVLVTQVLTS T0448 127 :WPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYR 2q0qA 129 :YPAPKVLVVSPPPLAPMPHPWFQLIFEGGEQKTTELARVYSALASFMKVPFFDAGS T0448 193 :QAAIYSVDTLHPNNAGHRVIARKLQSFLDSH 2q0qA 185 :VISTDGVDGIHFTEANNRDLGVALAEQVRSL Number of specific fragments extracted= 10 number of extra gaps= 1 total=101 # request to SCWRL produces command: ulimit -t 209 ; scwrl3 -i /var/tmp/to_scwrl_1199906068.pdb -s /var/tmp/to_scwrl_1199906068.seq -o /var/tmp/from_scwrl_1199906068.pdb > /var/tmp/scwrl_1199906068.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1199906068.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 16250.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 16250.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 16250.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 16250.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 16250.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 5.143 (unweighted)= 43.770 superimposing iter= 1 total_weight= 6139.568 rmsd (weighted)= 2.103 (unweighted)= 43.848 superimposing iter= 2 total_weight= 2105.585 rmsd (weighted)= 1.644 (unweighted)= 43.829 superimposing iter= 3 total_weight= 1409.559 rmsd (weighted)= 1.580 (unweighted)= 43.800 superimposing iter= 4 total_weight= 1360.575 rmsd (weighted)= 1.546 (unweighted)= 43.773 superimposing iter= 5 total_weight= 1356.795 rmsd (weighted)= 1.517 (unweighted)= 43.749 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.206 rmsd (weighted)= 6.739 (unweighted)= 35.193 superimposing iter= 1 total_weight= 7035.663 rmsd (weighted)= 2.511 (unweighted)= 35.100 superimposing iter= 2 total_weight= 3547.454 rmsd (weighted)= 1.475 (unweighted)= 35.050 superimposing iter= 3 total_weight= 2447.681 rmsd (weighted)= 1.084 (unweighted)= 35.016 superimposing iter= 4 total_weight= 1893.133 rmsd (weighted)= 0.921 (unweighted)= 34.997 superimposing iter= 5 total_weight= 1624.861 rmsd (weighted)= 0.847 (unweighted)= 34.987 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 6.038 (unweighted)= 25.835 superimposing iter= 1 total_weight= 7194.666 rmsd (weighted)= 2.263 (unweighted)= 26.055 superimposing iter= 2 total_weight= 3279.560 rmsd (weighted)= 1.422 (unweighted)= 26.166 superimposing iter= 3 total_weight= 1961.000 rmsd (weighted)= 1.182 (unweighted)= 26.192 superimposing iter= 4 total_weight= 1567.751 rmsd (weighted)= 1.103 (unweighted)= 26.196 superimposing iter= 5 total_weight= 1460.292 rmsd (weighted)= 1.067 (unweighted)= 26.192 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.171 rmsd (weighted)= 5.270 (unweighted)= 49.801 superimposing iter= 1 total_weight= 6675.053 rmsd (weighted)= 2.166 (unweighted)= 50.050 superimposing iter= 2 total_weight= 2587.999 rmsd (weighted)= 1.551 (unweighted)= 50.068 superimposing iter= 3 total_weight= 1637.447 rmsd (weighted)= 1.410 (unweighted)= 50.050 superimposing iter= 4 total_weight= 1461.286 rmsd (weighted)= 1.358 (unweighted)= 50.021 superimposing iter= 5 total_weight= 1430.867 rmsd (weighted)= 1.323 (unweighted)= 49.986 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.128 rmsd (weighted)= 5.110 (unweighted)= 33.193 superimposing iter= 1 total_weight= 5409.358 rmsd (weighted)= 2.291 (unweighted)= 32.796 superimposing iter= 2 total_weight= 2662.106 rmsd (weighted)= 1.549 (unweighted)= 32.619 superimposing iter= 3 total_weight= 1875.071 rmsd (weighted)= 1.278 (unweighted)= 32.580 superimposing iter= 4 total_weight= 1568.013 rmsd (weighted)= 1.159 (unweighted)= 32.591 superimposing iter= 5 total_weight= 1502.215 rmsd (weighted)= 1.076 (unweighted)= 32.612 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.251 rmsd (weighted)= 7.426 (unweighted)= 46.594 superimposing iter= 1 total_weight= 6238.454 rmsd (weighted)= 3.039 (unweighted)= 46.738 superimposing iter= 2 total_weight= 3330.881 rmsd (weighted)= 1.835 (unweighted)= 46.736 superimposing iter= 3 total_weight= 2466.411 rmsd (weighted)= 1.353 (unweighted)= 46.733 superimposing iter= 4 total_weight= 1918.136 rmsd (weighted)= 1.156 (unweighted)= 46.732 superimposing iter= 5 total_weight= 1614.962 rmsd (weighted)= 1.083 (unweighted)= 46.728 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.061 rmsd (weighted)= 6.436 (unweighted)= 46.512 superimposing iter= 1 total_weight= 6516.480 rmsd (weighted)= 2.381 (unweighted)= 46.266 superimposing iter= 2 total_weight= 2427.167 rmsd (weighted)= 1.643 (unweighted)= 46.169 superimposing iter= 3 total_weight= 1564.497 rmsd (weighted)= 1.433 (unweighted)= 46.074 superimposing iter= 4 total_weight= 1412.013 rmsd (weighted)= 1.324 (unweighted)= 45.986 superimposing iter= 5 total_weight= 1340.769 rmsd (weighted)= 1.258 (unweighted)= 45.908 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.219 rmsd (weighted)= 6.579 (unweighted)= 39.312 superimposing iter= 1 total_weight= 6704.744 rmsd (weighted)= 2.522 (unweighted)= 39.436 superimposing iter= 2 total_weight= 3548.951 rmsd (weighted)= 1.532 (unweighted)= 39.438 superimposing iter= 3 total_weight= 2019.280 rmsd (weighted)= 1.271 (unweighted)= 39.460 superimposing iter= 4 total_weight= 1560.768 rmsd (weighted)= 1.205 (unweighted)= 39.473 superimposing iter= 5 total_weight= 1445.418 rmsd (weighted)= 1.189 (unweighted)= 39.480 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.200 rmsd (weighted)= 5.250 (unweighted)= 29.028 superimposing iter= 1 total_weight= 7014.090 rmsd (weighted)= 2.118 (unweighted)= 29.077 superimposing iter= 2 total_weight= 2752.678 rmsd (weighted)= 1.483 (unweighted)= 29.048 superimposing iter= 3 total_weight= 1730.294 rmsd (weighted)= 1.322 (unweighted)= 29.028 superimposing iter= 4 total_weight= 1533.534 rmsd (weighted)= 1.255 (unweighted)= 29.014 superimposing iter= 5 total_weight= 1507.827 rmsd (weighted)= 1.201 (unweighted)= 29.002 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 5.094 (unweighted)= 25.088 superimposing iter= 1 total_weight= 7924.556 rmsd (weighted)= 1.974 (unweighted)= 25.192 superimposing iter= 2 total_weight= 3571.188 rmsd (weighted)= 1.279 (unweighted)= 25.221 superimposing iter= 3 total_weight= 2351.784 rmsd (weighted)= 1.040 (unweighted)= 25.235 superimposing iter= 4 total_weight= 2016.098 rmsd (weighted)= 0.919 (unweighted)= 25.242 superimposing iter= 5 total_weight= 1837.209 rmsd (weighted)= 0.854 (unweighted)= 25.246 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 3.082 (unweighted)= 33.847 superimposing iter= 1 total_weight= 6213.099 rmsd (weighted)= 1.252 (unweighted)= 33.992 superimposing iter= 2 total_weight= 2558.746 rmsd (weighted)= 0.879 (unweighted)= 34.011 superimposing iter= 3 total_weight= 1619.485 rmsd (weighted)= 0.785 (unweighted)= 34.017 superimposing iter= 4 total_weight= 1428.284 rmsd (weighted)= 0.748 (unweighted)= 34.017 superimposing iter= 5 total_weight= 1374.297 rmsd (weighted)= 0.728 (unweighted)= 34.016 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.258 rmsd (weighted)= 4.060 (unweighted)= 32.267 superimposing iter= 1 total_weight= 8277.895 rmsd (weighted)= 1.429 (unweighted)= 32.232 superimposing iter= 2 total_weight= 3595.564 rmsd (weighted)= 0.883 (unweighted)= 32.222 superimposing iter= 3 total_weight= 1979.993 rmsd (weighted)= 0.751 (unweighted)= 32.217 superimposing iter= 4 total_weight= 1614.293 rmsd (weighted)= 0.711 (unweighted)= 32.215 superimposing iter= 5 total_weight= 1514.102 rmsd (weighted)= 0.697 (unweighted)= 32.214 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 3.054 (unweighted)= 25.648 superimposing iter= 1 total_weight= 7000.857 rmsd (weighted)= 1.235 (unweighted)= 25.639 superimposing iter= 2 total_weight= 2772.641 rmsd (weighted)= 0.860 (unweighted)= 25.628 superimposing iter= 3 total_weight= 1764.465 rmsd (weighted)= 0.758 (unweighted)= 25.622 superimposing iter= 4 total_weight= 1533.368 rmsd (weighted)= 0.717 (unweighted)= 25.618 superimposing iter= 5 total_weight= 1447.150 rmsd (weighted)= 0.699 (unweighted)= 25.616 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.171 rmsd (weighted)= 3.265 (unweighted)= 42.423 superimposing iter= 1 total_weight= 7547.927 rmsd (weighted)= 1.180 (unweighted)= 42.529 superimposing iter= 2 total_weight= 3232.909 rmsd (weighted)= 0.748 (unweighted)= 42.559 superimposing iter= 3 total_weight= 1816.657 rmsd (weighted)= 0.643 (unweighted)= 42.568 superimposing iter= 4 total_weight= 1497.588 rmsd (weighted)= 0.611 (unweighted)= 42.572 superimposing iter= 5 total_weight= 1414.248 rmsd (weighted)= 0.597 (unweighted)= 42.574 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.143 rmsd (weighted)= 3.342 (unweighted)= 27.068 superimposing iter= 1 total_weight= 5619.218 rmsd (weighted)= 1.460 (unweighted)= 26.932 superimposing iter= 2 total_weight= 2990.678 rmsd (weighted)= 0.939 (unweighted)= 26.880 superimposing iter= 3 total_weight= 1952.850 rmsd (weighted)= 0.767 (unweighted)= 26.871 superimposing iter= 4 total_weight= 1583.019 rmsd (weighted)= 0.701 (unweighted)= 26.872 superimposing iter= 5 total_weight= 1446.418 rmsd (weighted)= 0.670 (unweighted)= 26.875 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.251 rmsd (weighted)= 4.325 (unweighted)= 32.926 superimposing iter= 1 total_weight= 7069.348 rmsd (weighted)= 1.634 (unweighted)= 32.897 superimposing iter= 2 total_weight= 3439.455 rmsd (weighted)= 1.015 (unweighted)= 32.912 superimposing iter= 3 total_weight= 2045.825 rmsd (weighted)= 0.846 (unweighted)= 32.917 superimposing iter= 4 total_weight= 1569.791 rmsd (weighted)= 0.809 (unweighted)= 32.918 superimposing iter= 5 total_weight= 1461.783 rmsd (weighted)= 0.802 (unweighted)= 32.917 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.121 rmsd (weighted)= 3.090 (unweighted)= 37.912 superimposing iter= 1 total_weight= 6390.634 rmsd (weighted)= 1.234 (unweighted)= 37.942 superimposing iter= 2 total_weight= 2630.998 rmsd (weighted)= 0.849 (unweighted)= 37.936 superimposing iter= 3 total_weight= 1638.111 rmsd (weighted)= 0.750 (unweighted)= 37.928 superimposing iter= 4 total_weight= 1392.893 rmsd (weighted)= 0.720 (unweighted)= 37.922 superimposing iter= 5 total_weight= 1329.506 rmsd (weighted)= 0.708 (unweighted)= 37.918 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.266 rmsd (weighted)= 3.651 (unweighted)= 29.752 superimposing iter= 1 total_weight= 6628.109 rmsd (weighted)= 1.526 (unweighted)= 29.639 superimposing iter= 2 total_weight= 3166.847 rmsd (weighted)= 1.015 (unweighted)= 29.629 superimposing iter= 3 total_weight= 2121.311 rmsd (weighted)= 0.837 (unweighted)= 29.627 superimposing iter= 4 total_weight= 1737.440 rmsd (weighted)= 0.766 (unweighted)= 29.626 superimposing iter= 5 total_weight= 1552.956 rmsd (weighted)= 0.739 (unweighted)= 29.626 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.200 rmsd (weighted)= 3.341 (unweighted)= 30.161 superimposing iter= 1 total_weight= 7907.207 rmsd (weighted)= 1.189 (unweighted)= 30.184 superimposing iter= 2 total_weight= 3418.401 rmsd (weighted)= 0.740 (unweighted)= 30.199 superimposing iter= 3 total_weight= 1912.337 rmsd (weighted)= 0.627 (unweighted)= 30.203 superimposing iter= 4 total_weight= 1552.603 rmsd (weighted)= 0.591 (unweighted)= 30.204 superimposing iter= 5 total_weight= 1450.779 rmsd (weighted)= 0.577 (unweighted)= 30.205 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 5.099 (unweighted)= 25.074 superimposing iter= 1 total_weight= 7940.493 rmsd (weighted)= 1.974 (unweighted)= 25.179 superimposing iter= 2 total_weight= 3568.689 rmsd (weighted)= 1.280 (unweighted)= 25.207 superimposing iter= 3 total_weight= 2356.624 rmsd (weighted)= 1.038 (unweighted)= 25.221 superimposing iter= 4 total_weight= 2019.671 rmsd (weighted)= 0.917 (unweighted)= 25.228 superimposing iter= 5 total_weight= 1838.864 rmsd (weighted)= 0.851 (unweighted)= 25.231 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 3.079 (unweighted)= 33.848 superimposing iter= 1 total_weight= 6206.165 rmsd (weighted)= 1.252 (unweighted)= 33.994 superimposing iter= 2 total_weight= 2543.783 rmsd (weighted)= 0.882 (unweighted)= 34.013 superimposing iter= 3 total_weight= 1614.860 rmsd (weighted)= 0.789 (unweighted)= 34.019 superimposing iter= 4 total_weight= 1421.458 rmsd (weighted)= 0.754 (unweighted)= 34.020 superimposing iter= 5 total_weight= 1369.413 rmsd (weighted)= 0.734 (unweighted)= 34.019 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.258 rmsd (weighted)= 4.062 (unweighted)= 32.258 superimposing iter= 1 total_weight= 8284.000 rmsd (weighted)= 1.429 (unweighted)= 32.222 superimposing iter= 2 total_weight= 3595.877 rmsd (weighted)= 0.883 (unweighted)= 32.212 superimposing iter= 3 total_weight= 1979.145 rmsd (weighted)= 0.751 (unweighted)= 32.207 superimposing iter= 4 total_weight= 1616.392 rmsd (weighted)= 0.710 (unweighted)= 32.205 superimposing iter= 5 total_weight= 1515.328 rmsd (weighted)= 0.695 (unweighted)= 32.205 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 3.056 (unweighted)= 25.647 superimposing iter= 1 total_weight= 7004.544 rmsd (weighted)= 1.236 (unweighted)= 25.639 superimposing iter= 2 total_weight= 2767.733 rmsd (weighted)= 0.862 (unweighted)= 25.628 superimposing iter= 3 total_weight= 1760.515 rmsd (weighted)= 0.760 (unweighted)= 25.621 superimposing iter= 4 total_weight= 1532.097 rmsd (weighted)= 0.720 (unweighted)= 25.617 superimposing iter= 5 total_weight= 1446.540 rmsd (weighted)= 0.702 (unweighted)= 25.616 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.171 rmsd (weighted)= 3.267 (unweighted)= 42.409 superimposing iter= 1 total_weight= 7537.059 rmsd (weighted)= 1.181 (unweighted)= 42.515 superimposing iter= 2 total_weight= 3240.093 rmsd (weighted)= 0.748 (unweighted)= 42.546 superimposing iter= 3 total_weight= 1827.782 rmsd (weighted)= 0.641 (unweighted)= 42.556 superimposing iter= 4 total_weight= 1497.686 rmsd (weighted)= 0.609 (unweighted)= 42.560 superimposing iter= 5 total_weight= 1413.120 rmsd (weighted)= 0.596 (unweighted)= 42.561 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.143 rmsd (weighted)= 3.338 (unweighted)= 27.080 superimposing iter= 1 total_weight= 5597.711 rmsd (weighted)= 1.462 (unweighted)= 26.945 superimposing iter= 2 total_weight= 2992.652 rmsd (weighted)= 0.939 (unweighted)= 26.893 superimposing iter= 3 total_weight= 1948.106 rmsd (weighted)= 0.768 (unweighted)= 26.883 superimposing iter= 4 total_weight= 1580.286 rmsd (weighted)= 0.702 (unweighted)= 26.884 superimposing iter= 5 total_weight= 1443.315 rmsd (weighted)= 0.672 (unweighted)= 26.887 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.251 rmsd (weighted)= 4.326 (unweighted)= 32.926 superimposing iter= 1 total_weight= 7049.178 rmsd (weighted)= 1.639 (unweighted)= 32.896 superimposing iter= 2 total_weight= 3446.042 rmsd (weighted)= 1.016 (unweighted)= 32.910 superimposing iter= 3 total_weight= 2049.165 rmsd (weighted)= 0.846 (unweighted)= 32.915 superimposing iter= 4 total_weight= 1571.212 rmsd (weighted)= 0.808 (unweighted)= 32.915 superimposing iter= 5 total_weight= 1462.858 rmsd (weighted)= 0.802 (unweighted)= 32.914 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.121 rmsd (weighted)= 3.080 (unweighted)= 37.895 superimposing iter= 1 total_weight= 6373.980 rmsd (weighted)= 1.233 (unweighted)= 37.927 superimposing iter= 2 total_weight= 2635.307 rmsd (weighted)= 0.847 (unweighted)= 37.922 superimposing iter= 3 total_weight= 1640.282 rmsd (weighted)= 0.746 (unweighted)= 37.915 superimposing iter= 4 total_weight= 1399.951 rmsd (weighted)= 0.713 (unweighted)= 37.908 superimposing iter= 5 total_weight= 1334.483 rmsd (weighted)= 0.698 (unweighted)= 37.904 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.266 rmsd (weighted)= 3.640 (unweighted)= 29.748 superimposing iter= 1 total_weight= 6598.549 rmsd (weighted)= 1.525 (unweighted)= 29.635 superimposing iter= 2 total_weight= 3149.849 rmsd (weighted)= 1.018 (unweighted)= 29.628 superimposing iter= 3 total_weight= 2099.498 rmsd (weighted)= 0.845 (unweighted)= 29.629 superimposing iter= 4 total_weight= 1727.222 rmsd (weighted)= 0.774 (unweighted)= 29.630 superimposing iter= 5 total_weight= 1550.979 rmsd (weighted)= 0.748 (unweighted)= 29.630 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.200 rmsd (weighted)= 3.344 (unweighted)= 30.139 superimposing iter= 1 total_weight= 7901.898 rmsd (weighted)= 1.190 (unweighted)= 30.162 superimposing iter= 2 total_weight= 3427.229 rmsd (weighted)= 0.740 (unweighted)= 30.177 superimposing iter= 3 total_weight= 1920.340 rmsd (weighted)= 0.625 (unweighted)= 30.182 superimposing iter= 4 total_weight= 1557.622 rmsd (weighted)= 0.588 (unweighted)= 30.183 superimposing iter= 5 total_weight= 1451.386 rmsd (weighted)= 0.574 (unweighted)= 30.184 superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 5.101 (unweighted)= 25.066 superimposing iter= 1 total_weight= 7941.719 rmsd (weighted)= 1.975 (unweighted)= 25.172 superimposing iter= 2 total_weight= 3568.867 rmsd (weighted)= 1.280 (unweighted)= 25.201 superimposing iter= 3 total_weight= 2356.219 rmsd (weighted)= 1.038 (unweighted)= 25.214 superimposing iter= 4 total_weight= 2019.862 rmsd (weighted)= 0.917 (unweighted)= 25.221 superimposing iter= 5 total_weight= 1839.155 rmsd (weighted)= 0.851 (unweighted)= 25.224 superimposing iter= 0 total_weight= 1.124 rmsd (weighted)= 3.079 (unweighted)= 33.847 superimposing iter= 1 total_weight= 6204.345 rmsd (weighted)= 1.252 (unweighted)= 33.993 superimposing iter= 2 total_weight= 2542.973 rmsd (weighted)= 0.882 (unweighted)= 34.012 superimposing iter= 3 total_weight= 1614.972 rmsd (weighted)= 0.789 (unweighted)= 34.018 superimposing iter= 4 total_weight= 1421.378 rmsd (weighted)= 0.754 (unweighted)= 34.019 superimposing iter= 5 total_weight= 1369.331 rmsd (weighted)= 0.735 (unweighted)= 34.018 superimposing iter= 0 total_weight= 1.258 rmsd (weighted)= 4.062 (unweighted)= 32.251 superimposing iter= 1 total_weight= 8285.007 rmsd (weighted)= 1.429 (unweighted)= 32.216 superimposing iter= 2 total_weight= 3595.435 rmsd (weighted)= 0.883 (unweighted)= 32.206 superimposing iter= 3 total_weight= 1979.262 rmsd (weighted)= 0.751 (unweighted)= 32.201 superimposing iter= 4 total_weight= 1616.370 rmsd (weighted)= 0.710 (unweighted)= 32.200 superimposing iter= 5 total_weight= 1515.157 rmsd (weighted)= 0.695 (unweighted)= 32.199 superimposing iter= 0 total_weight= 1.193 rmsd (weighted)= 3.056 (unweighted)= 25.649 superimposing iter= 1 total_weight= 7004.284 rmsd (weighted)= 1.236 (unweighted)= 25.641 superimposing iter= 2 total_weight= 2767.433 rmsd (weighted)= 0.862 (unweighted)= 25.631 superimposing iter= 3 total_weight= 1760.521 rmsd (weighted)= 0.760 (unweighted)= 25.624 superimposing iter= 4 total_weight= 1532.289 rmsd (weighted)= 0.720 (unweighted)= 25.620 superimposing iter= 5 total_weight= 1446.690 rmsd (weighted)= 0.702 (unweighted)= 25.618 superimposing iter= 0 total_weight= 1.171 rmsd (weighted)= 3.267 (unweighted)= 42.389 superimposing iter= 1 total_weight= 7537.492 rmsd (weighted)= 1.181 (unweighted)= 42.495 superimposing iter= 2 total_weight= 3239.831 rmsd (weighted)= 0.748 (unweighted)= 42.526 superimposing iter= 3 total_weight= 1828.186 rmsd (weighted)= 0.641 (unweighted)= 42.536 superimposing iter= 4 total_weight= 1497.965 rmsd (weighted)= 0.609 (unweighted)= 42.540 superimposing iter= 5 total_weight= 1413.012 rmsd (weighted)= 0.596 (unweighted)= 42.542 superimposing iter= 0 total_weight= 1.143 rmsd (weighted)= 3.337 (unweighted)= 27.084 superimposing iter= 1 total_weight= 5595.885 rmsd (weighted)= 1.461 (unweighted)= 26.949 superimposing iter= 2 total_weight= 2991.362 rmsd (weighted)= 0.939 (unweighted)= 26.898 superimposing iter= 3 total_weight= 1947.770 rmsd (weighted)= 0.769 (unweighted)= 26.888 superimposing iter= 4 total_weight= 1580.219 rmsd (weighted)= 0.702 (unweighted)= 26.889 superimposing iter= 5 total_weight= 1443.289 rmsd (weighted)= 0.673 (unweighted)= 26.892 superimposing iter= 0 total_weight= 1.251 rmsd (weighted)= 4.325 (unweighted)= 32.931 superimposing iter= 1 total_weight= 7049.343 rmsd (weighted)= 1.638 (unweighted)= 32.899 superimposing iter= 2 total_weight= 3446.268 rmsd (weighted)= 1.016 (unweighted)= 32.913 superimposing iter= 3 total_weight= 2048.625 rmsd (weighted)= 0.846 (unweighted)= 32.918 superimposing iter= 4 total_weight= 1570.812 rmsd (weighted)= 0.809 (unweighted)= 32.919 superimposing iter= 5 total_weight= 1462.755 rmsd (weighted)= 0.802 (unweighted)= 32.918 superimposing iter= 0 total_weight= 1.121 rmsd (weighted)= 3.081 (unweighted)= 37.882 superimposing iter= 1 total_weight= 6375.774 rmsd (weighted)= 1.232 (unweighted)= 37.914 superimposing iter= 2 total_weight= 2636.385 rmsd (weighted)= 0.847 (unweighted)= 37.909 superimposing iter= 3 total_weight= 1640.518 rmsd (weighted)= 0.745 (unweighted)= 37.902 superimposing iter= 4 total_weight= 1400.102 rmsd (weighted)= 0.712 (unweighted)= 37.896 superimposing iter= 5 total_weight= 1334.280 rmsd (weighted)= 0.697 (unweighted)= 37.891 superimposing iter= 0 total_weight= 1.266 rmsd (weighted)= 3.640 (unweighted)= 29.740 superimposing iter= 1 total_weight= 6598.513 rmsd (weighted)= 1.526 (unweighted)= 29.628 superimposing iter= 2 total_weight= 3122.736 rmsd (weighted)= 1.024 (unweighted)= 29.623 superimposing iter= 3 total_weight= 2052.827 rmsd (weighted)= 0.860 (unweighted)= 29.626 superimposing iter= 4 total_weight= 1733.724 rmsd (weighted)= 0.789 (unweighted)= 29.630 superimposing iter= 5 total_weight= 1553.618 rmsd (weighted)= 0.762 (unweighted)= 29.631 superimposing iter= 0 total_weight= 1.200 rmsd (weighted)= 3.345 (unweighted)= 30.132 superimposing iter= 1 total_weight= 7902.024 rmsd (weighted)= 1.190 (unweighted)= 30.155 superimposing iter= 2 total_weight= 3427.127 rmsd (weighted)= 0.740 (unweighted)= 30.170 superimposing iter= 3 total_weight= 1920.202 rmsd (weighted)= 0.625 (unweighted)= 30.175 superimposing iter= 4 total_weight= 1557.813 rmsd (weighted)= 0.588 (unweighted)= 30.176 superimposing iter= 5 total_weight= 1451.493 rmsd (weighted)= 0.574 (unweighted)= 30.177 # command:# Printing sheets for alignments to T0448.undertaker-align.sheets # command: