# command:# Seed set to 1279639118 # 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= 24.176 sec, elapsed time= 28.350 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= 37.267 sec, elapsed time= 45.411 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0627 numbered 1 through 261 Created new target T0627 from T0627.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.269 sec, elapsed time= 45.414 sec. # command:# Prefix for input files set to # command:# reading script from file T0627.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcwA/T0627-1rcwA-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 1rcwA expands to /projects/compbio/data/pdb/1rcw.pdb.gz 1rcwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 1rcwA/T0627-1rcwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcwA read from 1rcwA/T0627-1rcwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rcwA to template set # found chain 1rcwA in template set Warning: unaligning (T0627)N97 because of BadResidue code BAD_PEPTIDE in next template residue (1rcwA)E82 Warning: unaligning (T0627)I98 because of BadResidue code BAD_PEPTIDE at template residue (1rcwA)E82 Warning: unaligning (T0627)I244 because last residue in template chain is (1rcwA)L219 T0627 21 :AQQLIN 1rcwA 12 :LDLIIQ # choosing archetypes in rotamer library T0627 32 :KARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHP 1rcwA 18 :NKHMLEHTFYVKWSKGELTKEQLQAYAKDYYLHIKAFPKYLSAIHSRCDDLEAR T0627 88 :DMARRWLMR 1rcwA 72 :KLLLDNLMD T0627 99 :RVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAAT 1rcwA 83 :NGYPNHIDLWKQFVFALGVTPEELEAHEPSEAAKAKVATFMRWCTGDSLAAGVAAL T0627 156 :YAIEGATGEWSAVVCSTGVYAEAFAEETR 1rcwA 139 :YSYESQIPRIAREKIRGLTEYFGFSNPED T0627 188 :MKWLKMHAQYDDAHPWEALEIICTLVGNKPS 1rcwA 168 :YAYFTEHEEADVRHAREEKALIEMLLKDDAD T0627 224 :ELRQAVTKSYDYMYLFLERC 1rcwA 199 :KVLEASQEVTQSLYGFLDSF Number of specific fragments extracted= 7 number of extra gaps= 1 total=7 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_1577311264.pdb -s /var/tmp/to_scwrl_1577311264.seq -o /var/tmp/from_scwrl_1577311264.pdb > /var/tmp/scwrl_1577311264.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1577311264.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3mvuA/T0627-3mvuA-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 3mvuA expands to /projects/compbio/data/pdb/3mvu.pdb.gz 3mvuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 96, because occupancy 0.5 <= existing 0.500 in 3mvuA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 610, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 614, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 616, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 618, because occupancy 0.300 <= existing 0.450 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 620, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 713, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 717, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 721, because occupancy 0.370 <= existing 0.380 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1539, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1547, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1549, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1553, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 3mvuA/T0627-3mvuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mvuA read from 3mvuA/T0627-3mvuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3mvuA to template set # found chain 3mvuA in template set T0627 14 :ASSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3mvuA 2 :SEPYGKAFSLMRAEAEPAWRAYTHHAFVEGLKAGTLPREAFLHYLQQDYVFLIHFSRAWALAVVKS T0627 82 :GRHPGEDMARRWLMRNIRVE 3mvuA 68 :ETHSEMLAAVGTVNALVAEE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 3mvuA 88 :MQLHIGICEASGISQEALFATRERAENLAYTRFVLEAGYSGDLLDLLAALAPCV T0627 165 :WSAVVCSTGVYAEAF 3mvuA 142 :MGYGEIGKRLTAEAT T0627 184 :RKKSMKWLKMHAQYDDAHPW 3mvuA 157 :STLYGDWIDTYGGDDYQAAC T0627 204 :EALEIICTLVGNK 3mvuA 178 :AVGTLLDDALERR T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERC 3mvuA 196 :TSSPRWSRLCQTFHTATELEVGFWQMG Number of specific fragments extracted= 7 number of extra gaps= 0 total=14 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_1985021367.pdb -s /var/tmp/to_scwrl_1985021367.seq -o /var/tmp/from_scwrl_1985021367.pdb > /var/tmp/scwrl_1985021367.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1985021367.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qcxA/T0627-2qcxA-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 2qcxA expands to /projects/compbio/data/pdb/2qcx.pdb.gz 2qcxA:Skipped atom 1239, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 2qcxA # T0627 read from 2qcxA/T0627-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0627-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qcxA to template set # found chain 2qcxA in template set Warning: unaligning (T0627)S16 because first residue in template chain is (2qcxA)Q-1 Warning: unaligning (T0627)S251 because last residue in template chain is (2qcxA)D220 T0627 17 :YPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2qcxA 0 :GMKFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 82 :GRHPGEDMARRWLMRNIRVE 2qcxA 63 :KDLYTTGRMASHAQGTYEAE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 2qcxA 83 :MALHREFAELLEISEEERKAFKPSPTAYSFTSHMYRSVLSGNFAEILAALLPCY T0627 165 :WSAVVCSTG 2qcxA 137 :WLYYEVGEK T0627 175 :YAEAFAE 2qcxA 146 :LLHCDPG T0627 184 :RKKSMKWLKMHAQYDDAHPW 2qcxA 153 :HPIYQKWIGTYGGDWFRQQV T0627 204 :EALEIICTLVGN 2qcxA 174 :EQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 2qcxA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=22 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_2107553156.pdb -s /var/tmp/to_scwrl_2107553156.seq -o /var/tmp/from_scwrl_2107553156.pdb > /var/tmp/scwrl_2107553156.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2107553156.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yakA/T0627-1yakA-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 1yakA expands to /projects/compbio/data/pdb/1yak.pdb.gz 1yakA:# T0627 read from 1yakA/T0627-1yakA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yakA read from 1yakA/T0627-1yakA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yakA to template set # found chain 1yakA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1yakA)K2 Warning: unaligning (T0627)S251 because last residue in template chain is (1yakA)D220 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1yakA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 82 :G 1yakA 63 :K T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAA 1yakA 64 :DLYTTGRMASHAQGTYEAEMALHREFAE T0627 115 :HDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 1yakA 93 :LEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCY T0627 165 :WSAVVCSTG 1yakA 137 :WLYYEVGEK T0627 175 :YAEAFAE 1yakA 146 :LLHCDPG T0627 184 :RKKSMKWLKMHAQYDDAHPW 1yakA 153 :HPIYQKWIGTYGGDWFRQQV T0627 204 :EALEIICTLVGN 1yakA 174 :EQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 1yakA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 9 number of extra gaps= 0 total=31 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_95504763.pdb -s /var/tmp/to_scwrl_95504763.seq -o /var/tmp/from_scwrl_95504763.pdb > /var/tmp/scwrl_95504763.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_95504763.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rd3A/T0627-2rd3A-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 2rd3A expands to /projects/compbio/data/pdb/2rd3.pdb.gz 2rd3A:# T0627 read from 2rd3A/T0627-2rd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rd3A read from 2rd3A/T0627-2rd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rd3A to template set # found chain 2rd3A in template set Warning: unaligning (T0627)A14 because first residue in template chain is (2rd3A)D-3 Warning: unaligning (T0627)S15 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)P-2 Warning: unaligning (T0627)Y57 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)I41 Warning: unaligning (T0627)L58 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)I41 T0627 16 :SYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQ 2rd3A -1 :FTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRF T0627 59 :IGGWPVVEQFAVYMAKNLTKT 2rd3A 42 :IQDYLFLLEYAKVFALGVVKA T0627 82 :G 2rd3A 63 :C T0627 87 :EDMARRWLMRNIRVE 2rd3A 64 :DEAVMREFSNAIQDI T0627 105 :AD 2rd3A 79 :LN T0627 107 :YWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 2rd3A 85 :IHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCG T0627 165 :WSAVVCSTG 2rd3A 137 :WSYLVIAQN T0627 175 :YAEAFAEETRKKSMKWLKMHAQYDDAHPW 2rd3A 146 :LSQIPNALEHAFYGHWIKGYSSKEFQACV T0627 204 :EALEIICTLVGN 2rd3A 176 :WNINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCI 2rd3A 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAY Number of specific fragments extracted= 10 number of extra gaps= 1 total=41 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_2133935731.pdb -s /var/tmp/to_scwrl_2133935731.seq -o /var/tmp/from_scwrl_2133935731.pdb > /var/tmp/scwrl_2133935731.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2133935731.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ibxA/T0627-3ibxA-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 3ibxA expands to /projects/compbio/data/pdb/3ibx.pdb.gz 3ibxA:# T0627 read from 3ibxA/T0627-3ibxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ibxA read from 3ibxA/T0627-3ibxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ibxA to template set # found chain 3ibxA in template set Warning: unaligning (T0627)S15 because of BadResidue code BAD_PEPTIDE at template residue (3ibxA)P-2 T0627 16 :SYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3ibxA -1 :FTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLYLLEYAKVFALGVVKA T0627 82 :G 3ibxA 63 :C T0627 87 :EDMARRWLMRNIRVELNH 3ibxA 64 :DEAVMREFSNAIQDILNN T0627 107 :YWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 3ibxA 85 :IHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCG T0627 165 :WSAVVCSTG 3ibxA 137 :WSYLVIAQN T0627 175 :YAEAFAEETRKKSMKWLKMHAQYDDAHPW 3ibxA 146 :LSQIPNALEHAFYGHWIKGYSSKEFQACV T0627 204 :EALEIICTLVGN 3ibxA 176 :WNINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQ 3ibxA 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAYQ Number of specific fragments extracted= 8 number of extra gaps= 1 total=49 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_205997447.pdb -s /var/tmp/to_scwrl_205997447.seq -o /var/tmp/from_scwrl_205997447.pdb > /var/tmp/scwrl_205997447.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_205997447.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qzcA/T0627-2qzcA-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 2qzcA expands to /projects/compbio/data/pdb/2qzc.pdb.gz 2qzcA:Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2qzcA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 292, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 305, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 310, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 313, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 316, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 319, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 2qzcA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 463, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1124, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 2qzcA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1170, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1460, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1466, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1502, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1506, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1510, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1545, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1546, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1550, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1551, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1553, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1554, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1556, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1557, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1559, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1560, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1562, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1563, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1720, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2qzcA # T0627 read from 2qzcA/T0627-2qzcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzcA read from 2qzcA/T0627-2qzcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qzcA to template set # found chain 2qzcA in template set Warning: unaligning (T0627)R99 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qzcA)K83 T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 2qzcA 4 :VGNVENLINGVGELWNKYVKHEFILKMRDGSLPLDIFRYYLIQDGKYVEDMLRALLIASSKGP T0627 84 :HPGEDMARRWLMR 2qzcA 67 :IDKVTKILNLVFS T0627 100 :VELNHADYW 2qzcA 84 :GLETHGKLY T0627 113 :AAHDVTLEDLHDQRVAPELHALSHWCWQTSSS 2qzcA 93 :SKLDISRDVIVKTGYNLINYAYTRHLYYYANL T0627 146 :SLAVAMAATNYAIEG 2qzcA 125 :DWNKFLVAWTPCMFG T0627 162 :TGEWS 2qzcA 140 :YSIVG T0627 174 :VYAEAFA 2qzcA 145 :DYVIDSP T0627 184 :RKKSMKWLKMHAQY 2qzcA 152 :NEVYKTWASFYAST T0627 201 :HPWEALEIICTLVGN 2qzcA 166 :EYKKRIEAILYALDE T0627 216 :KPSLQ 2qzcA 182 :SITED T0627 225 :LRQAVTKSYDYMYLFLERCIQLDK 2qzcA 187 :LLNIFINSVRFEIGFWDASLRKDP Number of specific fragments extracted= 11 number of extra gaps= 0 total=60 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_1215272803.pdb -s /var/tmp/to_scwrl_1215272803.seq -o /var/tmp/from_scwrl_1215272803.pdb > /var/tmp/scwrl_1215272803.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1215272803.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hmlA/T0627-3hmlA-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 3hmlA expands to /projects/compbio/data/pdb/3hml.pdb.gz 3hmlA:Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 3hmlA # T0627 read from 3hmlA/T0627-3hmlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hmlA read from 3hmlA/T0627-3hmlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hmlA to template set # found chain 3hmlA in template set Warning: unaligning (T0627)N103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)G92 Warning: unaligning (T0627)T162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)P151 Warning: unaligning (T0627)G163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)P151 Warning: unaligning (T0627)T172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)S160 Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)D186 Warning: unaligning (T0627)H201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)D186 T0627 12 :MEASSY 3hmlA 4 :TDTLSP T0627 22 :QQLINDCSPAKARV 3hmlA 10 :QAFEEALRAKGDFY T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3hmlA 25 :IHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANC T0627 82 :G 3hmlA 69 :P T0627 87 :EDMARRWLMRNIRVEL 3hmlA 70 :DAQTRRKWVQRILDHD T0627 104 :HADYWVNWCAAHDVTLEDLHDQR 3hmlA 93 :GIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATNY 3hmlA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSLT T0627 159 :EGA 3hmlA 147 :ELF T0627 175 :YAEAFAE 3hmlA 161 :WPQHYPW T0627 183 :TRKKSMKWLKMHA 3hmlA 168 :IKEEGYFYFRSRL T0627 202 :PWEALEIICTLV 3hmlA 187 :VEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVAALE 3hmlA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDK Number of specific fragments extracted= 12 number of extra gaps= 2 total=72 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_2136088970.pdb -s /var/tmp/to_scwrl_2136088970.seq -o /var/tmp/from_scwrl_2136088970.pdb > /var/tmp/scwrl_2136088970.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2136088970.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hlxA/T0627-3hlxA-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 3hlxA expands to /projects/compbio/data/pdb/3hlx.pdb.gz 3hlxA:Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 283, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 287, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 289, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 291, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 293, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 320, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 324, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 326, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 328, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 330, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 332, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 334, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 336, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1830, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1928, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 3hlxA # T0627 read from 3hlxA/T0627-3hlxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hlxA read from 3hlxA/T0627-3hlxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hlxA to template set # found chain 3hlxA in template set Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3hlxA)R185 Warning: unaligning (T0627)A200 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3hlxA)R185 T0627 11 :LMEASSY 3hlxA 3 :ITDTLSP T0627 22 :QQLINDCSPAKARV 3hlxA 10 :QAFEEALRAKGDFY T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3hlxA 25 :IHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANC T0627 82 :G 3hlxA 69 :P T0627 87 :EDMARRWLMRNIRVEL 3hlxA 70 :DAQTRRKWVQRILDHD T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 3hlxA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATNY 3hlxA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSLT T0627 159 :EGATGEWSAVVCST 3hlxA 147 :ELFAPQIHQSRLDS T0627 175 :YAEAFAE 3hlxA 161 :WPQHYPW T0627 183 :TRKKSMKWLKMHAQYD 3hlxA 168 :IKEEGYFFFRSRLSQA T0627 201 :HPWEALEIICTLV 3hlxA 186 :DVEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVAALE 3hlxA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDK Number of specific fragments extracted= 12 number of extra gaps= 1 total=84 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_1585031776.pdb -s /var/tmp/to_scwrl_1585031776.seq -o /var/tmp/from_scwrl_1585031776.pdb > /var/tmp/scwrl_1585031776.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1585031776.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ddeA/T0627-3ddeA-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 3ddeA expands to /projects/compbio/data/pdb/3dde.pdb.gz 3ddeA:Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 238, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 669, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 703, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 707, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 711, because occupancy 0.370 <= existing 0.380 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 3ddeA/T0627-3ddeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ddeA read from 3ddeA/T0627-3ddeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ddeA to template set # found chain 3ddeA in template set T0627 21 :AQQLINDCSPAKARV 3ddeA 6 :LTKLEQKVATMWDSI T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3ddeA 22 :TNSPFIHEVLDGKATKALYAIYMTETYHYTKHNAKNQALVGIMG T0627 82 :GRH 3ddeA 66 :KDL T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 3ddeA 69 :PGKYLSFCFHHAHEEAGHELMALSDIASIGFDREDVLSSKPLPATETLIAYLYWISATGNPVQRLGYSYWA T0627 159 :EGATG 3ddeA 140 :ENVYG T0627 165 :WSAVVCST 3ddeA 145 :YIDPVLKA T0627 175 :YAEAFAE 3ddeA 153 :IQSTLDL T0627 184 :RKKSMKWLKMHAQYDDAHPWEALEIICTLV 3ddeA 160 :TPQSMKFFIAHSKIDAKHAEEVNEMLHEVC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDK 3ddeA 190 :KTQEDVDSVVAVMENSLVLTARILDDVWKEYQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=93 # request to SCWRL produces command: ulimit -t 235 ; scwrl4 -t -i /var/tmp/to_scwrl_1025228224.pdb -s /var/tmp/to_scwrl_1025228224.seq -o /var/tmp/from_scwrl_1025228224.pdb > /var/tmp/scwrl_1025228224.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1025228224.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.185 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 16730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 16730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 16730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 16730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 16730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.101 rmsd (weighted)= 5.007 (unweighted)= 46.052 superimposing iter= 1 total_weight= 6557.790 rmsd (weighted)= 2.136 (unweighted)= 46.846 superimposing iter= 2 total_weight= 2977.889 rmsd (weighted)= 1.507 (unweighted)= 46.990 superimposing iter= 3 total_weight= 1922.501 rmsd (weighted)= 1.343 (unweighted)= 47.067 superimposing iter= 4 total_weight= 1714.276 rmsd (weighted)= 1.272 (unweighted)= 47.120 superimposing iter= 5 total_weight= 1631.219 rmsd (weighted)= 1.235 (unweighted)= 47.155 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.100 rmsd (weighted)= 5.080 (unweighted)= 42.027 superimposing iter= 1 total_weight= 5982.381 rmsd (weighted)= 2.371 (unweighted)= 42.309 superimposing iter= 2 total_weight= 2643.134 rmsd (weighted)= 1.782 (unweighted)= 42.506 superimposing iter= 3 total_weight= 1822.903 rmsd (weighted)= 1.630 (unweighted)= 42.661 superimposing iter= 4 total_weight= 1686.319 rmsd (weighted)= 1.555 (unweighted)= 42.780 superimposing iter= 5 total_weight= 1661.633 rmsd (weighted)= 1.496 (unweighted)= 42.869 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.099 rmsd (weighted)= 5.213 (unweighted)= 54.263 superimposing iter= 1 total_weight= 6458.174 rmsd (weighted)= 2.311 (unweighted)= 54.400 superimposing iter= 2 total_weight= 2760.616 rmsd (weighted)= 1.707 (unweighted)= 54.513 superimposing iter= 3 total_weight= 1827.064 rmsd (weighted)= 1.563 (unweighted)= 54.600 superimposing iter= 4 total_weight= 1681.558 rmsd (weighted)= 1.495 (unweighted)= 54.667 superimposing iter= 5 total_weight= 1649.171 rmsd (weighted)= 1.445 (unweighted)= 54.720 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.079 rmsd (weighted)= 5.274 (unweighted)= 80.146 superimposing iter= 1 total_weight= 5985.780 rmsd (weighted)= 2.369 (unweighted)= 80.168 superimposing iter= 2 total_weight= 2865.460 rmsd (weighted)= 1.671 (unweighted)= 80.114 superimposing iter= 3 total_weight= 1976.065 rmsd (weighted)= 1.441 (unweighted)= 80.066 superimposing iter= 4 total_weight= 1692.328 rmsd (weighted)= 1.350 (unweighted)= 80.047 superimposing iter= 5 total_weight= 1590.276 rmsd (weighted)= 1.307 (unweighted)= 80.041 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.101 rmsd (weighted)= 5.284 (unweighted)= 77.117 superimposing iter= 1 total_weight= 6224.240 rmsd (weighted)= 2.353 (unweighted)= 77.124 superimposing iter= 2 total_weight= 3002.130 rmsd (weighted)= 1.639 (unweighted)= 77.067 superimposing iter= 3 total_weight= 2045.221 rmsd (weighted)= 1.404 (unweighted)= 77.032 superimposing iter= 4 total_weight= 1737.836 rmsd (weighted)= 1.310 (unweighted)= 77.019 superimposing iter= 5 total_weight= 1614.591 rmsd (weighted)= 1.272 (unweighted)= 77.015 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.053 rmsd (weighted)= 4.997 (unweighted)= 51.890 superimposing iter= 1 total_weight= 5402.043 rmsd (weighted)= 2.464 (unweighted)= 51.913 superimposing iter= 2 total_weight= 2187.570 rmsd (weighted)= 1.990 (unweighted)= 51.983 superimposing iter= 3 total_weight= 1799.489 rmsd (weighted)= 1.787 (unweighted)= 52.077 superimposing iter= 4 total_weight= 1736.042 rmsd (weighted)= 1.639 (unweighted)= 52.160 superimposing iter= 5 total_weight= 1689.573 rmsd (weighted)= 1.528 (unweighted)= 52.218 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.007 rmsd (weighted)= 4.448 (unweighted)= 42.017 superimposing iter= 1 total_weight= 7062.784 rmsd (weighted)= 1.795 (unweighted)= 42.028 superimposing iter= 2 total_weight= 2673.300 rmsd (weighted)= 1.292 (unweighted)= 42.018 superimposing iter= 3 total_weight= 1679.353 rmsd (weighted)= 1.184 (unweighted)= 42.017 superimposing iter= 4 total_weight= 1510.242 rmsd (weighted)= 1.146 (unweighted)= 42.020 superimposing iter= 5 total_weight= 1459.531 rmsd (weighted)= 1.129 (unweighted)= 42.025 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.096 rmsd (weighted)= 3.930 (unweighted)= 43.122 superimposing iter= 1 total_weight= 7937.580 rmsd (weighted)= 1.521 (unweighted)= 43.286 superimposing iter= 2 total_weight= 3210.792 rmsd (weighted)= 1.031 (unweighted)= 43.339 superimposing iter= 3 total_weight= 1987.128 rmsd (weighted)= 0.901 (unweighted)= 43.363 superimposing iter= 4 total_weight= 1695.952 rmsd (weighted)= 0.855 (unweighted)= 43.378 superimposing iter= 5 total_weight= 1605.115 rmsd (weighted)= 0.835 (unweighted)= 43.389 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.117 rmsd (weighted)= 4.254 (unweighted)= 51.816 superimposing iter= 1 total_weight= 6517.012 rmsd (weighted)= 1.921 (unweighted)= 51.890 superimposing iter= 2 total_weight= 2436.675 rmsd (weighted)= 1.532 (unweighted)= 51.876 superimposing iter= 3 total_weight= 1680.974 rmsd (weighted)= 1.476 (unweighted)= 51.872 superimposing iter= 4 total_weight= 1587.181 rmsd (weighted)= 1.465 (unweighted)= 51.874 superimposing iter= 5 total_weight= 1570.975 rmsd (weighted)= 1.463 (unweighted)= 51.878 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.185 rmsd (weighted)= 3.685 (unweighted)= 32.010 superimposing iter= 1 total_weight= 6890.840 rmsd (weighted)= 1.620 (unweighted)= 32.076 superimposing iter= 2 total_weight= 3111.269 rmsd (weighted)= 1.160 (unweighted)= 32.084 superimposing iter= 3 total_weight= 2131.977 rmsd (weighted)= 1.014 (unweighted)= 32.087 superimposing iter= 4 total_weight= 1938.902 rmsd (weighted)= 0.931 (unweighted)= 32.088 superimposing iter= 5 total_weight= 1830.954 rmsd (weighted)= 0.881 (unweighted)= 32.088 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.238 rmsd (weighted)= 3.204 (unweighted)= 37.975 superimposing iter= 1 total_weight= 7889.509 rmsd (weighted)= 1.380 (unweighted)= 38.116 superimposing iter= 2 total_weight= 3074.201 rmsd (weighted)= 1.024 (unweighted)= 38.166 superimposing iter= 3 total_weight= 2035.138 rmsd (weighted)= 0.944 (unweighted)= 38.191 superimposing iter= 4 total_weight= 1826.503 rmsd (weighted)= 0.919 (unweighted)= 38.209 superimposing iter= 5 total_weight= 1774.228 rmsd (weighted)= 0.908 (unweighted)= 38.221 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.264 rmsd (weighted)= 2.638 (unweighted)= 27.477 superimposing iter= 1 total_weight= 6481.334 rmsd (weighted)= 1.308 (unweighted)= 27.565 superimposing iter= 2 total_weight= 2875.927 rmsd (weighted)= 1.009 (unweighted)= 27.617 superimposing iter= 3 total_weight= 2170.097 rmsd (weighted)= 0.904 (unweighted)= 27.649 superimposing iter= 4 total_weight= 1955.878 rmsd (weighted)= 0.856 (unweighted)= 27.671 superimposing iter= 5 total_weight= 1874.760 rmsd (weighted)= 0.829 (unweighted)= 27.688 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.242 rmsd (weighted)= 2.399 (unweighted)= 38.315 superimposing iter= 1 total_weight= 6380.105 rmsd (weighted)= 1.180 (unweighted)= 38.307 superimposing iter= 2 total_weight= 2917.900 rmsd (weighted)= 0.901 (unweighted)= 38.300 superimposing iter= 3 total_weight= 2055.713 rmsd (weighted)= 0.826 (unweighted)= 38.297 superimposing iter= 4 total_weight= 1881.142 rmsd (weighted)= 0.792 (unweighted)= 38.297 superimposing iter= 5 total_weight= 1819.165 rmsd (weighted)= 0.773 (unweighted)= 38.299 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.209 rmsd (weighted)= 2.227 (unweighted)= 68.414 superimposing iter= 1 total_weight= 6328.182 rmsd (weighted)= 1.051 (unweighted)= 68.475 superimposing iter= 2 total_weight= 2852.274 rmsd (weighted)= 0.791 (unweighted)= 68.500 superimposing iter= 3 total_weight= 2052.494 rmsd (weighted)= 0.713 (unweighted)= 68.514 superimposing iter= 4 total_weight= 1828.118 rmsd (weighted)= 0.684 (unweighted)= 68.523 superimposing iter= 5 total_weight= 1735.525 rmsd (weighted)= 0.674 (unweighted)= 68.528 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.236 rmsd (weighted)= 2.240 (unweighted)= 65.323 superimposing iter= 1 total_weight= 6588.017 rmsd (weighted)= 1.051 (unweighted)= 65.396 superimposing iter= 2 total_weight= 3009.838 rmsd (weighted)= 0.782 (unweighted)= 65.423 superimposing iter= 3 total_weight= 2084.434 rmsd (weighted)= 0.710 (unweighted)= 65.433 superimposing iter= 4 total_weight= 1855.402 rmsd (weighted)= 0.685 (unweighted)= 65.437 superimposing iter= 5 total_weight= 1790.056 rmsd (weighted)= 0.674 (unweighted)= 65.439 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.170 rmsd (weighted)= 3.252 (unweighted)= 34.414 superimposing iter= 1 total_weight= 5894.697 rmsd (weighted)= 1.567 (unweighted)= 34.433 superimposing iter= 2 total_weight= 2861.159 rmsd (weighted)= 1.158 (unweighted)= 34.449 superimposing iter= 3 total_weight= 2089.138 rmsd (weighted)= 1.015 (unweighted)= 34.464 superimposing iter= 4 total_weight= 1908.475 rmsd (weighted)= 0.936 (unweighted)= 34.477 superimposing iter= 5 total_weight= 1757.643 rmsd (weighted)= 0.902 (unweighted)= 34.489 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.228 rmsd (weighted)= 3.461 (unweighted)= 28.409 superimposing iter= 1 total_weight= 6515.644 rmsd (weighted)= 1.652 (unweighted)= 28.195 superimposing iter= 2 total_weight= 2843.933 rmsd (weighted)= 1.258 (unweighted)= 28.109 superimposing iter= 3 total_weight= 2125.306 rmsd (weighted)= 1.113 (unweighted)= 28.068 superimposing iter= 4 total_weight= 1899.007 rmsd (weighted)= 1.042 (unweighted)= 28.046 superimposing iter= 5 total_weight= 1798.865 rmsd (weighted)= 1.004 (unweighted)= 28.035 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.323 rmsd (weighted)= 3.216 (unweighted)= 28.467 superimposing iter= 1 total_weight= 6447.492 rmsd (weighted)= 1.647 (unweighted)= 28.572 superimposing iter= 2 total_weight= 2703.065 rmsd (weighted)= 1.342 (unweighted)= 28.640 superimposing iter= 3 total_weight= 2229.229 rmsd (weighted)= 1.213 (unweighted)= 28.682 superimposing iter= 4 total_weight= 2116.286 rmsd (weighted)= 1.131 (unweighted)= 28.707 superimposing iter= 5 total_weight= 2071.706 rmsd (weighted)= 1.068 (unweighted)= 28.723 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 3.253 (unweighted)= 38.919 superimposing iter= 1 total_weight= 5977.849 rmsd (weighted)= 1.686 (unweighted)= 38.933 superimposing iter= 2 total_weight= 2568.985 rmsd (weighted)= 1.369 (unweighted)= 38.939 superimposing iter= 3 total_weight= 2068.590 rmsd (weighted)= 1.245 (unweighted)= 38.938 superimposing iter= 4 total_weight= 1908.704 rmsd (weighted)= 1.181 (unweighted)= 38.937 superimposing iter= 5 total_weight= 1824.305 rmsd (weighted)= 1.148 (unweighted)= 38.935 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.185 rmsd (weighted)= 3.684 (unweighted)= 32.006 superimposing iter= 1 total_weight= 6874.707 rmsd (weighted)= 1.624 (unweighted)= 32.071 superimposing iter= 2 total_weight= 3078.044 rmsd (weighted)= 1.170 (unweighted)= 32.076 superimposing iter= 3 total_weight= 2108.082 rmsd (weighted)= 1.028 (unweighted)= 32.076 superimposing iter= 4 total_weight= 1929.935 rmsd (weighted)= 0.947 (unweighted)= 32.078 superimposing iter= 5 total_weight= 1864.825 rmsd (weighted)= 0.888 (unweighted)= 32.081 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.238 rmsd (weighted)= 3.195 (unweighted)= 37.995 superimposing iter= 1 total_weight= 7866.392 rmsd (weighted)= 1.379 (unweighted)= 38.135 superimposing iter= 2 total_weight= 3059.084 rmsd (weighted)= 1.026 (unweighted)= 38.185 superimposing iter= 3 total_weight= 2030.436 rmsd (weighted)= 0.946 (unweighted)= 38.209 superimposing iter= 4 total_weight= 1824.617 rmsd (weighted)= 0.922 (unweighted)= 38.227 superimposing iter= 5 total_weight= 1775.853 rmsd (weighted)= 0.911 (unweighted)= 38.239 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.264 rmsd (weighted)= 2.637 (unweighted)= 27.481 superimposing iter= 1 total_weight= 6474.919 rmsd (weighted)= 1.308 (unweighted)= 27.567 superimposing iter= 2 total_weight= 2866.315 rmsd (weighted)= 1.011 (unweighted)= 27.619 superimposing iter= 3 total_weight= 2171.016 rmsd (weighted)= 0.906 (unweighted)= 27.652 superimposing iter= 4 total_weight= 1952.220 rmsd (weighted)= 0.859 (unweighted)= 27.674 superimposing iter= 5 total_weight= 1868.648 rmsd (weighted)= 0.833 (unweighted)= 27.691 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.242 rmsd (weighted)= 2.401 (unweighted)= 38.322 superimposing iter= 1 total_weight= 6357.106 rmsd (weighted)= 1.183 (unweighted)= 38.316 superimposing iter= 2 total_weight= 2915.938 rmsd (weighted)= 0.903 (unweighted)= 38.308 superimposing iter= 3 total_weight= 2061.002 rmsd (weighted)= 0.827 (unweighted)= 38.305 superimposing iter= 4 total_weight= 1875.009 rmsd (weighted)= 0.794 (unweighted)= 38.305 superimposing iter= 5 total_weight= 1814.806 rmsd (weighted)= 0.776 (unweighted)= 38.306 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.209 rmsd (weighted)= 2.222 (unweighted)= 68.425 superimposing iter= 1 total_weight= 6312.288 rmsd (weighted)= 1.050 (unweighted)= 68.487 superimposing iter= 2 total_weight= 2844.668 rmsd (weighted)= 0.792 (unweighted)= 68.511 superimposing iter= 3 total_weight= 2043.013 rmsd (weighted)= 0.715 (unweighted)= 68.525 superimposing iter= 4 total_weight= 1827.394 rmsd (weighted)= 0.686 (unweighted)= 68.534 superimposing iter= 5 total_weight= 1736.378 rmsd (weighted)= 0.676 (unweighted)= 68.539 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.236 rmsd (weighted)= 2.239 (unweighted)= 65.336 superimposing iter= 1 total_weight= 6590.959 rmsd (weighted)= 1.050 (unweighted)= 65.409 superimposing iter= 2 total_weight= 3005.157 rmsd (weighted)= 0.783 (unweighted)= 65.435 superimposing iter= 3 total_weight= 2081.480 rmsd (weighted)= 0.711 (unweighted)= 65.444 superimposing iter= 4 total_weight= 1853.663 rmsd (weighted)= 0.687 (unweighted)= 65.448 superimposing iter= 5 total_weight= 1788.214 rmsd (weighted)= 0.676 (unweighted)= 65.449 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.170 rmsd (weighted)= 3.247 (unweighted)= 34.398 superimposing iter= 1 total_weight= 5864.414 rmsd (weighted)= 1.569 (unweighted)= 34.417 superimposing iter= 2 total_weight= 2840.994 rmsd (weighted)= 1.165 (unweighted)= 34.434 superimposing iter= 3 total_weight= 2077.137 rmsd (weighted)= 1.024 (unweighted)= 34.450 superimposing iter= 4 total_weight= 1913.775 rmsd (weighted)= 0.943 (unweighted)= 34.464 superimposing iter= 5 total_weight= 1765.020 rmsd (weighted)= 0.906 (unweighted)= 34.477 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.228 rmsd (weighted)= 3.456 (unweighted)= 28.438 superimposing iter= 1 total_weight= 6528.316 rmsd (weighted)= 1.642 (unweighted)= 28.230 superimposing iter= 2 total_weight= 2883.565 rmsd (weighted)= 1.236 (unweighted)= 28.152 superimposing iter= 3 total_weight= 2126.036 rmsd (weighted)= 1.091 (unweighted)= 28.118 superimposing iter= 4 total_weight= 1890.978 rmsd (weighted)= 1.024 (unweighted)= 28.101 superimposing iter= 5 total_weight= 1793.746 rmsd (weighted)= 0.989 (unweighted)= 28.093 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.323 rmsd (weighted)= 3.213 (unweighted)= 28.473 superimposing iter= 1 total_weight= 6592.927 rmsd (weighted)= 1.621 (unweighted)= 28.574 superimposing iter= 2 total_weight= 2869.170 rmsd (weighted)= 1.281 (unweighted)= 28.642 superimposing iter= 3 total_weight= 2377.953 rmsd (weighted)= 1.120 (unweighted)= 28.682 superimposing iter= 4 total_weight= 2159.932 rmsd (weighted)= 1.031 (unweighted)= 28.704 superimposing iter= 5 total_weight= 2017.478 rmsd (weighted)= 0.982 (unweighted)= 28.715 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 3.250 (unweighted)= 38.959 superimposing iter= 1 total_weight= 5978.268 rmsd (weighted)= 1.684 (unweighted)= 38.972 superimposing iter= 2 total_weight= 2568.080 rmsd (weighted)= 1.367 (unweighted)= 38.977 superimposing iter= 3 total_weight= 2064.565 rmsd (weighted)= 1.245 (unweighted)= 38.977 superimposing iter= 4 total_weight= 1906.638 rmsd (weighted)= 1.182 (unweighted)= 38.976 superimposing iter= 5 total_weight= 1823.820 rmsd (weighted)= 1.148 (unweighted)= 38.974 superimposing iter= 0 total_weight= 1.185 rmsd (weighted)= 3.684 (unweighted)= 32.005 superimposing iter= 1 total_weight= 6874.984 rmsd (weighted)= 1.625 (unweighted)= 32.069 superimposing iter= 2 total_weight= 3072.817 rmsd (weighted)= 1.171 (unweighted)= 32.074 superimposing iter= 3 total_weight= 2103.327 rmsd (weighted)= 1.031 (unweighted)= 32.073 superimposing iter= 4 total_weight= 1920.130 rmsd (weighted)= 0.952 (unweighted)= 32.074 superimposing iter= 5 total_weight= 1866.792 rmsd (weighted)= 0.893 (unweighted)= 32.078 superimposing iter= 0 total_weight= 1.238 rmsd (weighted)= 3.195 (unweighted)= 38.016 superimposing iter= 1 total_weight= 7867.858 rmsd (weighted)= 1.379 (unweighted)= 38.155 superimposing iter= 2 total_weight= 3056.865 rmsd (weighted)= 1.026 (unweighted)= 38.205 superimposing iter= 3 total_weight= 2030.296 rmsd (weighted)= 0.947 (unweighted)= 38.229 superimposing iter= 4 total_weight= 1824.700 rmsd (weighted)= 0.922 (unweighted)= 38.247 superimposing iter= 5 total_weight= 1776.180 rmsd (weighted)= 0.911 (unweighted)= 38.260 superimposing iter= 0 total_weight= 1.264 rmsd (weighted)= 2.635 (unweighted)= 27.487 superimposing iter= 1 total_weight= 6471.439 rmsd (weighted)= 1.308 (unweighted)= 27.573 superimposing iter= 2 total_weight= 2863.669 rmsd (weighted)= 1.011 (unweighted)= 27.624 superimposing iter= 3 total_weight= 2169.466 rmsd (weighted)= 0.906 (unweighted)= 27.657 superimposing iter= 4 total_weight= 1952.568 rmsd (weighted)= 0.859 (unweighted)= 27.679 superimposing iter= 5 total_weight= 1867.704 rmsd (weighted)= 0.834 (unweighted)= 27.696 superimposing iter= 0 total_weight= 1.242 rmsd (weighted)= 2.400 (unweighted)= 38.335 superimposing iter= 1 total_weight= 6353.341 rmsd (weighted)= 1.183 (unweighted)= 38.328 superimposing iter= 2 total_weight= 2916.819 rmsd (weighted)= 0.903 (unweighted)= 38.320 superimposing iter= 3 total_weight= 2057.875 rmsd (weighted)= 0.827 (unweighted)= 38.317 superimposing iter= 4 total_weight= 1873.934 rmsd (weighted)= 0.795 (unweighted)= 38.316 superimposing iter= 5 total_weight= 1815.124 rmsd (weighted)= 0.777 (unweighted)= 38.317 superimposing iter= 0 total_weight= 1.209 rmsd (weighted)= 2.223 (unweighted)= 68.422 superimposing iter= 1 total_weight= 6311.709 rmsd (weighted)= 1.050 (unweighted)= 68.484 superimposing iter= 2 total_weight= 2847.619 rmsd (weighted)= 0.792 (unweighted)= 68.508 superimposing iter= 3 total_weight= 2043.261 rmsd (weighted)= 0.715 (unweighted)= 68.522 superimposing iter= 4 total_weight= 1827.700 rmsd (weighted)= 0.685 (unweighted)= 68.531 superimposing iter= 5 total_weight= 1736.532 rmsd (weighted)= 0.676 (unweighted)= 68.536 superimposing iter= 0 total_weight= 1.236 rmsd (weighted)= 2.239 (unweighted)= 65.333 superimposing iter= 1 total_weight= 6592.242 rmsd (weighted)= 1.050 (unweighted)= 65.406 superimposing iter= 2 total_weight= 3008.230 rmsd (weighted)= 0.782 (unweighted)= 65.432 superimposing iter= 3 total_weight= 2082.591 rmsd (weighted)= 0.710 (unweighted)= 65.441 superimposing iter= 4 total_weight= 1855.271 rmsd (weighted)= 0.686 (unweighted)= 65.445 superimposing iter= 5 total_weight= 1788.323 rmsd (weighted)= 0.675 (unweighted)= 65.446 superimposing iter= 0 total_weight= 1.170 rmsd (weighted)= 3.245 (unweighted)= 34.394 superimposing iter= 1 total_weight= 5862.568 rmsd (weighted)= 1.569 (unweighted)= 34.412 superimposing iter= 2 total_weight= 2838.282 rmsd (weighted)= 1.165 (unweighted)= 34.429 superimposing iter= 3 total_weight= 2075.871 rmsd (weighted)= 1.024 (unweighted)= 34.445 superimposing iter= 4 total_weight= 1914.469 rmsd (weighted)= 0.944 (unweighted)= 34.460 superimposing iter= 5 total_weight= 1765.509 rmsd (weighted)= 0.907 (unweighted)= 34.473 superimposing iter= 0 total_weight= 1.228 rmsd (weighted)= 3.455 (unweighted)= 28.450 superimposing iter= 1 total_weight= 6535.650 rmsd (weighted)= 1.638 (unweighted)= 28.246 superimposing iter= 2 total_weight= 2903.169 rmsd (weighted)= 1.227 (unweighted)= 28.174 superimposing iter= 3 total_weight= 2145.175 rmsd (weighted)= 1.078 (unweighted)= 28.141 superimposing iter= 4 total_weight= 1899.795 rmsd (weighted)= 1.009 (unweighted)= 28.126 superimposing iter= 5 total_weight= 1796.697 rmsd (weighted)= 0.974 (unweighted)= 28.119 superimposing iter= 0 total_weight= 1.323 rmsd (weighted)= 3.211 (unweighted)= 28.478 superimposing iter= 1 total_weight= 6640.599 rmsd (weighted)= 1.611 (unweighted)= 28.576 superimposing iter= 2 total_weight= 2973.828 rmsd (weighted)= 1.250 (unweighted)= 28.641 superimposing iter= 3 total_weight= 2393.988 rmsd (weighted)= 1.089 (unweighted)= 28.677 superimposing iter= 4 total_weight= 2146.692 rmsd (weighted)= 1.004 (unweighted)= 28.696 superimposing iter= 5 total_weight= 1976.960 rmsd (weighted)= 0.965 (unweighted)= 28.707 superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 3.251 (unweighted)= 38.981 superimposing iter= 1 total_weight= 5977.138 rmsd (weighted)= 1.684 (unweighted)= 38.995 superimposing iter= 2 total_weight= 2568.510 rmsd (weighted)= 1.367 (unweighted)= 39.000 superimposing iter= 3 total_weight= 2064.333 rmsd (weighted)= 1.245 (unweighted)= 39.000 superimposing iter= 4 total_weight= 1906.310 rmsd (weighted)= 1.182 (unweighted)= 38.998 superimposing iter= 5 total_weight= 1823.506 rmsd (weighted)= 1.148 (unweighted)= 38.997 # command:# Printing sheets for alignments to T0627.undertaker-align.sheets # command: