# command:# Seed set to 1274644602 # 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= 24.242 sec, elapsed time= 29.392 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= 37.365 sec, elapsed time= 46.712 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0545 numbered 1 through 158 Created new target T0545 from T0545.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.366 sec, elapsed time= 46.721 sec. # command:# Prefix for input files set to # command:# reading script from file T0545.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mugA/T0545-1mugA-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 # T0545 read from 1mugA/T0545-1mugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mugA read from 1mugA/T0545-1mugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mugA in training set Warning: unaligning (T0545)G5 because first residue in template chain is (1mugA)M1 T0545 6 :FPAVLDENTEILILGSLPSDESIRKQQYYGNPGNDFWRLVGH 1mugA 2 :VEDILAPGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQ # choosing archetypes in rotamer library T0545 49 :IGENLQDMAYEKK 1mugA 44 :AGFTDRQLKPQEA T0545 63 :KTLKHNRIGLWDVFKAGSR 1mugA 57 :QHLLDYRCGVTKLVDRPTV T0545 82 :EGSQDSKIGDEEINDFSGLKEMVP 1mugA 78 :NEVSKQELHAGGRKLIEKIEDYQP T0545 108 :RLICFNGRKAGEYEPLLRGM 1mugA 102 :QALAILGKQAYEQGFSQRGA T0545 128 :GYETKVLPSSSGANRRFSKNRESEWEAVFR 1mugA 132 :STQIWVLPNPSGLSRVSLEKLVEAYRELDQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_1657318593.pdb -s /var/tmp/to_scwrl_1657318593.seq -o /var/tmp/from_scwrl_1657318593.pdb > /var/tmp/scwrl_1657318593.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1657318593.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c2pA/T0545-2c2pA-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 2c2pA expands to /projects/compbio/data/pdb/2c2p.pdb.gz 2c2pA:# T0545 read from 2c2pA/T0545-2c2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c2pA read from 2c2pA/T0545-2c2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c2pA to template set # found chain 2c2pA in template set Warning: unaligning (T0545)P7 because of BadResidue code BAD_PEPTIDE in next template residue (2c2pA)D20 Warning: unaligning (T0545)A8 because of BadResidue code BAD_PEPTIDE at template residue (2c2pA)D20 T0545 5 :GF 2c2pA 17 :LV T0545 9 :VLDENTEILILGSLPSDESIRKQQYYGNPGNDFWRLVGH 2c2pA 21 :VLQPGLTLVLVGTAPSGISARARAYYANPENKFWRTLHA T0545 49 :IGENLQDMAYEKKLK 2c2pA 60 :VGLTPRQLVPQEYAT T0545 65 :LKHNRIGLWDVFKA 2c2pA 75 :LPQYGLGLTDVAKR T0545 83 :GS 2c2pA 89 :HS T0545 85 :QDSKI 2c2pA 92 :VDAAL T0545 91 :DEEINDFSGLKE 2c2pA 97 :PGEAWRPDELRR T0545 103 :M 2c2pA 113 :Y T0545 106 :KLRLICFNGRKAGEYEPLLRGM 2c2pA 114 :RPRIVAFTSKRGASETLGVPTG T0545 128 :GYETKVLPSSSGANR 2c2pA 151 :ETELWVLPSTSPLGH T0545 143 :RFSKNRESEWEAVFR 2c2pA 171 :EPWQALGDRVRELRG Number of specific fragments extracted= 11 number of extra gaps= 1 total=17 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_1276727089.pdb -s /var/tmp/to_scwrl_1276727089.seq -o /var/tmp/from_scwrl_1276727089.pdb > /var/tmp/scwrl_1276727089.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1276727089.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c2qA/T0545-2c2qA-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 2c2qA expands to /projects/compbio/data/pdb/2c2q.pdb.gz 2c2qA:# T0545 read from 2c2qA/T0545-2c2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c2qA read from 2c2qA/T0545-2c2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c2qA to template set # found chain 2c2qA in template set Warning: unaligning (T0545)P7 because of BadResidue code BAD_PEPTIDE in next template residue (2c2qA)D20 Warning: unaligning (T0545)A8 because of BadResidue code BAD_PEPTIDE at template residue (2c2qA)D20 Warning: unaligning (T0545)P23 because of BadResidue code BAD_PEPTIDE in next template residue (2c2qA)S36 Warning: unaligning (T0545)S24 because of BadResidue code BAD_PEPTIDE at template residue (2c2qA)S36 Warning: unaligning (T0545)R142 because of BadResidue code BAD_PEPTIDE in next template residue (2c2qA)N166 Warning: unaligning (T0545)R143 because of BadResidue code BAD_PEPTIDE at template residue (2c2qA)N166 T0545 5 :GF 2c2qA 17 :LV T0545 9 :VLDENTEILILGSL 2c2qA 21 :VLQPGLTLVLVGTA T0545 25 :DESIRKQQYYGNPGNDFWRLVGH 2c2qA 37 :GISARARAYYANPENKFWRTLHA T0545 49 :IGENLQDMAYEKKLK 2c2qA 60 :VGLTPRQLVPQEYAT T0545 65 :LKHNRIGLWDVFKA 2c2qA 75 :LPQYGLGLTDVAKR T0545 83 :GSQDSKIGDEEINDFSGLKE 2c2qA 89 :HSGVAAALPGEAWRPDELRR T0545 104 :V 2c2qA 113 :Y T0545 106 :KLRLICFNGRKAGEYEPLLRGM 2c2qA 114 :RPRIVAFTSKRGASETLGVPTG T0545 128 :GYETKVLPSSSGAN 2c2qA 151 :ETELWVLPSTSPLG T0545 144 :F 2c2qA 167 :H T0545 145 :SKNRESEWEAVFR 2c2qA 173 :WQALGDRVRELRG Number of specific fragments extracted= 11 number of extra gaps= 3 total=28 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_891219792.pdb -s /var/tmp/to_scwrl_891219792.seq -o /var/tmp/from_scwrl_891219792.pdb > /var/tmp/scwrl_891219792.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_891219792.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rbaA/T0545-2rbaA-t2k-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2rbaA expands to /projects/compbio/data/pdb/2rba.pdb.gz 2rbaA:# T0545 read from 2rbaA/T0545-2rbaA-t2k-global-adpstyle1.a2m # 2rbaA read from 2rbaA/T0545-2rbaA-t2k-global-adpstyle1.a2m # adding 2rbaA to template set # found chain 2rbaA in template set Warning: unaligning (T0545)G5 because first residue in template chain is (2rbaA)T123 Warning: unaligning (T0545)E15 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)I134 Warning: unaligning (T0545)I16 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)I134 Warning: unaligning (T0545)N36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)P155 Warning: unaligning (T0545)P37 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)P155 Warning: unaligning (T0545)G38 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)G156 Warning: unaligning (T0545)N39 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)N157 Warning: unaligning (T0545)T64 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)P182 Warning: unaligning (T0545)L65 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)P182 Warning: unaligning (T0545)S80 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)P198 Warning: unaligning (T0545)R81 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)P198 Warning: unaligning (T0545)E82 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)G199 Warning: unaligning (T0545)G83 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)S200 Warning: unaligning (T0545)R115 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)C233 Warning: unaligning (T0545)K116 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)C233 Warning: unaligning (T0545)R148 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)S272 Warning: unaligning (T0545)E149 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)S272 Warning: unaligning (T0545)W152 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rbaA)C276 Warning: unaligning (T0545)E153 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rbaA)C276 T0545 6 :FPAVLDENT 2rbaA 124 :LPDILTFNL T0545 17 :LILGSLPSDESIRKQQYYG 2rbaA 135 :VIIGINPGLMAAYKGHHYP T0545 40 :DFWRLVGHAIGENLQD 2rbaA 158 :HFWKCLFMSGLSEVQL T0545 57 :AYEKKLK 2rbaA 174 :NHMDDHT T0545 66 :KHNRIGLWDVFKAG 2rbaA 183 :GKYGIGFTNMVERT T0545 84 :SQDSKIGDEEINDFSGLKEMVPKLRLICFNG 2rbaA 201 :KDLSSKEFREGGRILVQKLQKYQPRIAVFNG T0545 117 :AGEYEPLLR 2rbaA 234 :IYEIFSKEV T0545 126 :GMGYETKVLPSSSGANRRFSKN 2rbaA 249 :NLEFGLQPHKIPDTETLCYVMP T0545 150 :SE 2rbaA 273 :SA T0545 154 :AVFRH 2rbaA 277 :AQFPR Number of specific fragments extracted= 10 number of extra gaps= 7 total=38 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_632639758.pdb -s /var/tmp/to_scwrl_632639758.seq -o /var/tmp/from_scwrl_632639758.pdb > /var/tmp/scwrl_632639758.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_632639758.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ikbA/T0545-3ikbA-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 3ikbA expands to /projects/compbio/data/pdb/3ikb.pdb.gz 3ikbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 170, because occupancy 0.5 <= existing 0.500 in 3ikbA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 3ikbA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 860, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1393, because occupancy 0.500 <= existing 0.500 in 3ikbA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1426, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1441, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1443, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1445, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1447, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1449, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1451, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1510, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1520, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1522, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1546, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1550, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1552, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1554, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1556, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1652, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1656, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1658, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1660, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1662, because occupancy 0.500 <= existing 0.500 in 3ikbA Skipped atom 1664, because occupancy 0.500 <= existing 0.500 in 3ikbA # T0545 read from 3ikbA/T0545-3ikbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ikbA read from 3ikbA/T0545-3ikbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ikbA to template set # found chain 3ikbA in template set Warning: unaligning (T0545)N95 because of BadResidue code BAD_PEPTIDE in next template residue (3ikbA)W108 Warning: unaligning (T0545)D96 because of BadResidue code BAD_PEPTIDE at template residue (3ikbA)W108 T0545 5 :GFPAVL 3ikbA 24 :NIEPLF T0545 11 :DENTEILILGSLPSDESIRKQQYYGNPGND 3ikbA 32 :PKTARINIVGQAPGIKAQESRLYWNDKSGD T0545 44 :LVGHAIGENLQDMAY 3ikbA 62 :RLREWMGVDYDTFYH T0545 69 :RIGLWDV 3ikbA 79 :YFAVIPM T0545 76 :FKAGSREGSQDSKIGDE 3ikbA 87 :FYYPGKGKSGDLPPRKG T0545 93 :EI 3ikbA 105 :AQ T0545 97 :FSGLKEMVPKLRLICFNGRKAGEYEPLLRGM 3ikbA 109 :HQPILDLLPDIQLTILIGNYAQKYYLHQKSS T0545 128 :G 3ikbA 155 :D T0545 131 :TKVLPSSSGANRRFSKN 3ikbA 156 :YFPLVHPSPRNQIWMSR T0545 148 :RESEWEAVFRH 3ikbA 184 :LKKIIQQIIQS Number of specific fragments extracted= 10 number of extra gaps= 1 total=48 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_1650637774.pdb -s /var/tmp/to_scwrl_1650637774.seq -o /var/tmp/from_scwrl_1650637774.pdb > /var/tmp/scwrl_1650637774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1650637774.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d3yA/T0545-2d3yA-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 2d3yA expands to /projects/compbio/data/pdb/2d3y.pdb.gz 2d3yA:# T0545 read from 2d3yA/T0545-2d3yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d3yA read from 2d3yA/T0545-2d3yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d3yA to template set # found chain 2d3yA in template set T0545 2 :IKRGFPAVLDENTEILILGSLPSDE 2d3yA 39 :WARPVPGFGDPEARILLFGLAPGAH T0545 27 :SIRKQQYY 2d3yA 65 :SNRTGRPF T0545 35 :GNPGNDF 2d3yA 74 :GDASGAF T0545 42 :WRLVGH 2d3yA 82 :YPLLHE T0545 49 :IGENLQD 2d3yA 98 :PGDDLRL T0545 68 :NRIGLWDVFKAGSREGSQDSKIGDEEINDFSGLKEMVPKLRLICFNGRKAGEYEPLLRGM 2d3yA 105 :YGVYLTAAVRCAPPKNKPTPEELRACARWTEVELGLLPEVRVYVALGRIALEALLAHFGL T0545 128 :GYETKVLPSSSGANR 2d3yA 182 :GRHLLASYHVSRQNT T0545 147 :NRESEWEAVF 2d3yA 201 :LTREMFLEVL Number of specific fragments extracted= 8 number of extra gaps= 0 total=56 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_1761457317.pdb -s /var/tmp/to_scwrl_1761457317.seq -o /var/tmp/from_scwrl_1761457317.pdb > /var/tmp/scwrl_1761457317.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1761457317.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oe4A/T0545-1oe4A-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 1oe4A expands to /projects/compbio/data/pdb/1oe4.pdb.gz 1oe4A:Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1oe4A # T0545 read from 1oe4A/T0545-1oe4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oe4A read from 1oe4A/T0545-1oe4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oe4A to template set # found chain 1oe4A in template set T0545 13 :NTEILILGSLPSDES 1oe4A 87 :KKEVLFLGMNPGPFG T0545 28 :IRKQQYYGNP 1oe4A 103 :AQTGVPFGEV T0545 40 :DFWRLVGHAIG 1oe4A 151 :RFWSLFKSLCG T0545 57 :AYEKK 1oe4A 162 :QPETF T0545 66 :KH 1oe4A 167 :FK T0545 69 :RIGLWDV 1oe4A 169 :HCFVHNH T0545 78 :AGS 1oe4A 176 :CPL T0545 81 :REGSQDSKIGDEEINDFSGLKEMV 1oe4A 182 :NHSGKNLTPTDLPKAQRDTLLEIC T0545 106 :KLRLICFNGRKAGEYEPLL 1oe4A 217 :GVKLVIGVGRFSEQRARKA T0545 125 :RGMGYETKVLPSSSGANRRFSKNRESEWEA 1oe4A 239 :EGIDVTVKGIMHPSPRNPQANKGWEGIVRG T0545 155 :VF 1oe4A 270 :LL Number of specific fragments extracted= 11 number of extra gaps= 0 total=67 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_1000717981.pdb -s /var/tmp/to_scwrl_1000717981.seq -o /var/tmp/from_scwrl_1000717981.pdb > /var/tmp/scwrl_1000717981.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1000717981.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4eugA/T0545-4eugA-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 # T0545 read from 4eugA/T0545-4eugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 4eugA read from 4eugA/T0545-4eugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 4eugA in training set Warning: unaligning (T0545)E153 because of BadResidue code BAD_PEPTIDE in next template residue (4eugA)Q212 Warning: unaligning (T0545)A154 because of BadResidue code BAD_PEPTIDE at template residue (4eugA)Q212 T0545 13 :NTEILILGSLPS 4eugA 55 :DVKVVILGQDPY T0545 28 :IRKQQYYG 4eugA 71 :QAHGLAFS T0545 36 :NPGN 4eugA 80 :RPGI T0545 40 :DFWRLVGHAIGE 4eugA 91 :NMYKELENTIPG T0545 52 :NLQDMAYEKK 4eugA 105 :RPNHGYLESW T0545 66 :KHNRIGLWDVFKAGSREGS 4eugA 115 :ARQGVLLLNTVLTVRAGQA T0545 85 :QDSKIG 4eugA 135 :SHASLG T0545 91 :DEEINDFSGLKEMVPKL 4eugA 143 :TFTDKVISLINQHREGV T0545 109 :LICFNGRKAGEYEPLLRGMGYETKVLPSSSGANRRF 4eugA 160 :VFLLWGSHAQKKGAIIDKQRHHVLKAPQPSPLSAHR T0545 145 :SKNRESEW 4eugA 203 :FVLANQWL Number of specific fragments extracted= 10 number of extra gaps= 1 total=77 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_549570986.pdb -s /var/tmp/to_scwrl_549570986.seq -o /var/tmp/from_scwrl_549570986.pdb > /var/tmp/scwrl_549570986.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_549570986.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h4tA/T0545-3h4tA-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 3h4tA expands to /projects/compbio/data/pdb/3h4t.pdb.gz 3h4tA:Skipped atom 26, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 29, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 900, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 902, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1049, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1051, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1053, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1055, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1140, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1142, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1174, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1176, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1391, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1393, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1908, because occupancy 0.300 <= existing 0.400 in 3h4tA Skipped atom 1911, because occupancy 0.300 <= existing 0.400 in 3h4tA Skipped atom 1958, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1960, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1962, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1964, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 1966, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 2017, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 2019, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 2538, because occupancy 0.350 <= existing 0.650 in 3h4tA Skipped atom 2540, because occupancy 0.350 <= existing 0.650 in 3h4tA # T0545 read from 3h4tA/T0545-3h4tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h4tA read from 3h4tA/T0545-3h4tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h4tA to template set # found chain 3h4tA in template set Warning: unaligning (T0545)E15 because first residue in template chain is (3h4tA)G2 T0545 16 :ILILGSLPSDESI 3h4tA 3 :VLITGCGSRGDTE T0545 40 :DFWRLVGH 3h4tA 19 :ALAARLRE T0545 49 :IGEN 3h4tA 27 :LGAD T0545 53 :LQDM 3h4tA 36 :PPDY T0545 62 :LKTLKHNRIGLWDVFKAGSR 3h4tA 40 :VERCAEVGVPMVPVGRAVRA T0545 82 :EGSQDSKIGDEEIN 3h4tA 64 :PGELPPGAAEVVTE T0545 96 :DFSGLKEMVPKLRLICFNGRKAGEYEPLLRGM 3h4tA 82 :WFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAE T0545 128 :GYETKVLPSSSGANR 3h4tA 116 :GIPYRYTVLSPDHLP T0545 143 :RFSKNRESEWEA 3h4tA 132 :EQSQAERDMYNQ T0545 155 :V 3h4tA 145 :A Number of specific fragments extracted= 10 number of extra gaps= 0 total=87 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_1180816833.pdb -s /var/tmp/to_scwrl_1180816833.seq -o /var/tmp/from_scwrl_1180816833.pdb > /var/tmp/scwrl_1180816833.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1180816833.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2owrA/T0545-2owrA-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 2owrA expands to /projects/compbio/data/pdb/2owr.pdb.gz 2owrA:# T0545 read from 2owrA/T0545-2owrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2owrA read from 2owrA/T0545-2owrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2owrA to template set # found chain 2owrA in template set Warning: unaligning (T0545)L123 because of BadResidue code BAD_PEPTIDE in next template residue (2owrA)K169 Warning: unaligning (T0545)L124 because of BadResidue code BAD_PEPTIDE at template residue (2owrA)K169 Warning: unaligning (T0545)R125 because of BadResidue code BAD_PEPTIDE at template residue (2owrA)L170 Warning: unaligning (T0545)G139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2owrA)F189 T0545 12 :ENTEILILGSLPSDE 2owrA 58 :RNKRVCVCGIDPYPK T0545 30 :KQQYYGNPGN 2owrA 75 :TGVPFESPNF T0545 52 :NLQD 2owrA 85 :TKKS T0545 58 :YEKKLKTLKHN 2owrA 89 :IKEIASSISRL T0545 69 :RIGLWDVFKAGSREGSQD 2owrA 115 :GVIPWNYYLSCKLGETKS T0545 89 :I 2owrA 133 :H T0545 94 :INDFSGLKEMV 2owrA 134 :AIYWDKISKLL T0545 105 :PKLRLICFNGRKAGEYEP 2owrA 150 :KHVSVLYCLGKTDFSNIR T0545 126 :GMGYETKVLPSSS 2owrA 171 :ESPVTTIVGYHPA Number of specific fragments extracted= 9 number of extra gaps= 1 total=96 # request to SCWRL produces command: ulimit -t 143 ; scwrl4 -t -i /var/tmp/to_scwrl_919019573.pdb -s /var/tmp/to_scwrl_919019573.seq -o /var/tmp/from_scwrl_919019573.pdb > /var/tmp/scwrl_919019573.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_919019573.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.403 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 11910.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 11910.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 11910.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 11910.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 11910.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.319 rmsd (weighted)= 4.758 (unweighted)= 28.622 superimposing iter= 1 total_weight= 4063.344 rmsd (weighted)= 2.045 (unweighted)= 28.604 superimposing iter= 2 total_weight= 3360.949 rmsd (weighted)= 1.071 (unweighted)= 28.566 superimposing iter= 3 total_weight= 1954.593 rmsd (weighted)= 0.793 (unweighted)= 28.549 superimposing iter= 4 total_weight= 1380.081 rmsd (weighted)= 0.708 (unweighted)= 28.543 superimposing iter= 5 total_weight= 1224.556 rmsd (weighted)= 0.673 (unweighted)= 28.540 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.284 rmsd (weighted)= 4.855 (unweighted)= 31.343 superimposing iter= 1 total_weight= 4270.710 rmsd (weighted)= 2.019 (unweighted)= 31.239 superimposing iter= 2 total_weight= 3183.616 rmsd (weighted)= 1.077 (unweighted)= 31.175 superimposing iter= 3 total_weight= 1886.514 rmsd (weighted)= 0.799 (unweighted)= 31.143 superimposing iter= 4 total_weight= 1362.887 rmsd (weighted)= 0.706 (unweighted)= 31.127 superimposing iter= 5 total_weight= 1232.748 rmsd (weighted)= 0.659 (unweighted)= 31.118 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.217 rmsd (weighted)= 9.633 (unweighted)= 38.434 superimposing iter= 1 total_weight= 6114.254 rmsd (weighted)= 2.935 (unweighted)= 38.379 superimposing iter= 2 total_weight= 4020.893 rmsd (weighted)= 1.329 (unweighted)= 38.387 superimposing iter= 3 total_weight= 2301.317 rmsd (weighted)= 0.863 (unweighted)= 38.386 superimposing iter= 4 total_weight= 1427.001 rmsd (weighted)= 0.725 (unweighted)= 38.387 superimposing iter= 5 total_weight= 1149.972 rmsd (weighted)= 0.681 (unweighted)= 38.388 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.234 rmsd (weighted)= 5.764 (unweighted)= 31.908 superimposing iter= 1 total_weight= 3723.934 rmsd (weighted)= 2.865 (unweighted)= 31.929 superimposing iter= 2 total_weight= 1749.540 rmsd (weighted)= 2.161 (unweighted)= 31.920 superimposing iter= 3 total_weight= 1298.344 rmsd (weighted)= 1.908 (unweighted)= 31.904 superimposing iter= 4 total_weight= 1166.826 rmsd (weighted)= 1.784 (unweighted)= 31.889 superimposing iter= 5 total_weight= 1116.348 rmsd (weighted)= 1.709 (unweighted)= 31.875 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 5.582 (unweighted)= 32.202 superimposing iter= 1 total_weight= 3988.070 rmsd (weighted)= 2.598 (unweighted)= 32.380 superimposing iter= 2 total_weight= 1931.830 rmsd (weighted)= 1.830 (unweighted)= 32.472 superimposing iter= 3 total_weight= 1619.881 rmsd (weighted)= 1.426 (unweighted)= 32.528 superimposing iter= 4 total_weight= 1453.770 rmsd (weighted)= 1.185 (unweighted)= 32.557 superimposing iter= 5 total_weight= 1293.254 rmsd (weighted)= 1.052 (unweighted)= 32.572 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.183 rmsd (weighted)= 7.940 (unweighted)= 35.962 superimposing iter= 1 total_weight= 4378.618 rmsd (weighted)= 3.308 (unweighted)= 35.958 superimposing iter= 2 total_weight= 2419.357 rmsd (weighted)= 2.028 (unweighted)= 35.940 superimposing iter= 3 total_weight= 1575.443 rmsd (weighted)= 1.590 (unweighted)= 35.946 superimposing iter= 4 total_weight= 1210.230 rmsd (weighted)= 1.433 (unweighted)= 35.952 superimposing iter= 5 total_weight= 1070.569 rmsd (weighted)= 1.376 (unweighted)= 35.954 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.220 rmsd (weighted)= 7.112 (unweighted)= 35.528 superimposing iter= 1 total_weight= 3409.580 rmsd (weighted)= 3.650 (unweighted)= 35.642 superimposing iter= 2 total_weight= 1639.196 rmsd (weighted)= 2.853 (unweighted)= 35.695 superimposing iter= 3 total_weight= 1217.521 rmsd (weighted)= 2.611 (unweighted)= 35.722 superimposing iter= 4 total_weight= 1113.057 rmsd (weighted)= 2.505 (unweighted)= 35.732 superimposing iter= 5 total_weight= 1061.889 rmsd (weighted)= 2.462 (unweighted)= 35.734 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.127 rmsd (weighted)= 10.870 (unweighted)= 32.733 superimposing iter= 1 total_weight= 2777.972 rmsd (weighted)= 5.911 (unweighted)= 32.357 superimposing iter= 2 total_weight= 1564.320 rmsd (weighted)= 4.515 (unweighted)= 32.247 superimposing iter= 3 total_weight= 1165.731 rmsd (weighted)= 4.046 (unweighted)= 32.204 superimposing iter= 4 total_weight= 1066.877 rmsd (weighted)= 3.808 (unweighted)= 32.182 superimposing iter= 5 total_weight= 1014.243 rmsd (weighted)= 3.680 (unweighted)= 32.170 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.919 rmsd (weighted)= 8.459 (unweighted)= 50.920 superimposing iter= 1 total_weight= 2887.757 rmsd (weighted)= 3.706 (unweighted)= 51.868 superimposing iter= 2 total_weight= 2212.766 rmsd (weighted)= 2.048 (unweighted)= 52.106 superimposing iter= 3 total_weight= 1330.218 rmsd (weighted)= 1.531 (unweighted)= 52.196 superimposing iter= 4 total_weight= 985.204 rmsd (weighted)= 1.338 (unweighted)= 52.277 superimposing iter= 5 total_weight= 909.373 rmsd (weighted)= 1.218 (unweighted)= 52.348 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.403 rmsd (weighted)= 3.838 (unweighted)= 24.717 superimposing iter= 1 total_weight= 4040.367 rmsd (weighted)= 1.944 (unweighted)= 24.710 superimposing iter= 2 total_weight= 2015.829 rmsd (weighted)= 1.458 (unweighted)= 24.712 superimposing iter= 3 total_weight= 1476.116 rmsd (weighted)= 1.292 (unweighted)= 24.716 superimposing iter= 4 total_weight= 1298.467 rmsd (weighted)= 1.224 (unweighted)= 24.719 superimposing iter= 5 total_weight= 1242.560 rmsd (weighted)= 1.187 (unweighted)= 24.723 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.354 rmsd (weighted)= 4.131 (unweighted)= 17.775 superimposing iter= 1 total_weight= 4333.681 rmsd (weighted)= 1.963 (unweighted)= 17.802 superimposing iter= 2 total_weight= 2040.442 rmsd (weighted)= 1.439 (unweighted)= 17.825 superimposing iter= 3 total_weight= 1406.377 rmsd (weighted)= 1.288 (unweighted)= 17.838 superimposing iter= 4 total_weight= 1232.855 rmsd (weighted)= 1.234 (unweighted)= 17.847 superimposing iter= 5 total_weight= 1185.539 rmsd (weighted)= 1.206 (unweighted)= 17.854 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.319 rmsd (weighted)= 4.057 (unweighted)= 21.814 superimposing iter= 1 total_weight= 4222.045 rmsd (weighted)= 1.925 (unweighted)= 21.785 superimposing iter= 2 total_weight= 1953.173 rmsd (weighted)= 1.425 (unweighted)= 21.780 superimposing iter= 3 total_weight= 1355.107 rmsd (weighted)= 1.282 (unweighted)= 21.777 superimposing iter= 4 total_weight= 1188.314 rmsd (weighted)= 1.235 (unweighted)= 21.775 superimposing iter= 5 total_weight= 1143.971 rmsd (weighted)= 1.214 (unweighted)= 21.773 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.264 rmsd (weighted)= 8.398 (unweighted)= 33.856 superimposing iter= 1 total_weight= 6304.382 rmsd (weighted)= 2.805 (unweighted)= 33.746 superimposing iter= 2 total_weight= 2948.593 rmsd (weighted)= 1.628 (unweighted)= 33.730 superimposing iter= 3 total_weight= 1518.967 rmsd (weighted)= 1.351 (unweighted)= 33.729 superimposing iter= 4 total_weight= 1188.556 rmsd (weighted)= 1.272 (unweighted)= 33.730 superimposing iter= 5 total_weight= 1111.279 rmsd (weighted)= 1.239 (unweighted)= 33.731 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 5.145 (unweighted)= 19.099 superimposing iter= 1 total_weight= 4192.017 rmsd (weighted)= 2.418 (unweighted)= 19.168 superimposing iter= 2 total_weight= 1933.692 rmsd (weighted)= 1.765 (unweighted)= 19.200 superimposing iter= 3 total_weight= 1315.378 rmsd (weighted)= 1.578 (unweighted)= 19.213 superimposing iter= 4 total_weight= 1135.104 rmsd (weighted)= 1.523 (unweighted)= 19.217 superimposing iter= 5 total_weight= 1081.921 rmsd (weighted)= 1.506 (unweighted)= 19.218 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.297 rmsd (weighted)= 4.483 (unweighted)= 19.907 superimposing iter= 1 total_weight= 4265.818 rmsd (weighted)= 2.077 (unweighted)= 19.854 superimposing iter= 2 total_weight= 2054.570 rmsd (weighted)= 1.473 (unweighted)= 19.827 superimposing iter= 3 total_weight= 1525.446 rmsd (weighted)= 1.227 (unweighted)= 19.814 superimposing iter= 4 total_weight= 1352.541 rmsd (weighted)= 1.091 (unweighted)= 19.807 superimposing iter= 5 total_weight= 1299.683 rmsd (weighted)= 0.989 (unweighted)= 19.804 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.210 rmsd (weighted)= 5.757 (unweighted)= 26.644 superimposing iter= 1 total_weight= 4111.305 rmsd (weighted)= 2.631 (unweighted)= 26.681 superimposing iter= 2 total_weight= 1982.943 rmsd (weighted)= 1.834 (unweighted)= 26.712 superimposing iter= 3 total_weight= 1420.775 rmsd (weighted)= 1.534 (unweighted)= 26.736 superimposing iter= 4 total_weight= 1244.115 rmsd (weighted)= 1.378 (unweighted)= 26.753 superimposing iter= 5 total_weight= 1147.400 rmsd (weighted)= 1.291 (unweighted)= 26.766 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.247 rmsd (weighted)= 5.499 (unweighted)= 24.594 superimposing iter= 1 total_weight= 2948.932 rmsd (weighted)= 3.111 (unweighted)= 24.477 superimposing iter= 2 total_weight= 1547.782 rmsd (weighted)= 2.529 (unweighted)= 24.460 superimposing iter= 3 total_weight= 1211.585 rmsd (weighted)= 2.342 (unweighted)= 24.459 superimposing iter= 4 total_weight= 1109.955 rmsd (weighted)= 2.271 (unweighted)= 24.462 superimposing iter= 5 total_weight= 1076.526 rmsd (weighted)= 2.238 (unweighted)= 24.466 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.157 rmsd (weighted)= 9.359 (unweighted)= 25.833 superimposing iter= 1 total_weight= 3298.388 rmsd (weighted)= 4.602 (unweighted)= 25.641 superimposing iter= 2 total_weight= 1851.946 rmsd (weighted)= 3.245 (unweighted)= 25.581 superimposing iter= 3 total_weight= 1368.216 rmsd (weighted)= 2.704 (unweighted)= 25.549 superimposing iter= 4 total_weight= 1193.841 rmsd (weighted)= 2.419 (unweighted)= 25.534 superimposing iter= 5 total_weight= 1101.764 rmsd (weighted)= 2.252 (unweighted)= 25.530 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.948 rmsd (weighted)= 6.004 (unweighted)= 45.816 superimposing iter= 1 total_weight= 2876.373 rmsd (weighted)= 2.721 (unweighted)= 46.774 superimposing iter= 2 total_weight= 1920.457 rmsd (weighted)= 1.638 (unweighted)= 47.192 superimposing iter= 3 total_weight= 1319.036 rmsd (weighted)= 1.240 (unweighted)= 47.327 superimposing iter= 4 total_weight= 1006.500 rmsd (weighted)= 1.087 (unweighted)= 47.380 superimposing iter= 5 total_weight= 881.352 rmsd (weighted)= 1.021 (unweighted)= 47.403 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.403 rmsd (weighted)= 3.876 (unweighted)= 24.746 superimposing iter= 1 total_weight= 4010.829 rmsd (weighted)= 1.964 (unweighted)= 24.736 superimposing iter= 2 total_weight= 2047.199 rmsd (weighted)= 1.461 (unweighted)= 24.740 superimposing iter= 3 total_weight= 1484.988 rmsd (weighted)= 1.290 (unweighted)= 24.745 superimposing iter= 4 total_weight= 1300.868 rmsd (weighted)= 1.222 (unweighted)= 24.749 superimposing iter= 5 total_weight= 1236.320 rmsd (weighted)= 1.189 (unweighted)= 24.752 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.354 rmsd (weighted)= 4.128 (unweighted)= 17.782 superimposing iter= 1 total_weight= 4306.292 rmsd (weighted)= 1.972 (unweighted)= 17.808 superimposing iter= 2 total_weight= 2015.411 rmsd (weighted)= 1.456 (unweighted)= 17.832 superimposing iter= 3 total_weight= 1397.187 rmsd (weighted)= 1.307 (unweighted)= 17.846 superimposing iter= 4 total_weight= 1232.806 rmsd (weighted)= 1.253 (unweighted)= 17.856 superimposing iter= 5 total_weight= 1185.904 rmsd (weighted)= 1.226 (unweighted)= 17.863 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.319 rmsd (weighted)= 4.056 (unweighted)= 21.821 superimposing iter= 1 total_weight= 4203.922 rmsd (weighted)= 1.934 (unweighted)= 21.791 superimposing iter= 2 total_weight= 1930.486 rmsd (weighted)= 1.441 (unweighted)= 21.787 superimposing iter= 3 total_weight= 1345.955 rmsd (weighted)= 1.301 (unweighted)= 21.784 superimposing iter= 4 total_weight= 1190.935 rmsd (weighted)= 1.252 (unweighted)= 21.782 superimposing iter= 5 total_weight= 1147.793 rmsd (weighted)= 1.229 (unweighted)= 21.780 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.264 rmsd (weighted)= 8.397 (unweighted)= 33.824 superimposing iter= 1 total_weight= 6277.201 rmsd (weighted)= 2.816 (unweighted)= 33.713 superimposing iter= 2 total_weight= 2947.874 rmsd (weighted)= 1.633 (unweighted)= 33.700 superimposing iter= 3 total_weight= 1526.163 rmsd (weighted)= 1.351 (unweighted)= 33.700 superimposing iter= 4 total_weight= 1197.474 rmsd (weighted)= 1.267 (unweighted)= 33.702 superimposing iter= 5 total_weight= 1114.627 rmsd (weighted)= 1.233 (unweighted)= 33.703 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 5.151 (unweighted)= 19.116 superimposing iter= 1 total_weight= 4165.141 rmsd (weighted)= 2.431 (unweighted)= 19.187 superimposing iter= 2 total_weight= 1918.121 rmsd (weighted)= 1.783 (unweighted)= 19.224 superimposing iter= 3 total_weight= 1305.899 rmsd (weighted)= 1.600 (unweighted)= 19.237 superimposing iter= 4 total_weight= 1132.688 rmsd (weighted)= 1.545 (unweighted)= 19.242 superimposing iter= 5 total_weight= 1081.529 rmsd (weighted)= 1.527 (unweighted)= 19.244 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.297 rmsd (weighted)= 4.489 (unweighted)= 19.911 superimposing iter= 1 total_weight= 4249.744 rmsd (weighted)= 2.088 (unweighted)= 19.858 superimposing iter= 2 total_weight= 2057.426 rmsd (weighted)= 1.479 (unweighted)= 19.830 superimposing iter= 3 total_weight= 1555.792 rmsd (weighted)= 1.218 (unweighted)= 19.816 superimposing iter= 4 total_weight= 1360.263 rmsd (weighted)= 1.076 (unweighted)= 19.808 superimposing iter= 5 total_weight= 1280.211 rmsd (weighted)= 0.979 (unweighted)= 19.803 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.210 rmsd (weighted)= 5.755 (unweighted)= 26.623 superimposing iter= 1 total_weight= 4126.473 rmsd (weighted)= 2.629 (unweighted)= 26.663 superimposing iter= 2 total_weight= 1962.279 rmsd (weighted)= 1.844 (unweighted)= 26.694 superimposing iter= 3 total_weight= 1410.636 rmsd (weighted)= 1.549 (unweighted)= 26.718 superimposing iter= 4 total_weight= 1249.423 rmsd (weighted)= 1.389 (unweighted)= 26.737 superimposing iter= 5 total_weight= 1150.219 rmsd (weighted)= 1.301 (unweighted)= 26.750 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.247 rmsd (weighted)= 5.502 (unweighted)= 24.564 superimposing iter= 1 total_weight= 2947.516 rmsd (weighted)= 3.110 (unweighted)= 24.444 superimposing iter= 2 total_weight= 1557.177 rmsd (weighted)= 2.520 (unweighted)= 24.426 superimposing iter= 3 total_weight= 1209.336 rmsd (weighted)= 2.336 (unweighted)= 24.424 superimposing iter= 4 total_weight= 1106.048 rmsd (weighted)= 2.270 (unweighted)= 24.427 superimposing iter= 5 total_weight= 1074.188 rmsd (weighted)= 2.239 (unweighted)= 24.430 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.157 rmsd (weighted)= 9.352 (unweighted)= 25.817 superimposing iter= 1 total_weight= 3315.740 rmsd (weighted)= 4.577 (unweighted)= 25.630 superimposing iter= 2 total_weight= 1880.142 rmsd (weighted)= 3.202 (unweighted)= 25.572 superimposing iter= 3 total_weight= 1373.038 rmsd (weighted)= 2.665 (unweighted)= 25.541 superimposing iter= 4 total_weight= 1184.414 rmsd (weighted)= 2.393 (unweighted)= 25.527 superimposing iter= 5 total_weight= 1098.201 rmsd (weighted)= 2.231 (unweighted)= 25.522 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.948 rmsd (weighted)= 5.942 (unweighted)= 45.838 superimposing iter= 1 total_weight= 2865.688 rmsd (weighted)= 2.703 (unweighted)= 46.788 superimposing iter= 2 total_weight= 1896.439 rmsd (weighted)= 1.637 (unweighted)= 47.209 superimposing iter= 3 total_weight= 1305.395 rmsd (weighted)= 1.247 (unweighted)= 47.347 superimposing iter= 4 total_weight= 996.860 rmsd (weighted)= 1.098 (unweighted)= 47.403 superimposing iter= 5 total_weight= 872.321 rmsd (weighted)= 1.038 (unweighted)= 47.428 superimposing iter= 0 total_weight= 1.403 rmsd (weighted)= 3.880 (unweighted)= 24.760 superimposing iter= 1 total_weight= 4005.505 rmsd (weighted)= 1.967 (unweighted)= 24.749 superimposing iter= 2 total_weight= 2048.740 rmsd (weighted)= 1.462 (unweighted)= 24.754 superimposing iter= 3 total_weight= 1485.658 rmsd (weighted)= 1.291 (unweighted)= 24.759 superimposing iter= 4 total_weight= 1301.432 rmsd (weighted)= 1.223 (unweighted)= 24.763 superimposing iter= 5 total_weight= 1236.352 rmsd (weighted)= 1.190 (unweighted)= 24.766 superimposing iter= 0 total_weight= 1.354 rmsd (weighted)= 4.128 (unweighted)= 17.782 superimposing iter= 1 total_weight= 4306.693 rmsd (weighted)= 1.973 (unweighted)= 17.808 superimposing iter= 2 total_weight= 2013.105 rmsd (weighted)= 1.458 (unweighted)= 17.831 superimposing iter= 3 total_weight= 1396.119 rmsd (weighted)= 1.309 (unweighted)= 17.846 superimposing iter= 4 total_weight= 1231.583 rmsd (weighted)= 1.256 (unweighted)= 17.856 superimposing iter= 5 total_weight= 1185.732 rmsd (weighted)= 1.228 (unweighted)= 17.863 superimposing iter= 0 total_weight= 1.319 rmsd (weighted)= 4.057 (unweighted)= 21.821 superimposing iter= 1 total_weight= 4203.812 rmsd (weighted)= 1.935 (unweighted)= 21.791 superimposing iter= 2 total_weight= 1927.913 rmsd (weighted)= 1.442 (unweighted)= 21.787 superimposing iter= 3 total_weight= 1345.089 rmsd (weighted)= 1.303 (unweighted)= 21.784 superimposing iter= 4 total_weight= 1190.824 rmsd (weighted)= 1.254 (unweighted)= 21.782 superimposing iter= 5 total_weight= 1147.478 rmsd (weighted)= 1.231 (unweighted)= 21.780 superimposing iter= 0 total_weight= 1.264 rmsd (weighted)= 8.395 (unweighted)= 33.829 superimposing iter= 1 total_weight= 6274.024 rmsd (weighted)= 2.816 (unweighted)= 33.717 superimposing iter= 2 total_weight= 2947.004 rmsd (weighted)= 1.634 (unweighted)= 33.704 superimposing iter= 3 total_weight= 1525.288 rmsd (weighted)= 1.352 (unweighted)= 33.705 superimposing iter= 4 total_weight= 1197.765 rmsd (weighted)= 1.268 (unweighted)= 33.707 superimposing iter= 5 total_weight= 1114.222 rmsd (weighted)= 1.234 (unweighted)= 33.708 superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 5.153 (unweighted)= 19.114 superimposing iter= 1 total_weight= 4165.429 rmsd (weighted)= 2.431 (unweighted)= 19.185 superimposing iter= 2 total_weight= 1917.814 rmsd (weighted)= 1.784 (unweighted)= 19.222 superimposing iter= 3 total_weight= 1304.724 rmsd (weighted)= 1.601 (unweighted)= 19.235 superimposing iter= 4 total_weight= 1132.560 rmsd (weighted)= 1.546 (unweighted)= 19.240 superimposing iter= 5 total_weight= 1081.384 rmsd (weighted)= 1.529 (unweighted)= 19.241 superimposing iter= 0 total_weight= 1.297 rmsd (weighted)= 4.492 (unweighted)= 19.913 superimposing iter= 1 total_weight= 4228.807 rmsd (weighted)= 2.098 (unweighted)= 19.861 superimposing iter= 2 total_weight= 2004.671 rmsd (weighted)= 1.507 (unweighted)= 19.833 superimposing iter= 3 total_weight= 1547.202 rmsd (weighted)= 1.246 (unweighted)= 19.819 superimposing iter= 4 total_weight= 1405.934 rmsd (weighted)= 1.084 (unweighted)= 19.812 superimposing iter= 5 total_weight= 1290.553 rmsd (weighted)= 0.983 (unweighted)= 19.808 superimposing iter= 0 total_weight= 1.210 rmsd (weighted)= 5.757 (unweighted)= 26.617 superimposing iter= 1 total_weight= 4128.514 rmsd (weighted)= 2.630 (unweighted)= 26.657 superimposing iter= 2 total_weight= 1960.566 rmsd (weighted)= 1.846 (unweighted)= 26.689 superimposing iter= 3 total_weight= 1410.221 rmsd (weighted)= 1.550 (unweighted)= 26.712 superimposing iter= 4 total_weight= 1249.953 rmsd (weighted)= 1.390 (unweighted)= 26.731 superimposing iter= 5 total_weight= 1149.345 rmsd (weighted)= 1.302 (unweighted)= 26.744 superimposing iter= 0 total_weight= 1.247 rmsd (weighted)= 5.503 (unweighted)= 24.552 superimposing iter= 1 total_weight= 2947.378 rmsd (weighted)= 3.111 (unweighted)= 24.432 superimposing iter= 2 total_weight= 1557.509 rmsd (weighted)= 2.520 (unweighted)= 24.413 superimposing iter= 3 total_weight= 1208.927 rmsd (weighted)= 2.337 (unweighted)= 24.412 superimposing iter= 4 total_weight= 1105.894 rmsd (weighted)= 2.271 (unweighted)= 24.414 superimposing iter= 5 total_weight= 1073.994 rmsd (weighted)= 2.240 (unweighted)= 24.418 superimposing iter= 0 total_weight= 1.157 rmsd (weighted)= 9.355 (unweighted)= 25.818 superimposing iter= 1 total_weight= 3317.265 rmsd (weighted)= 4.577 (unweighted)= 25.631 superimposing iter= 2 total_weight= 1882.754 rmsd (weighted)= 3.200 (unweighted)= 25.573 superimposing iter= 3 total_weight= 1373.257 rmsd (weighted)= 2.662 (unweighted)= 25.542 superimposing iter= 4 total_weight= 1184.057 rmsd (weighted)= 2.391 (unweighted)= 25.527 superimposing iter= 5 total_weight= 1097.603 rmsd (weighted)= 2.230 (unweighted)= 25.523 superimposing iter= 0 total_weight= 0.948 rmsd (weighted)= 5.934 (unweighted)= 45.847 superimposing iter= 1 total_weight= 2865.308 rmsd (weighted)= 2.700 (unweighted)= 46.794 superimposing iter= 2 total_weight= 1894.744 rmsd (weighted)= 1.636 (unweighted)= 47.214 superimposing iter= 3 total_weight= 1303.731 rmsd (weighted)= 1.247 (unweighted)= 47.351 superimposing iter= 4 total_weight= 996.029 rmsd (weighted)= 1.099 (unweighted)= 47.408 superimposing iter= 5 total_weight= 871.966 rmsd (weighted)= 1.039 (unweighted)= 47.433 # command:# Printing sheets for alignments to T0545.undertaker-align.sheets # command: