# command:# Seed set to 1276051573 # 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= 22.920 sec, elapsed time= 23.150 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= 35.676 sec, elapsed time= 39.318 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0573 numbered 1 through 311 Created new target T0573 from T0573.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 35.678 sec, elapsed time= 39.321 sec. # command:# Prefix for input files set to # command:# reading script from file T0573.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gp6A/T0573-1gp6A-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 # T0573 read from 1gp6A/T0573-1gp6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gp6A read from 1gp6A/T0573-1gp6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gp6A in training set T0573 2 :STSAIDPVSFSLYA 1gp6A 46 :QVPTIDLKNIESDD # choosing archetypes in rotamer library T0573 16 :KDFTRFAQELGASFERYGFAVLSDYDLDQARIDAAVDSAKAFFALPVETKKQYAGVKGGARGYIPFGVETAKGADHYDLKEFWHMGR 1gp6A 61 :KIRENCIEELKKASLDWGVMHLINHGIPADLMERVKKAGEEFFSLSVEEKEKYANDQATGKIQGYGSKLANNASGQLEWEDYFFHLA T0573 109 :RFRAHMADNVWPAEIPAFKHDVSWLYNSLDGMGGKVLEAIATYLKLERDFFKPTV 1gp6A 148 :YPEEKRDLSIWPKTPSDYIEATSEYAKCLRLLATKVFKALSVGLGLEPDRLEKEV T0573 164 :QDGNSVLRLLHYPPIPKDATGVRAGAHGDINTITLLLGAEEGGLEVL 1gp6A 206 :EELLLQMKINYYPKCPQPELALGVEAHTDVSALTFILHNMVPGLQLF T0573 212 :RDGQWLPINPPPGCLVINIGDMLERLTNNVLPSTVHRVVNPPPE 1gp6A 253 :YEGKWVTAKCVPDSIVMHIGDTLEILSNGKYKSILHRGLVNKEK T0573 260 :PRYSTPFFLHFASD 1gp6A 297 :VRISWAVFCEPPKD T0573 274 :YEIKTLQNCVTAENPDRYPESITADEFLQQRLRE 1gp6A 312 :IVLKPLPEMVSVESPAKFPPRTFAQHIEHKLFGK Number of specific fragments extracted= 7 number of extra gaps= 0 total=7 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_1411170445.pdb -s /var/tmp/to_scwrl_1411170445.seq -o /var/tmp/from_scwrl_1411170445.pdb > /var/tmp/scwrl_1411170445.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1411170445.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g19A/T0573-2g19A-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 2g19A expands to /projects/compbio/data/pdb/2g19.pdb.gz 2g19A:# T0573 read from 2g19A/T0573-2g19A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g19A read from 2g19A/T0573-2g19A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g19A to template set # found chain 2g19A in template set T0573 17 :DFTRFA 2g19A 189 :PALKLA T0573 23 :QELGASFERYGFAVLSDY 2g19A 196 :EYIVPCMNKHGICVVDDF T0573 42 :LDQARIDAAVDSAKAFFA 2g19A 214 :LGKETGQQIGDEVRALHD T0573 69 :AGVKGGARGYIPFGVETAKGADH 2g19A 243 :QKSDSSKDIRGDKITWIEGKEPG T0573 127 :KHDVSWLYNSLDGMGGKV 2g19A 266 :CETIGLLMSSMDDLIRHC T0573 153 :KLE 2g19A 289 :SYK T0573 165 :DGNSVLRLLHYPPIPKDATGVRAGAHGDINTITLLLG 2g19A 293 :NGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYY T0573 204 :EGGLEVLDRD 2g19A 340 :GGILRIFPEG T0573 214 :GQWLPINPPPGCLVINIGD 2g19A 351 :AQFADIEPKFDRLLFFWSD T0573 243 :PSTVHRVVN 2g19A 370 :RRNPHEVQP T0573 257 :RGVPRYSTPFFLH 2g19A 379 :AYATRYAITVWYF Number of specific fragments extracted= 11 number of extra gaps= 0 total=18 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_1944517798.pdb -s /var/tmp/to_scwrl_1944517798.seq -o /var/tmp/from_scwrl_1944517798.pdb > /var/tmp/scwrl_1944517798.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1944517798.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hbtA/T0573-2hbtA-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 2hbtA expands to /projects/compbio/data/pdb/2hbt.pdb.gz 2hbtA:Skipped atom 82, because occupancy 0.5 <= existing 0.500 in 2hbtA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 991, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1097, because occupancy 0.200 <= existing 0.800 in 2hbtA Skipped atom 1101, because occupancy 0.200 <= existing 0.800 in 2hbtA Skipped atom 1103, because occupancy 0.200 <= existing 0.800 in 2hbtA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1146, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1742, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1746, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2hbtA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2hbtA # T0573 read from 2hbtA/T0573-2hbtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hbtA read from 2hbtA/T0573-2hbtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hbtA to template set # found chain 2hbtA in template set Warning: unaligning (T0573)D43 because of BadResidue code BAD_PEPTIDE in next template residue (2hbtA)K216 Warning: unaligning (T0573)Q44 because of BadResidue code BAD_PEPTIDE at template residue (2hbtA)K216 Warning: unaligning (T0573)G70 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hbtA)S245 Warning: unaligning (T0573)V71 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hbtA)S245 Warning: unaligning (T0573)K72 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hbtA)D246 Warning: unaligning (T0573)P161 because of BadResidue code BAD_PEPTIDE in next template residue (2hbtA)K286 Warning: unaligning (T0573)T162 because of BadResidue code BAD_PEPTIDE at template residue (2hbtA)K286 Warning: unaligning (T0573)V169 because of BadResidue code BAD_PEPTIDE at template residue (2hbtA)K297 Warning: unaligning (T0573)G201 because of BadResidue code BAD_PEPTIDE in next template residue (2hbtA)L330 Warning: unaligning (T0573)D213 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hbtA)K350 Warning: unaligning (T0573)G214 because of BadResidue code BAD_PEPTIDE at template residue (2hbtA)A351 Warning: unaligning (T0573)Q215 because of BadResidue code BAD_PEPTIDE at template residue (2hbtA)Q352 T0573 25 :LGASFERYGFAVLSDY 2hbtA 198 :IVPCMNKHGICVVDDF T0573 42 :L 2hbtA 214 :L T0573 45 :ARIDAAVDSAKAFFA 2hbtA 217 :ETGQQIGDEVRALHD T0573 68 :YA 2hbtA 241 :VS T0573 73 :GGARGYIPFGVETAKGAD 2hbtA 247 :SSKDIRGDKITWIEGKEP T0573 125 :A 2hbtA 265 :G T0573 127 :KHDVSWLYNSLDGMGGK 2hbtA 266 :CETIGLLMSSMDDLIRH T0573 159 :FK 2hbtA 283 :CN T0573 163 :VQDGNS 2hbtA 287 :LGSYKI T0573 170 :LRLLHYPPIPKDATGVRAGAHGDINTITLLL 2hbtA 298 :AMVACYPGNGTGYVRHVDNPNGDGRCVTCIY T0573 204 :EGGLEVLDR 2hbtA 340 :GGILRIFPE T0573 216 :WLPINPPPGCLVINIGD 2hbtA 353 :FADIEPKFDRLLFFWSD T0573 243 :PSTVHRVVN 2hbtA 370 :RRNPHEVQP T0573 257 :RGVPRYSTPFFLH 2hbtA 379 :AYATRYAITVWYF Number of specific fragments extracted= 14 number of extra gaps= 7 total=32 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_1230115671.pdb -s /var/tmp/to_scwrl_1230115671.seq -o /var/tmp/from_scwrl_1230115671.pdb > /var/tmp/scwrl_1230115671.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1230115671.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3emrA/T0573-3emrA-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 3emrA expands to /projects/compbio/data/pdb/3emr.pdb.gz 3emrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 493, because occupancy 0.500 <= existing 0.500 in 3emrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 3emrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 3emrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 3emrA Skipped atom 581, because occupancy 0.450 <= existing 0.550 in 3emrA Skipped atom 583, because occupancy 0.450 <= existing 0.550 in 3emrA Skipped atom 799, because occupancy 0.310 <= existing 0.690 in 3emrA Skipped atom 803, because occupancy 0.310 <= existing 0.690 in 3emrA Skipped atom 805, because occupancy 0.310 <= existing 0.690 in 3emrA Skipped atom 807, because occupancy 0.310 <= existing 0.690 in 3emrA Skipped atom 809, because occupancy 0.310 <= existing 0.690 in 3emrA Skipped atom 994, because occupancy 0.400 <= existing 0.600 in 3emrA Skipped atom 998, because occupancy 0.400 <= existing 0.600 in 3emrA Skipped atom 1000, because occupancy 0.400 <= existing 0.600 in 3emrA Skipped atom 1002, because occupancy 0.400 <= existing 0.600 in 3emrA Skipped atom 1004, because occupancy 0.400 <= existing 0.600 in 3emrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1383, because occupancy 0.350 <= existing 0.650 in 3emrA Skipped atom 1387, because occupancy 0.350 <= existing 0.650 in 3emrA Skipped atom 1389, because occupancy 0.350 <= existing 0.650 in 3emrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1699, because occupancy 0.470 <= existing 0.530 in 3emrA Skipped atom 1701, because occupancy 0.470 <= existing 0.530 in 3emrA Skipped atom 1703, because occupancy 0.470 <= existing 0.530 in 3emrA Skipped atom 1705, because occupancy 0.470 <= existing 0.530 in 3emrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0573 read from 3emrA/T0573-3emrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3emrA read from 3emrA/T0573-3emrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3emrA to template set # found chain 3emrA in template set Warning: unaligning (T0573)M100 because of BadResidue code BAD_PEPTIDE in next template residue (3emrA)H98 Warning: unaligning (T0573)G101 because of BadResidue code BAD_PEPTIDE at template residue (3emrA)H98 T0573 9 :VSFSLYAKDFTR 3emrA 31 :NQAPITKEQLDS T0573 29 :FERYGFAVLSDY 3emrA 43 :YEKNGFLQIKNF T0573 42 :LDQARIDAAVDSAKAFFA 3emrA 55 :FSEDEVIDMQKAIFELQD T0573 67 :QYAGVKGGARGYI 3emrA 73 :SIKDVASDKVIRE T0573 89 :ADHYDLKEFWH 3emrA 86 :PESNDIRSIFH T0573 102 :RD 3emrA 99 :QD T0573 123 :IPAFKHDV 3emrA 101 :DNYFQDVA T0573 142 :GKVLEAIATYLKLE 3emrA 111 :KRILDIVRHLLGSD T0573 167 :NSVLRLLHYPPIPKDA 3emrA 127 :VHQSRINYKPGFKGKE T0573 183 :TGVR 3emrA 157 :GMPR T0573 193 :INTITLLLG 3emrA 161 :MRAISVSIA T0573 202 :AEEGGLEVLDR 3emrA 175 :SFNGPLMLIPG T0573 213 :DGQ 3emrA 227 :GGI T0573 220 :NPPPGCLVINIG 3emrA 233 :TGKAGSVTLFES T0573 244 :STVHRVVNPPPE 3emrA 245 :NTMHGSTSNITP T0573 259 :VPRYSTPFFLHFASDYEIKT 3emrA 257 :YPRNNLFMVYNSVKNRLVEP T0573 282 :CVTAENPDRY 3emrA 277 :FSGGEKRPEY Number of specific fragments extracted= 17 number of extra gaps= 1 total=49 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_1856542323.pdb -s /var/tmp/to_scwrl_1856542323.seq -o /var/tmp/from_scwrl_1856542323.pdb > /var/tmp/scwrl_1856542323.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1856542323.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rdqA/T0573-2rdqA-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 2rdqA expands to /projects/compbio/data/pdb/2rdq.pdb.gz 2rdqA:Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 991, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2078, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2080, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2082, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2084, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2086, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2088, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2090, because occupancy 0.500 <= existing 0.500 in 2rdqA Skipped atom 2092, because occupancy 0.500 <= existing 0.500 in 2rdqA # T0573 read from 2rdqA/T0573-2rdqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rdqA read from 2rdqA/T0573-2rdqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rdqA to template set # found chain 2rdqA in template set T0573 7 :DPVSFSLYAKDFTRFAQ 2rdqA 10 :DCTPLLGDRAALDSFYE T0573 31 :RYGFAVLSDY 2rdqA 27 :EHGYLFLRNV T0573 42 :LDQARIDAAVDSAKAF 2rdqA 37 :LDRDLVKTVAEQMREG T0573 65 :KKQYAGVKGGARGYIPFGVETAK 2rdqA 53 :LVALGAADPHATLEELTIDSFES T0573 92 :YDLKEFWHMGRDLPPG 2rdqA 76 :VDEVAMHDYVKYDAFW T0573 122 :EIPAFKHDVSWLY 2rdqA 92 :NNPSTIKVFEQVF T0573 164 :QDGNS 2rdqA 105 :GEPVF T0573 169 :VLRLLHYPPIPK 2rdqA 113 :STTIRYYPSQAG T0573 181 :DA 2rdqA 126 :EE T0573 183 :TGVRAGAHGD 2rdqA 130 :FHYLTPFHQD T0573 193 :INTITLLLG 2rdqA 147 :QDFRTFWIP T0573 202 :AEEGGLEVLDR 2rdqA 161 :RESGGVALADG T0573 213 :DGQWLPINPPPGCLVINIGD 2rdqA 204 :DEHLLHSPMEPGDILLFHAH T0573 245 :TVHRVVNPPPERRGVPRYSTPFFLHFASD 2rdqA 224 :MCHKSIPNLSKDPRLMRMSMDTRVQPAKS Number of specific fragments extracted= 14 number of extra gaps= 0 total=63 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_856036397.pdb -s /var/tmp/to_scwrl_856036397.seq -o /var/tmp/from_scwrl_856036397.pdb > /var/tmp/scwrl_856036397.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_856036397.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rg4A/T0573-2rg4A-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 2rg4A expands to /projects/compbio/data/pdb/2rg4.pdb.gz 2rg4A:Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 2rg4A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2rg4A # T0573 read from 2rg4A/T0573-2rg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rg4A read from 2rg4A/T0573-2rg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rg4A to template set # found chain 2rg4A in template set Warning: unaligning (T0573)D39 because of BadResidue code BAD_PEPTIDE at template residue (2rg4A)G23 Warning: unaligning (T0573)G74 because of BadResidue code BAD_PEPTIDE in next template residue (2rg4A)G56 Warning: unaligning (T0573)A75 because of BadResidue code BAD_PEPTIDE at template residue (2rg4A)G56 Warning: unaligning (T0573)R76 because of BadResidue code BAD_PEPTIDE at template residue (2rg4A)Y57 Warning: unaligning (T0573)G77 because of BadResidue code BAD_PEPTIDE at template residue (2rg4A)T58 Warning: unaligning (T0573)Y78 because of BadResidue code BAD_PEPTIDE in next template residue (2rg4A)Y60 Warning: unaligning (T0573)I79 because of BadResidue code BAD_PEPTIDE at template residue (2rg4A)Y60 Warning: unaligning (T0573)D165 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rg4A)K98 Warning: unaligning (T0573)G166 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rg4A)K98 Warning: unaligning (T0573)I196 because of BadResidue code BAD_PEPTIDE in next template residue (2rg4A)T130 Warning: unaligning (T0573)T197 because of BadResidue code BAD_PEPTIDE at template residue (2rg4A)T130 Warning: unaligning (T0573)G201 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rg4A)P135 Warning: unaligning (T0573)A202 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rg4A)E136 Warning: unaligning (T0573)E203 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rg4A)G137 Warning: unaligning (T0573)E204 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rg4A)T138 Warning: unaligning (T0573)F270 because last residue in template chain is (2rg4A)W207 T0573 40 :YDLDQA 2rg4A 24 :PALDPA T0573 49 :AAVDSAKAFFALPVETKKQYAGVKG 2rg4A 30 :EFAASCYSIAEDDDAGQEWCEREGY T0573 80 :PFGVE 2rg4A 61 :ASLTD T0573 123 :IPAFKHDVSWLYNSLDGMGG 2rg4A 66 :LPWRFPIFADLVKSLDAHVA T0573 147 :AIATYLKLE 2rg4A 86 :AFAEDLEFE T0573 163 :VQ 2rg4A 95 :LD T0573 167 :NSVLRLLHYPPIPKDA 2rg4A 99 :ALRLEDIWINILPEGG T0573 183 :TGVRAGAHGDINT 2rg4A 116 :HGSHIHPHSVISG T0573 198 :LLL 2rg4A 131 :YVA T0573 205 :GGLEVLDR 2rg4A 139 :SALKLEDP T0573 213 :DGQ 2rg4A 160 :GAR T0573 216 :WLPINPPPGCLVIN 2rg4A 168 :FRSVAPKVGDVLLW T0573 245 :TVHRVVNPPPE 2rg4A 185 :LRHEVPMNMAE T0573 259 :VPRYSTPFFLH 2rg4A 196 :EDRISVSFNYA Number of specific fragments extracted= 14 number of extra gaps= 6 total=77 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_1545686322.pdb -s /var/tmp/to_scwrl_1545686322.seq -o /var/tmp/from_scwrl_1545686322.pdb > /var/tmp/scwrl_1545686322.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1545686322.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2opwA/T0573-2opwA-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 2opwA expands to /projects/compbio/data/pdb/2opw.pdb.gz 2opwA:Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 2opwA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2opwA # T0573 read from 2opwA/T0573-2opwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2opwA read from 2opwA/T0573-2opwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2opwA to template set # found chain 2opwA in template set Warning: unaligning (T0573)V209 because of BadResidue code BAD_PEPTIDE in next template residue (2opwA)I190 Warning: unaligning (T0573)L210 because of BadResidue code BAD_PEPTIDE at template residue (2opwA)I190 T0573 26 :GASFERYGFAVLSDY 2opwA 9 :LQKFQQDGFLVLEGF T0573 42 :LDQARIDAAVDSAKAFFA 2opwA 24 :LSAEECVAMQQRIGEIVA T0573 60 :LPVETKKQYAGV 2opwA 54 :STQEEEQLRAQG T0573 72 :KGGARGYIPFGVETAKGA 2opwA 72 :SSGDKIRFFFEKGVFDEK T0573 113 :HMADNVWPA 2opwA 90 :GNFLVPPEK T0573 122 :EIPAFKHDV 2opwA 110 :HDPVFKSIT T0573 135 :NSLDGMGG 2opwA 121 :FKVQTLAR T0573 151 :YLKLE 2opwA 129 :SLGLQ T0573 166 :GNSVLRLLHYPPI 2opwA 134 :MPVVVQSMYIFKQ T0573 181 :DATGVRAGAHGDIN 2opwA 147 :PHFGGEVSPHQDAS T0573 195 :TITLLLG 2opwA 170 :VLGVWIA T0573 202 :AEEGGLE 2opwA 182 :LENGCLW T0573 211 :DR 2opwA 191 :PG T0573 216 :WLPINPPPGCLVINIGD 2opwA 227 :FVPTPVQRGALVLIHGE T0573 245 :TVHRVVNPPPE 2opwA 244 :VVHKSKQNLSD T0573 259 :VPRYSTPFFLHFASDYEI 2opwA 255 :RSRQAYTFHLMEASGTTW T0573 279 :LQNC 2opwA 273 :SPEN Number of specific fragments extracted= 17 number of extra gaps= 1 total=94 # request to SCWRL produces command: ulimit -t 280 ; scwrl4 -t -i /var/tmp/to_scwrl_1763731190.pdb -s /var/tmp/to_scwrl_1763731190.seq -o /var/tmp/from_scwrl_1763731190.pdb > /var/tmp/scwrl_1763731190.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1763731190.pdb Number of alignments=7 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.431 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 23300.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 23300.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 23300.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 23300.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 23300.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.806 rmsd (weighted)= 9.795 (unweighted)= 48.761 superimposing iter= 1 total_weight= 7403.338 rmsd (weighted)= 3.406 (unweighted)= 48.974 superimposing iter= 2 total_weight= 3065.434 rmsd (weighted)= 2.150 (unweighted)= 48.994 superimposing iter= 3 total_weight= 1703.050 rmsd (weighted)= 1.857 (unweighted)= 49.018 superimposing iter= 4 total_weight= 1443.482 rmsd (weighted)= 1.752 (unweighted)= 49.031 superimposing iter= 5 total_weight= 1372.826 rmsd (weighted)= 1.696 (unweighted)= 49.037 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.725 rmsd (weighted)= 9.867 (unweighted)= 44.690 superimposing iter= 1 total_weight= 7215.229 rmsd (weighted)= 3.194 (unweighted)= 44.792 superimposing iter= 2 total_weight= 3061.953 rmsd (weighted)= 1.919 (unweighted)= 44.863 superimposing iter= 3 total_weight= 1526.692 rmsd (weighted)= 1.667 (unweighted)= 44.908 superimposing iter= 4 total_weight= 1260.742 rmsd (weighted)= 1.597 (unweighted)= 44.932 superimposing iter= 5 total_weight= 1213.011 rmsd (weighted)= 1.562 (unweighted)= 44.948 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.895 rmsd (weighted)= 9.898 (unweighted)= 44.822 superimposing iter= 1 total_weight= 5618.824 rmsd (weighted)= 4.582 (unweighted)= 44.116 superimposing iter= 2 total_weight= 2770.296 rmsd (weighted)= 3.177 (unweighted)= 43.755 superimposing iter= 3 total_weight= 2114.758 rmsd (weighted)= 2.585 (unweighted)= 43.596 superimposing iter= 4 total_weight= 1741.350 rmsd (weighted)= 2.343 (unweighted)= 43.524 superimposing iter= 5 total_weight= 1556.827 rmsd (weighted)= 2.254 (unweighted)= 43.483 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.886 rmsd (weighted)= 9.837 (unweighted)= 32.864 superimposing iter= 1 total_weight= 4744.414 rmsd (weighted)= 4.867 (unweighted)= 33.742 superimposing iter= 2 total_weight= 2937.734 rmsd (weighted)= 3.212 (unweighted)= 34.255 superimposing iter= 3 total_weight= 2258.152 rmsd (weighted)= 2.495 (unweighted)= 34.543 superimposing iter= 4 total_weight= 1813.253 rmsd (weighted)= 2.189 (unweighted)= 34.717 superimposing iter= 5 total_weight= 1685.795 rmsd (weighted)= 2.000 (unweighted)= 34.821 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.687 rmsd (weighted)= 7.365 (unweighted)= 74.148 superimposing iter= 1 total_weight= 4144.578 rmsd (weighted)= 3.565 (unweighted)= 74.112 superimposing iter= 2 total_weight= 1908.010 rmsd (weighted)= 2.666 (unweighted)= 74.112 superimposing iter= 3 total_weight= 1387.091 rmsd (weighted)= 2.359 (unweighted)= 74.115 superimposing iter= 4 total_weight= 1216.049 rmsd (weighted)= 2.234 (unweighted)= 74.119 superimposing iter= 5 total_weight= 1153.663 rmsd (weighted)= 2.174 (unweighted)= 74.124 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.878 rmsd (weighted)= 10.247 (unweighted)= 38.877 superimposing iter= 1 total_weight= 6825.176 rmsd (weighted)= 3.956 (unweighted)= 38.844 superimposing iter= 2 total_weight= 3606.038 rmsd (weighted)= 2.362 (unweighted)= 38.825 superimposing iter= 3 total_weight= 2207.278 rmsd (weighted)= 1.857 (unweighted)= 38.816 superimposing iter= 4 total_weight= 1705.515 rmsd (weighted)= 1.672 (unweighted)= 38.807 superimposing iter= 5 total_weight= 1545.748 rmsd (weighted)= 1.583 (unweighted)= 38.800 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.431 rmsd (weighted)= 6.456 (unweighted)= 10.525 superimposing iter= 1 total_weight= 10265.494 rmsd (weighted)= 2.683 (unweighted)= 10.596 superimposing iter= 2 total_weight= 6284.639 rmsd (weighted)= 1.502 (unweighted)= 10.645 superimposing iter= 3 total_weight= 4681.931 rmsd (weighted)= 0.981 (unweighted)= 10.651 superimposing iter= 4 total_weight= 4023.228 rmsd (weighted)= 0.691 (unweighted)= 10.652 superimposing iter= 5 total_weight= 3709.896 rmsd (weighted)= 0.508 (unweighted)= 10.652 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.825 rmsd (weighted)= 5.466 (unweighted)= 47.184 superimposing iter= 1 total_weight= 8034.780 rmsd (weighted)= 1.915 (unweighted)= 47.125 superimposing iter= 2 total_weight= 2889.394 rmsd (weighted)= 1.262 (unweighted)= 47.118 superimposing iter= 3 total_weight= 1759.837 rmsd (weighted)= 1.079 (unweighted)= 47.118 superimposing iter= 4 total_weight= 1506.051 rmsd (weighted)= 1.002 (unweighted)= 47.115 superimposing iter= 5 total_weight= 1412.039 rmsd (weighted)= 0.963 (unweighted)= 47.109 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.744 rmsd (weighted)= 5.167 (unweighted)= 43.675 superimposing iter= 1 total_weight= 7422.506 rmsd (weighted)= 1.745 (unweighted)= 43.684 superimposing iter= 2 total_weight= 2754.667 rmsd (weighted)= 1.123 (unweighted)= 43.670 superimposing iter= 3 total_weight= 1552.096 rmsd (weighted)= 0.977 (unweighted)= 43.667 superimposing iter= 4 total_weight= 1309.441 rmsd (weighted)= 0.929 (unweighted)= 43.669 superimposing iter= 5 total_weight= 1233.182 rmsd (weighted)= 0.911 (unweighted)= 43.670 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.909 rmsd (weighted)= 5.812 (unweighted)= 42.436 superimposing iter= 1 total_weight= 6382.396 rmsd (weighted)= 2.481 (unweighted)= 42.000 superimposing iter= 2 total_weight= 3149.938 rmsd (weighted)= 1.612 (unweighted)= 41.784 superimposing iter= 3 total_weight= 2457.541 rmsd (weighted)= 1.213 (unweighted)= 41.702 superimposing iter= 4 total_weight= 1975.330 rmsd (weighted)= 1.032 (unweighted)= 41.680 superimposing iter= 5 total_weight= 1694.773 rmsd (weighted)= 0.952 (unweighted)= 41.678 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.933 rmsd (weighted)= 6.323 (unweighted)= 30.799 superimposing iter= 1 total_weight= 4614.280 rmsd (weighted)= 3.319 (unweighted)= 31.327 superimposing iter= 2 total_weight= 2653.351 rmsd (weighted)= 2.349 (unweighted)= 31.688 superimposing iter= 3 total_weight= 2574.170 rmsd (weighted)= 1.728 (unweighted)= 31.880 superimposing iter= 4 total_weight= 2173.478 rmsd (weighted)= 1.409 (unweighted)= 31.975 superimposing iter= 5 total_weight= 1843.646 rmsd (weighted)= 1.259 (unweighted)= 32.026 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.697 rmsd (weighted)= 4.944 (unweighted)= 71.550 superimposing iter= 1 total_weight= 4195.221 rmsd (weighted)= 2.296 (unweighted)= 71.527 superimposing iter= 2 total_weight= 2252.018 rmsd (weighted)= 1.584 (unweighted)= 71.542 superimposing iter= 3 total_weight= 1449.869 rmsd (weighted)= 1.381 (unweighted)= 71.555 superimposing iter= 4 total_weight= 1242.847 rmsd (weighted)= 1.303 (unweighted)= 71.566 superimposing iter= 5 total_weight= 1181.610 rmsd (weighted)= 1.263 (unweighted)= 71.573 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.887 rmsd (weighted)= 6.792 (unweighted)= 37.347 superimposing iter= 1 total_weight= 7093.071 rmsd (weighted)= 2.450 (unweighted)= 37.418 superimposing iter= 2 total_weight= 4056.892 rmsd (weighted)= 1.382 (unweighted)= 37.430 superimposing iter= 3 total_weight= 2160.483 rmsd (weighted)= 1.107 (unweighted)= 37.434 superimposing iter= 4 total_weight= 1658.929 rmsd (weighted)= 1.017 (unweighted)= 37.435 superimposing iter= 5 total_weight= 1500.215 rmsd (weighted)= 0.985 (unweighted)= 37.435 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.431 rmsd (weighted)= 6.538 (unweighted)= 10.529 superimposing iter= 1 total_weight= 10320.336 rmsd (weighted)= 2.706 (unweighted)= 10.599 superimposing iter= 2 total_weight= 6295.943 rmsd (weighted)= 1.511 (unweighted)= 10.648 superimposing iter= 3 total_weight= 4680.776 rmsd (weighted)= 0.986 (unweighted)= 10.655 superimposing iter= 4 total_weight= 4032.632 rmsd (weighted)= 0.694 (unweighted)= 10.657 superimposing iter= 5 total_weight= 3721.273 rmsd (weighted)= 0.508 (unweighted)= 10.658 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.825 rmsd (weighted)= 5.424 (unweighted)= 47.235 superimposing iter= 1 total_weight= 7968.954 rmsd (weighted)= 1.915 (unweighted)= 47.177 superimposing iter= 2 total_weight= 2885.110 rmsd (weighted)= 1.263 (unweighted)= 47.169 superimposing iter= 3 total_weight= 1762.577 rmsd (weighted)= 1.079 (unweighted)= 47.171 superimposing iter= 4 total_weight= 1510.696 rmsd (weighted)= 1.000 (unweighted)= 47.167 superimposing iter= 5 total_weight= 1401.269 rmsd (weighted)= 0.964 (unweighted)= 47.161 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.744 rmsd (weighted)= 5.141 (unweighted)= 43.698 superimposing iter= 1 total_weight= 7419.208 rmsd (weighted)= 1.740 (unweighted)= 43.692 superimposing iter= 2 total_weight= 2730.949 rmsd (weighted)= 1.125 (unweighted)= 43.677 superimposing iter= 3 total_weight= 1542.552 rmsd (weighted)= 0.981 (unweighted)= 43.673 superimposing iter= 4 total_weight= 1310.352 rmsd (weighted)= 0.932 (unweighted)= 43.673 superimposing iter= 5 total_weight= 1237.609 rmsd (weighted)= 0.912 (unweighted)= 43.675 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.909 rmsd (weighted)= 5.787 (unweighted)= 42.350 superimposing iter= 1 total_weight= 6405.982 rmsd (weighted)= 2.460 (unweighted)= 41.926 superimposing iter= 2 total_weight= 3196.715 rmsd (weighted)= 1.587 (unweighted)= 41.723 superimposing iter= 3 total_weight= 2444.202 rmsd (weighted)= 1.198 (unweighted)= 41.648 superimposing iter= 4 total_weight= 1952.875 rmsd (weighted)= 1.025 (unweighted)= 41.630 superimposing iter= 5 total_weight= 1683.791 rmsd (weighted)= 0.948 (unweighted)= 41.628 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.933 rmsd (weighted)= 6.331 (unweighted)= 30.711 superimposing iter= 1 total_weight= 4599.529 rmsd (weighted)= 3.327 (unweighted)= 31.242 superimposing iter= 2 total_weight= 2679.010 rmsd (weighted)= 2.339 (unweighted)= 31.609 superimposing iter= 3 total_weight= 2627.310 rmsd (weighted)= 1.696 (unweighted)= 31.808 superimposing iter= 4 total_weight= 2296.717 rmsd (weighted)= 1.338 (unweighted)= 31.908 superimposing iter= 5 total_weight= 1930.689 rmsd (weighted)= 1.160 (unweighted)= 31.949 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.697 rmsd (weighted)= 4.957 (unweighted)= 71.549 superimposing iter= 1 total_weight= 4170.943 rmsd (weighted)= 2.310 (unweighted)= 71.527 superimposing iter= 2 total_weight= 2251.238 rmsd (weighted)= 1.595 (unweighted)= 71.540 superimposing iter= 3 total_weight= 1453.484 rmsd (weighted)= 1.389 (unweighted)= 71.551 superimposing iter= 4 total_weight= 1245.399 rmsd (weighted)= 1.309 (unweighted)= 71.560 superimposing iter= 5 total_weight= 1184.032 rmsd (weighted)= 1.267 (unweighted)= 71.567 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.887 rmsd (weighted)= 6.713 (unweighted)= 37.339 superimposing iter= 1 total_weight= 7112.575 rmsd (weighted)= 2.419 (unweighted)= 37.419 superimposing iter= 2 total_weight= 4025.209 rmsd (weighted)= 1.377 (unweighted)= 37.431 superimposing iter= 3 total_weight= 2103.805 rmsd (weighted)= 1.117 (unweighted)= 37.431 superimposing iter= 4 total_weight= 1647.233 rmsd (weighted)= 1.030 (unweighted)= 37.431 superimposing iter= 5 total_weight= 1508.094 rmsd (weighted)= 0.994 (unweighted)= 37.430 superimposing iter= 0 total_weight= 1.431 rmsd (weighted)= 6.542 (unweighted)= 10.523 superimposing iter= 1 total_weight= 10336.362 rmsd (weighted)= 2.705 (unweighted)= 10.594 superimposing iter= 2 total_weight= 6275.431 rmsd (weighted)= 1.513 (unweighted)= 10.641 superimposing iter= 3 total_weight= 4673.020 rmsd (weighted)= 0.987 (unweighted)= 10.649 superimposing iter= 4 total_weight= 4032.935 rmsd (weighted)= 0.694 (unweighted)= 10.651 superimposing iter= 5 total_weight= 3720.870 rmsd (weighted)= 0.509 (unweighted)= 10.652 superimposing iter= 0 total_weight= 0.825 rmsd (weighted)= 5.418 (unweighted)= 47.247 superimposing iter= 1 total_weight= 7958.048 rmsd (weighted)= 1.916 (unweighted)= 47.189 superimposing iter= 2 total_weight= 2875.525 rmsd (weighted)= 1.265 (unweighted)= 47.182 superimposing iter= 3 total_weight= 1762.973 rmsd (weighted)= 1.081 (unweighted)= 47.183 superimposing iter= 4 total_weight= 1510.669 rmsd (weighted)= 1.002 (unweighted)= 47.180 superimposing iter= 5 total_weight= 1400.656 rmsd (weighted)= 0.966 (unweighted)= 47.174 superimposing iter= 0 total_weight= 0.744 rmsd (weighted)= 5.138 (unweighted)= 43.698 superimposing iter= 1 total_weight= 7416.983 rmsd (weighted)= 1.740 (unweighted)= 43.691 superimposing iter= 2 total_weight= 2720.346 rmsd (weighted)= 1.128 (unweighted)= 43.675 superimposing iter= 3 total_weight= 1540.158 rmsd (weighted)= 0.984 (unweighted)= 43.672 superimposing iter= 4 total_weight= 1308.786 rmsd (weighted)= 0.935 (unweighted)= 43.672 superimposing iter= 5 total_weight= 1236.360 rmsd (weighted)= 0.915 (unweighted)= 43.673 superimposing iter= 0 total_weight= 0.909 rmsd (weighted)= 5.787 (unweighted)= 42.352 superimposing iter= 1 total_weight= 6399.486 rmsd (weighted)= 2.461 (unweighted)= 41.929 superimposing iter= 2 total_weight= 3203.449 rmsd (weighted)= 1.585 (unweighted)= 41.727 superimposing iter= 3 total_weight= 2443.968 rmsd (weighted)= 1.197 (unweighted)= 41.652 superimposing iter= 4 total_weight= 1951.602 rmsd (weighted)= 1.024 (unweighted)= 41.634 superimposing iter= 5 total_weight= 1682.300 rmsd (weighted)= 0.948 (unweighted)= 41.632 superimposing iter= 0 total_weight= 0.933 rmsd (weighted)= 6.332 (unweighted)= 30.701 superimposing iter= 1 total_weight= 4597.309 rmsd (weighted)= 3.329 (unweighted)= 31.232 superimposing iter= 2 total_weight= 2677.308 rmsd (weighted)= 2.341 (unweighted)= 31.600 superimposing iter= 3 total_weight= 2639.547 rmsd (weighted)= 1.693 (unweighted)= 31.801 superimposing iter= 4 total_weight= 2301.768 rmsd (weighted)= 1.332 (unweighted)= 31.897 superimposing iter= 5 total_weight= 1912.296 rmsd (weighted)= 1.159 (unweighted)= 31.934 superimposing iter= 0 total_weight= 0.697 rmsd (weighted)= 4.957 (unweighted)= 71.548 superimposing iter= 1 total_weight= 4165.905 rmsd (weighted)= 2.311 (unweighted)= 71.525 superimposing iter= 2 total_weight= 2248.512 rmsd (weighted)= 1.597 (unweighted)= 71.537 superimposing iter= 3 total_weight= 1454.892 rmsd (weighted)= 1.390 (unweighted)= 71.549 superimposing iter= 4 total_weight= 1246.727 rmsd (weighted)= 1.310 (unweighted)= 71.558 superimposing iter= 5 total_weight= 1185.054 rmsd (weighted)= 1.266 (unweighted)= 71.564 superimposing iter= 0 total_weight= 0.887 rmsd (weighted)= 6.705 (unweighted)= 37.341 superimposing iter= 1 total_weight= 7114.594 rmsd (weighted)= 2.416 (unweighted)= 37.420 superimposing iter= 2 total_weight= 4021.828 rmsd (weighted)= 1.376 (unweighted)= 37.432 superimposing iter= 3 total_weight= 2100.289 rmsd (weighted)= 1.118 (unweighted)= 37.432 superimposing iter= 4 total_weight= 1645.331 rmsd (weighted)= 1.031 (unweighted)= 37.432 superimposing iter= 5 total_weight= 1507.847 rmsd (weighted)= 0.996 (unweighted)= 37.431 # command:# Printing sheets for alignments to T0573.undertaker-align.sheets # command: