# command:# Seed set to 1213834684 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 27.337 sec, elapsed time= 27.467 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0459 numbered 1 through 111 Created new target T0459 from T0459.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.704 sec, elapsed time= 37.943 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1957 20 (100.000%) # n-terminus 2 1932 333 (83.250%) # middle 1 481122 20 (100.000%) # middle 2 474896 400 (100.000%) # middle 3 468898 7988 (99.850%) # middle 4 463038 120397 (75.248%) # c-terminus 1 1914 20 (100.000%) # c-terminus 2 1887 372 (93.000%) # ss-bonds 1042 # command:CPU_time= 47.429 sec, elapsed time= 47.675 sec. # command:# Prefix for input files set to # command:# reading script from file T0459.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hztA/T0459-2hztA-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 2hztA expands to /projects/compbio/data/pdb/2hzt.pdb.gz 2hztA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: S for alphabet: pdb_atoms Bad short name: OD3 for alphabet: pdb_atoms Bad short name: S for alphabet: pdb_atoms Bad short name: OD3 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 703, because occupancy 0.5 <= existing 0.500 in 2hztA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2hztA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2hztA # T0459 read from 2hztA/T0459-2hztA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hztA read from 2hztA/T0459-2hztA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hztA to template set # found chain 2hztA in template set Warning: unaligning (T0459)T29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2hztA)V18 Warning: unaligning (T0459)L31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2hztA)V18 Warning: unaligning (T0459)I33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2hztA)H22 Warning: unaligning (T0459)V35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2hztA)H22 Warning: unaligning (T0459)L99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2hztA)A90 Warning: unaligning (T0459)Q101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2hztA)A90 Warning: unaligning (T0459)R108 because last residue in template chain is (2hztA)R98 T0459 15 :DPSESVLHLLGKKY 2hztA 2 :SLVEATLEVIGGKW # choosing archetypes in rotamer library T0459 32 :I 2hztA 19 :I T0459 36 :LGNGSTR 2hztA 23 :LTHGKKR T0459 45 :FNDIRSSIPGISSTILSRRIKDLIDSGLVERR 2hztA 30 :TSELKRLMPNITQKMLTQQLRELEADGVINRI T0459 77 :SGQITTYALTEKGMNVRNSLMP 2hztA 66 :VPPKVEYELSEYGRSLEGILDM T0459 102 :YI 2hztA 91 :WG T0459 104 :SVLD 2hztA 94 :NHIN Number of specific fragments extracted= 7 number of extra gaps= 0 total=7 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_1128959911.pdb -s /var/tmp/to_scwrl_1128959911.seq -o /var/tmp/from_scwrl_1128959911.pdb > /var/tmp/scwrl_1128959911.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1128959911.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fswA/T0459-2fswA-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 2fswA expands to /projects/compbio/data/pdb/2fsw.pdb.gz 2fswA:Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 179, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 397, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 401, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 413, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 415, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 417, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 524, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 896, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 900, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.300 <= existing 0.340 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fswA # T0459 read from 2fswA/T0459-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0459-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fswA to template set # found chain 2fswA in template set Warning: unaligning (T0459)G8 because first residue in template chain is (2fswA)R3 Warning: unaligning (T0459)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fswA)K4 T0459 10 :TEICIDPSESVLHLLGKKYTMLIISVLG 2fswA 5 :ISDEECPVRKSMQIFAGKWTLLIIFQIN T0459 40 :STRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRS 2fswA 33 :RRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQ T0459 78 :GQITTYALTEKGMNVRNSLMPLLQY 2fswA 75 :PPRVEYSLTPLGEKVLPIIDEIAKF Number of specific fragments extracted= 3 number of extra gaps= 0 total=10 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_1085948714.pdb -s /var/tmp/to_scwrl_1085948714.seq -o /var/tmp/from_scwrl_1085948714.pdb > /var/tmp/scwrl_1085948714.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1085948714.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub9A/T0459-1ub9A-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 1ub9A expands to /projects/compbio/data/pdb/1ub9.pdb.gz 1ub9A:# T0459 read from 1ub9A/T0459-1ub9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub9A read from 1ub9A/T0459-1ub9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ub9A to template set # found chain 1ub9A in template set T0459 23 :LLGKKYTMLIISVLG 1ub9A 12 :ILGNPVRLGIMIFLL T0459 39 :GSTRQNFNDIRSSI 1ub9A 27 :PRRKAPFSQIQKVL T0459 54 :GISSTILSRRIKDLIDSGLVERRS 1ub9A 41 :DLTPGNLDSHIRVLERNGLVKTYK T0459 78 :GQITTYALTEKGMNVRNSLMPLLQYI 1ub9A 69 :RPRTVVEITDFGMEEAKRFLSSLKAV Number of specific fragments extracted= 4 number of extra gaps= 0 total=14 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_1629735656.pdb -s /var/tmp/to_scwrl_1629735656.seq -o /var/tmp/from_scwrl_1629735656.pdb > /var/tmp/scwrl_1629735656.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1629735656.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bpvA/T0459-3bpvA-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 3bpvA expands to /projects/compbio/data/pdb/3bpv.pdb.gz 3bpvA:# T0459 read from 3bpvA/T0459-3bpvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bpvA read from 3bpvA/T0459-3bpvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bpvA to template set # found chain 3bpvA in template set T0459 29 :TMLIISVLG 3bpvA 35 :QVACLLRIH T0459 39 :GSTRQNFNDIRSSI 3bpvA 44 :REPGIKQDELATFF T0459 54 :GISSTILSRRIKDLIDSGLVERRS 3bpvA 58 :HVDKGTIARTLRRLEESGFIEREQ T0459 78 :GQITTYALTEKGMNVRNSLMPLLQYISVLDRNG 3bpvA 86 :RRRYILEVTRRGEEIIPLILKVEERWEDLLFRD Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_249537115.pdb -s /var/tmp/to_scwrl_249537115.seq -o /var/tmp/from_scwrl_249537115.pdb > /var/tmp/scwrl_249537115.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_249537115.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1tA/T0459-1r1tA-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 # T0459 read from 1r1tA/T0459-1r1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1tA read from 1r1tA/T0459-1r1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r1tA in training set T0459 14 :IDPSESVLHLLGKKYTMLIISVLG 1r1tA 33 :AQSLAEFFAVLADPNRLRLLSLLA T0459 40 :STRQNFNDIRSSI 1r1tA 57 :RSELCVGDLAQAI T0459 54 :GISSTILSRRIKDLIDSGLVERRS 1r1tA 70 :GVSESAVSHQLRSLRNLRLVSYRK T0459 78 :GQITTYALTEK 1r1tA 95 :GRHVYYQLQDH T0459 94 :NSLMPLLQYISVL 1r1tA 106 :HIVALYQNALDHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=23 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_158371456.pdb -s /var/tmp/to_scwrl_158371456.seq -o /var/tmp/from_scwrl_158371456.pdb > /var/tmp/scwrl_158371456.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_158371456.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bj6A/T0459-3bj6A-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 3bj6A expands to /projects/compbio/data/pdb/3bj6.pdb.gz 3bj6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 141, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 143, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 145, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 147, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 149, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 151, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 153, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 155, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 157, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 159, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 161, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 186, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 188, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 190, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 192, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 194, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 196, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 198, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 200, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 202, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 204, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 206, because occupancy 0.300 <= existing 0.700 in 3bj6A Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 3bj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 541, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 543, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 545, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 547, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 549, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 551, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 553, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 555, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 557, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 803, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 805, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 807, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 809, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 811, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 813, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 815, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 817, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 819, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 821, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 823, because occupancy 0.400 <= existing 0.600 in 3bj6A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 3bj6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1076, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 3bj6A Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 3bj6A # T0459 read from 3bj6A/T0459-3bj6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bj6A read from 3bj6A/T0459-3bj6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bj6A to template set # found chain 3bj6A in template set T0459 29 :TMLIISVLG 3bj6A 39 :QRAILEGLS T0459 39 :GSTRQNFNDIRSSI 3bj6A 48 :LTPGATAPQLGAAL T0459 54 :GISSTILSRRIKDLIDSGLVERRS 3bj6A 62 :QMKRQYISRILQEVQRAGLIERRT T0459 78 :GQITTYALTEKGMNV 3bj6A 90 :ARSHRYWLTPRGEAI T0459 96 :LMPLLQYISV 3bj6A 105 :ITAIRADEMA Number of specific fragments extracted= 5 number of extra gaps= 0 total=28 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_1914093096.pdb -s /var/tmp/to_scwrl_1914093096.seq -o /var/tmp/from_scwrl_1914093096.pdb > /var/tmp/scwrl_1914093096.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1914093096.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pexA/T0459-2pexA-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 2pexA expands to /projects/compbio/data/pdb/2pex.pdb.gz 2pexA:Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2pexA # T0459 read from 2pexA/T0459-2pexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pexA read from 2pexA/T0459-2pexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pexA to template set # found chain 2pexA in template set Warning: unaligning (T0459)S77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pexA)V103 Warning: unaligning (T0459)T81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pexA)V103 T0459 28 :YTMLIISVLG 2pexA 48 :PQYLVMLVLW T0459 39 :GSTRQNFNDIRSSI 2pexA 58 :ETDERSVSEIGERL T0459 54 :GISSTILSRRIKDLIDSGLVERR 2pexA 72 :YLDSATLTPLLKRLQAAGLVTRT T0459 82 :TYALTEKGMNVR 2pexA 104 :IIALTETGRALR Number of specific fragments extracted= 4 number of extra gaps= 0 total=32 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_1126068032.pdb -s /var/tmp/to_scwrl_1126068032.seq -o /var/tmp/from_scwrl_1126068032.pdb > /var/tmp/scwrl_1126068032.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1126068032.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gxgA/T0459-2gxgA-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 2gxgA expands to /projects/compbio/data/pdb/2gxg.pdb.gz 2gxgA:# T0459 read from 2gxgA/T0459-2gxgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gxgA read from 2gxgA/T0459-2gxgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gxgA to template set # found chain 2gxgA in template set T0459 17 :SESVLHLLGK 2gxgA 23 :SRELNRRLGE T0459 27 :KYTMLIISVLG 2gxgA 37 :YLDFLVLRATS T0459 40 :STRQNFNDIRSSI 2gxgA 48 :DGPKTMAYLANRY T0459 54 :GISSTILSRRIKDLIDSGLVERRS 2gxgA 61 :FVTQSAITASVDKLEEMGLVVRVR T0459 78 :GQITTYALTEKGMNVRNSLMPLLQ 2gxgA 89 :RRKILIEITEKGLETFNKGIEIYK T0459 102 :YISVLDRN 2gxgA 114 :LANEVTGD Number of specific fragments extracted= 6 number of extra gaps= 0 total=38 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_2043006148.pdb -s /var/tmp/to_scwrl_2043006148.seq -o /var/tmp/from_scwrl_2043006148.pdb > /var/tmp/scwrl_2043006148.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2043006148.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cjnA/T0459-3cjnA-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 3cjnA expands to /projects/compbio/data/pdb/3cjn.pdb.gz 3cjnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 408, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 3cjnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1125, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 3cjnA # T0459 read from 3cjnA/T0459-3cjnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cjnA read from 3cjnA/T0459-3cjnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cjnA to template set # found chain 3cjnA in template set Warning: unaligning (T0459)S77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cjnA)D98 T0459 27 :KYTMLIISVLG 3cjnA 49 :TAKMRALAILS T0459 39 :GSTRQNFNDIRSSI 3cjnA 60 :AKDGLPIGTLGIFA T0459 54 :GISSTILSRRIKDLIDSGLVERR 3cjnA 74 :VVEQSTLSRALDGLQADGLVRRE T0459 78 :GQITTYALTEKGMNVRNSLM 3cjnA 102 :QRSSRVYLTPAGRAVYDRLW T0459 98 :PLLQYISVLDRNG 3cjnA 123 :HMRASHDRMFQGI Number of specific fragments extracted= 5 number of extra gaps= 1 total=43 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_323410230.pdb -s /var/tmp/to_scwrl_323410230.seq -o /var/tmp/from_scwrl_323410230.pdb > /var/tmp/scwrl_323410230.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_323410230.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cdhA/T0459-3cdhA-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 3cdhA expands to /projects/compbio/data/pdb/3cdh.pdb.gz 3cdhA:Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 222, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 224, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 3cdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 453, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 3cdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 560, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 562, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 564, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 566, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 568, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 3cdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 590, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 3cdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 757, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 759, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 761, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 763, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 765, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 767, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 769, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 771, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 773, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 775, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 777, because occupancy 0.400 <= existing 0.600 in 3cdhA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1124, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1128, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1130, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1132, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1134, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 3cdhA Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 3cdhA # T0459 read from 3cdhA/T0459-3cdhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cdhA read from 3cdhA/T0459-3cdhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cdhA to template set # found chain 3cdhA in template set Warning: unaligning (T0459)S77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3cdhA)R95 Warning: unaligning (T0459)I80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3cdhA)R95 T0459 17 :SESVLHLLGK 3cdhA 26 :SAQFHDHIRA T0459 28 :YTMLIISVLG 3cdhA 41 :PEWRVLACLV T0459 39 :GSTRQNFNDIRSSI 3cdhA 51 :DNDAMMITRLAKLS T0459 54 :GISSTILSRRIKDLIDSGLVERR 3cdhA 65 :LMEQSRMTRIVDQMDARGLVTRV T0459 81 :TTYALTEKGMN 3cdhA 96 :VRVRLTDDGRA T0459 95 :SLMPLLQYISVL 3cdhA 107 :LAESLVASARAH Number of specific fragments extracted= 6 number of extra gaps= 0 total=49 # request to SCWRL produces command: ulimit -t 100 ; scwrl3 -i /var/tmp/to_scwrl_1225065970.pdb -s /var/tmp/to_scwrl_1225065970.seq -o /var/tmp/from_scwrl_1225065970.pdb > /var/tmp/scwrl_1225065970.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1225065970.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.120 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 6350.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 6350.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 6350.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 6350.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 6350.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.030 rmsd (weighted)= 2.717 (unweighted)= 58.513 superimposing iter= 1 total_weight= 3125.014 rmsd (weighted)= 1.026 (unweighted)= 58.545 superimposing iter= 2 total_weight= 1179.260 rmsd (weighted)= 0.697 (unweighted)= 58.529 superimposing iter= 3 total_weight= 807.033 rmsd (weighted)= 0.582 (unweighted)= 58.549 superimposing iter= 4 total_weight= 690.471 rmsd (weighted)= 0.530 (unweighted)= 58.566 superimposing iter= 5 total_weight= 635.932 rmsd (weighted)= 0.504 (unweighted)= 58.578 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.933 rmsd (weighted)= 3.325 (unweighted)= 40.887 superimposing iter= 1 total_weight= 2372.606 rmsd (weighted)= 1.350 (unweighted)= 40.530 superimposing iter= 2 total_weight= 1213.666 rmsd (weighted)= 0.845 (unweighted)= 40.254 superimposing iter= 3 total_weight= 799.937 rmsd (weighted)= 0.676 (unweighted)= 40.073 superimposing iter= 4 total_weight= 624.413 rmsd (weighted)= 0.618 (unweighted)= 39.970 superimposing iter= 5 total_weight= 564.786 rmsd (weighted)= 0.596 (unweighted)= 39.909 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.899 rmsd (weighted)= 3.362 (unweighted)= 47.670 superimposing iter= 1 total_weight= 2430.273 rmsd (weighted)= 1.368 (unweighted)= 47.039 superimposing iter= 2 total_weight= 1052.723 rmsd (weighted)= 0.909 (unweighted)= 46.470 superimposing iter= 3 total_weight= 730.966 rmsd (weighted)= 0.735 (unweighted)= 45.985 superimposing iter= 4 total_weight= 654.546 rmsd (weighted)= 0.634 (unweighted)= 45.633 superimposing iter= 5 total_weight= 599.746 rmsd (weighted)= 0.576 (unweighted)= 45.389 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.002 rmsd (weighted)= 4.535 (unweighted)= 52.343 superimposing iter= 1 total_weight= 1874.991 rmsd (weighted)= 2.298 (unweighted)= 53.203 superimposing iter= 2 total_weight= 1053.436 rmsd (weighted)= 1.584 (unweighted)= 53.865 superimposing iter= 3 total_weight= 1000.567 rmsd (weighted)= 1.130 (unweighted)= 54.269 superimposing iter= 4 total_weight= 974.797 rmsd (weighted)= 0.836 (unweighted)= 54.466 superimposing iter= 5 total_weight= 760.102 rmsd (weighted)= 0.715 (unweighted)= 54.527 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.828 rmsd (weighted)= 3.372 (unweighted)= 52.234 superimposing iter= 1 total_weight= 2447.612 rmsd (weighted)= 1.198 (unweighted)= 52.535 superimposing iter= 2 total_weight= 1364.735 rmsd (weighted)= 0.664 (unweighted)= 52.648 superimposing iter= 3 total_weight= 776.367 rmsd (weighted)= 0.504 (unweighted)= 52.664 superimposing iter= 4 total_weight= 580.338 rmsd (weighted)= 0.446 (unweighted)= 52.665 superimposing iter= 5 total_weight= 517.204 rmsd (weighted)= 0.418 (unweighted)= 52.664 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.703 rmsd (weighted)= 2.690 (unweighted)= 43.713 superimposing iter= 1 total_weight= 2122.478 rmsd (weighted)= 0.966 (unweighted)= 43.821 superimposing iter= 2 total_weight= 1034.707 rmsd (weighted)= 0.571 (unweighted)= 43.878 superimposing iter= 3 total_weight= 635.706 rmsd (weighted)= 0.445 (unweighted)= 43.906 superimposing iter= 4 total_weight= 494.811 rmsd (weighted)= 0.396 (unweighted)= 43.922 superimposing iter= 5 total_weight= 438.737 rmsd (weighted)= 0.376 (unweighted)= 43.935 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.057 rmsd (weighted)= 5.004 (unweighted)= 52.044 superimposing iter= 1 total_weight= 2831.330 rmsd (weighted)= 1.780 (unweighted)= 52.637 superimposing iter= 2 total_weight= 1748.976 rmsd (weighted)= 0.997 (unweighted)= 52.801 superimposing iter= 3 total_weight= 868.579 rmsd (weighted)= 0.816 (unweighted)= 52.915 superimposing iter= 4 total_weight= 686.033 rmsd (weighted)= 0.757 (unweighted)= 52.993 superimposing iter= 5 total_weight= 634.447 rmsd (weighted)= 0.732 (unweighted)= 53.046 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.921 rmsd (weighted)= 2.833 (unweighted)= 59.832 superimposing iter= 1 total_weight= 2415.012 rmsd (weighted)= 1.189 (unweighted)= 59.926 superimposing iter= 2 total_weight= 1022.036 rmsd (weighted)= 0.832 (unweighted)= 59.992 superimposing iter= 3 total_weight= 667.771 rmsd (weighted)= 0.729 (unweighted)= 60.066 superimposing iter= 4 total_weight= 599.637 rmsd (weighted)= 0.677 (unweighted)= 60.133 superimposing iter= 5 total_weight= 584.743 rmsd (weighted)= 0.638 (unweighted)= 60.191 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.943 rmsd (weighted)= 6.044 (unweighted)= 69.191 superimposing iter= 1 total_weight= 2274.193 rmsd (weighted)= 2.237 (unweighted)= 68.733 superimposing iter= 2 total_weight= 1653.622 rmsd (weighted)= 1.152 (unweighted)= 69.031 superimposing iter= 3 total_weight= 1072.789 rmsd (weighted)= 0.785 (unweighted)= 69.195 superimposing iter= 4 total_weight= 770.703 rmsd (weighted)= 0.641 (unweighted)= 69.206 superimposing iter= 5 total_weight= 648.083 rmsd (weighted)= 0.575 (unweighted)= 69.172 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.120 rmsd (weighted)= 3.052 (unweighted)= 27.303 superimposing iter= 1 total_weight= 3166.995 rmsd (weighted)= 1.126 (unweighted)= 27.212 superimposing iter= 2 total_weight= 1840.323 rmsd (weighted)= 0.620 (unweighted)= 27.187 superimposing iter= 3 total_weight= 1100.087 rmsd (weighted)= 0.461 (unweighted)= 27.186 superimposing iter= 4 total_weight= 794.893 rmsd (weighted)= 0.405 (unweighted)= 27.186 superimposing iter= 5 total_weight= 700.525 rmsd (weighted)= 0.380 (unweighted)= 27.185 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.249 rmsd (weighted)= 2.462 (unweighted)= 52.476 superimposing iter= 1 total_weight= 3702.830 rmsd (weighted)= 0.899 (unweighted)= 53.162 superimposing iter= 2 total_weight= 1982.848 rmsd (weighted)= 0.514 (unweighted)= 53.354 superimposing iter= 3 total_weight= 1097.091 rmsd (weighted)= 0.406 (unweighted)= 53.446 superimposing iter= 4 total_weight= 848.534 rmsd (weighted)= 0.364 (unweighted)= 53.484 superimposing iter= 5 total_weight= 763.446 rmsd (weighted)= 0.344 (unweighted)= 53.497 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.084 rmsd (weighted)= 2.159 (unweighted)= 38.409 superimposing iter= 1 total_weight= 2789.289 rmsd (weighted)= 0.860 (unweighted)= 37.893 superimposing iter= 2 total_weight= 1382.826 rmsd (weighted)= 0.547 (unweighted)= 37.722 superimposing iter= 3 total_weight= 928.340 rmsd (weighted)= 0.437 (unweighted)= 37.644 superimposing iter= 4 total_weight= 765.998 rmsd (weighted)= 0.388 (unweighted)= 37.599 superimposing iter= 5 total_weight= 688.436 rmsd (weighted)= 0.364 (unweighted)= 37.573 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.091 rmsd (weighted)= 2.140 (unweighted)= 43.044 superimposing iter= 1 total_weight= 1968.333 rmsd (weighted)= 1.082 (unweighted)= 42.287 superimposing iter= 2 total_weight= 1139.103 rmsd (weighted)= 0.746 (unweighted)= 41.736 superimposing iter= 3 total_weight= 961.907 rmsd (weighted)= 0.583 (unweighted)= 41.509 superimposing iter= 4 total_weight= 745.060 rmsd (weighted)= 0.527 (unweighted)= 41.410 superimposing iter= 5 total_weight= 660.662 rmsd (weighted)= 0.507 (unweighted)= 41.346 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.167 rmsd (weighted)= 3.311 (unweighted)= 43.755 superimposing iter= 1 total_weight= 1894.285 rmsd (weighted)= 1.819 (unweighted)= 44.114 superimposing iter= 2 total_weight= 1057.730 rmsd (weighted)= 1.375 (unweighted)= 44.613 superimposing iter= 3 total_weight= 894.602 rmsd (weighted)= 1.118 (unweighted)= 45.211 superimposing iter= 4 total_weight= 1008.007 rmsd (weighted)= 0.860 (unweighted)= 45.638 superimposing iter= 5 total_weight= 1023.748 rmsd (weighted)= 0.673 (unweighted)= 45.793 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.979 rmsd (weighted)= 1.491 (unweighted)= 40.777 superimposing iter= 1 total_weight= 2232.800 rmsd (weighted)= 0.680 (unweighted)= 40.944 superimposing iter= 2 total_weight= 1090.766 rmsd (weighted)= 0.470 (unweighted)= 41.023 superimposing iter= 3 total_weight= 768.806 rmsd (weighted)= 0.394 (unweighted)= 41.050 superimposing iter= 4 total_weight= 637.394 rmsd (weighted)= 0.364 (unweighted)= 41.063 superimposing iter= 5 total_weight= 583.753 rmsd (weighted)= 0.352 (unweighted)= 41.071 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.812 rmsd (weighted)= 1.142 (unweighted)= 37.872 superimposing iter= 1 total_weight= 2108.279 rmsd (weighted)= 0.483 (unweighted)= 37.864 superimposing iter= 2 total_weight= 983.095 rmsd (weighted)= 0.322 (unweighted)= 37.894 superimposing iter= 3 total_weight= 658.455 rmsd (weighted)= 0.266 (unweighted)= 37.912 superimposing iter= 4 total_weight= 571.178 rmsd (weighted)= 0.237 (unweighted)= 37.920 superimposing iter= 5 total_weight= 510.188 rmsd (weighted)= 0.223 (unweighted)= 37.924 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 2.801 (unweighted)= 46.604 superimposing iter= 1 total_weight= 3051.925 rmsd (weighted)= 1.165 (unweighted)= 47.003 superimposing iter= 2 total_weight= 1413.746 rmsd (weighted)= 0.773 (unweighted)= 47.265 superimposing iter= 3 total_weight= 1107.390 rmsd (weighted)= 0.597 (unweighted)= 47.389 superimposing iter= 4 total_weight= 907.310 rmsd (weighted)= 0.519 (unweighted)= 47.426 superimposing iter= 5 total_weight= 783.677 rmsd (weighted)= 0.488 (unweighted)= 47.436 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.113 rmsd (weighted)= 2.244 (unweighted)= 50.950 superimposing iter= 1 total_weight= 2141.457 rmsd (weighted)= 1.059 (unweighted)= 50.746 superimposing iter= 2 total_weight= 1228.095 rmsd (weighted)= 0.721 (unweighted)= 50.624 superimposing iter= 3 total_weight= 912.294 rmsd (weighted)= 0.589 (unweighted)= 50.613 superimposing iter= 4 total_weight= 752.623 rmsd (weighted)= 0.536 (unweighted)= 50.636 superimposing iter= 5 total_weight= 687.682 rmsd (weighted)= 0.511 (unweighted)= 50.665 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.094 rmsd (weighted)= 3.604 (unweighted)= 66.029 superimposing iter= 1 total_weight= 2790.144 rmsd (weighted)= 1.323 (unweighted)= 66.417 superimposing iter= 2 total_weight= 1645.877 rmsd (weighted)= 0.766 (unweighted)= 66.396 superimposing iter= 3 total_weight= 933.287 rmsd (weighted)= 0.614 (unweighted)= 66.402 superimposing iter= 4 total_weight= 700.292 rmsd (weighted)= 0.571 (unweighted)= 66.403 superimposing iter= 5 total_weight= 643.545 rmsd (weighted)= 0.555 (unweighted)= 66.405 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.120 rmsd (weighted)= 3.036 (unweighted)= 27.293 superimposing iter= 1 total_weight= 3159.788 rmsd (weighted)= 1.121 (unweighted)= 27.206 superimposing iter= 2 total_weight= 1840.337 rmsd (weighted)= 0.618 (unweighted)= 27.182 superimposing iter= 3 total_weight= 1100.695 rmsd (weighted)= 0.459 (unweighted)= 27.181 superimposing iter= 4 total_weight= 797.099 rmsd (weighted)= 0.403 (unweighted)= 27.180 superimposing iter= 5 total_weight= 705.686 rmsd (weighted)= 0.377 (unweighted)= 27.179 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.249 rmsd (weighted)= 2.442 (unweighted)= 52.528 superimposing iter= 1 total_weight= 3690.693 rmsd (weighted)= 0.893 (unweighted)= 53.175 superimposing iter= 2 total_weight= 2000.389 rmsd (weighted)= 0.507 (unweighted)= 53.351 superimposing iter= 3 total_weight= 1123.806 rmsd (weighted)= 0.394 (unweighted)= 53.439 superimposing iter= 4 total_weight= 863.955 rmsd (weighted)= 0.349 (unweighted)= 53.482 superimposing iter= 5 total_weight= 773.360 rmsd (weighted)= 0.327 (unweighted)= 53.502 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.084 rmsd (weighted)= 2.158 (unweighted)= 38.391 superimposing iter= 1 total_weight= 2783.210 rmsd (weighted)= 0.861 (unweighted)= 37.883 superimposing iter= 2 total_weight= 1373.123 rmsd (weighted)= 0.550 (unweighted)= 37.713 superimposing iter= 3 total_weight= 930.680 rmsd (weighted)= 0.439 (unweighted)= 37.628 superimposing iter= 4 total_weight= 769.538 rmsd (weighted)= 0.388 (unweighted)= 37.581 superimposing iter= 5 total_weight= 691.730 rmsd (weighted)= 0.364 (unweighted)= 37.556 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.091 rmsd (weighted)= 2.139 (unweighted)= 43.058 superimposing iter= 1 total_weight= 1941.815 rmsd (weighted)= 1.088 (unweighted)= 42.286 superimposing iter= 2 total_weight= 1132.108 rmsd (weighted)= 0.752 (unweighted)= 41.732 superimposing iter= 3 total_weight= 963.781 rmsd (weighted)= 0.587 (unweighted)= 41.500 superimposing iter= 4 total_weight= 749.756 rmsd (weighted)= 0.529 (unweighted)= 41.397 superimposing iter= 5 total_weight= 662.410 rmsd (weighted)= 0.508 (unweighted)= 41.332 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.167 rmsd (weighted)= 3.309 (unweighted)= 43.843 superimposing iter= 1 total_weight= 1893.305 rmsd (weighted)= 1.816 (unweighted)= 44.188 superimposing iter= 2 total_weight= 1055.756 rmsd (weighted)= 1.375 (unweighted)= 44.671 superimposing iter= 3 total_weight= 884.981 rmsd (weighted)= 1.126 (unweighted)= 45.259 superimposing iter= 4 total_weight= 996.838 rmsd (weighted)= 0.870 (unweighted)= 45.696 superimposing iter= 5 total_weight= 1026.981 rmsd (weighted)= 0.679 (unweighted)= 45.856 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.979 rmsd (weighted)= 1.497 (unweighted)= 40.797 superimposing iter= 1 total_weight= 2233.077 rmsd (weighted)= 0.682 (unweighted)= 40.968 superimposing iter= 2 total_weight= 1095.194 rmsd (weighted)= 0.470 (unweighted)= 41.048 superimposing iter= 3 total_weight= 770.934 rmsd (weighted)= 0.393 (unweighted)= 41.075 superimposing iter= 4 total_weight= 637.963 rmsd (weighted)= 0.363 (unweighted)= 41.088 superimposing iter= 5 total_weight= 583.472 rmsd (weighted)= 0.351 (unweighted)= 41.096 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.812 rmsd (weighted)= 1.137 (unweighted)= 37.899 superimposing iter= 1 total_weight= 2105.708 rmsd (weighted)= 0.481 (unweighted)= 37.893 superimposing iter= 2 total_weight= 976.140 rmsd (weighted)= 0.323 (unweighted)= 37.923 superimposing iter= 3 total_weight= 652.043 rmsd (weighted)= 0.268 (unweighted)= 37.941 superimposing iter= 4 total_weight= 567.859 rmsd (weighted)= 0.239 (unweighted)= 37.949 superimposing iter= 5 total_weight= 511.108 rmsd (weighted)= 0.225 (unweighted)= 37.953 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 2.801 (unweighted)= 46.567 superimposing iter= 1 total_weight= 3063.337 rmsd (weighted)= 1.161 (unweighted)= 46.973 superimposing iter= 2 total_weight= 1414.108 rmsd (weighted)= 0.771 (unweighted)= 47.232 superimposing iter= 3 total_weight= 1106.139 rmsd (weighted)= 0.596 (unweighted)= 47.353 superimposing iter= 4 total_weight= 908.202 rmsd (weighted)= 0.519 (unweighted)= 47.389 superimposing iter= 5 total_weight= 778.112 rmsd (weighted)= 0.490 (unweighted)= 47.403 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.113 rmsd (weighted)= 2.219 (unweighted)= 50.922 superimposing iter= 1 total_weight= 2123.327 rmsd (weighted)= 1.056 (unweighted)= 50.737 superimposing iter= 2 total_weight= 1219.449 rmsd (weighted)= 0.721 (unweighted)= 50.621 superimposing iter= 3 total_weight= 913.895 rmsd (weighted)= 0.589 (unweighted)= 50.612 superimposing iter= 4 total_weight= 754.789 rmsd (weighted)= 0.535 (unweighted)= 50.636 superimposing iter= 5 total_weight= 688.257 rmsd (weighted)= 0.510 (unweighted)= 50.667 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.094 rmsd (weighted)= 3.617 (unweighted)= 66.043 superimposing iter= 1 total_weight= 2771.648 rmsd (weighted)= 1.332 (unweighted)= 66.408 superimposing iter= 2 total_weight= 1647.722 rmsd (weighted)= 0.769 (unweighted)= 66.384 superimposing iter= 3 total_weight= 937.033 rmsd (weighted)= 0.616 (unweighted)= 66.387 superimposing iter= 4 total_weight= 700.141 rmsd (weighted)= 0.573 (unweighted)= 66.388 superimposing iter= 5 total_weight= 642.380 rmsd (weighted)= 0.557 (unweighted)= 66.389 superimposing iter= 0 total_weight= 1.120 rmsd (weighted)= 3.037 (unweighted)= 27.282 superimposing iter= 1 total_weight= 3159.750 rmsd (weighted)= 1.122 (unweighted)= 27.196 superimposing iter= 2 total_weight= 1843.201 rmsd (weighted)= 0.618 (unweighted)= 27.171 superimposing iter= 3 total_weight= 1102.342 rmsd (weighted)= 0.459 (unweighted)= 27.170 superimposing iter= 4 total_weight= 798.956 rmsd (weighted)= 0.403 (unweighted)= 27.170 superimposing iter= 5 total_weight= 708.412 rmsd (weighted)= 0.376 (unweighted)= 27.169 superimposing iter= 0 total_weight= 1.249 rmsd (weighted)= 2.442 (unweighted)= 52.539 superimposing iter= 1 total_weight= 3690.983 rmsd (weighted)= 0.892 (unweighted)= 53.169 superimposing iter= 2 total_weight= 2014.163 rmsd (weighted)= 0.503 (unweighted)= 53.332 superimposing iter= 3 total_weight= 1147.098 rmsd (weighted)= 0.387 (unweighted)= 53.416 superimposing iter= 4 total_weight= 876.111 rmsd (weighted)= 0.340 (unweighted)= 53.460 superimposing iter= 5 total_weight= 783.749 rmsd (weighted)= 0.317 (unweighted)= 53.481 superimposing iter= 0 total_weight= 1.084 rmsd (weighted)= 2.157 (unweighted)= 38.359 superimposing iter= 1 total_weight= 2781.815 rmsd (weighted)= 0.861 (unweighted)= 37.852 superimposing iter= 2 total_weight= 1372.874 rmsd (weighted)= 0.550 (unweighted)= 37.683 superimposing iter= 3 total_weight= 931.319 rmsd (weighted)= 0.439 (unweighted)= 37.597 superimposing iter= 4 total_weight= 770.108 rmsd (weighted)= 0.388 (unweighted)= 37.551 superimposing iter= 5 total_weight= 691.777 rmsd (weighted)= 0.364 (unweighted)= 37.526 superimposing iter= 0 total_weight= 1.091 rmsd (weighted)= 2.139 (unweighted)= 43.024 superimposing iter= 1 total_weight= 1939.064 rmsd (weighted)= 1.089 (unweighted)= 42.251 superimposing iter= 2 total_weight= 1130.814 rmsd (weighted)= 0.753 (unweighted)= 41.696 superimposing iter= 3 total_weight= 964.172 rmsd (weighted)= 0.588 (unweighted)= 41.462 superimposing iter= 4 total_weight= 750.762 rmsd (weighted)= 0.529 (unweighted)= 41.360 superimposing iter= 5 total_weight= 662.512 rmsd (weighted)= 0.508 (unweighted)= 41.295 superimposing iter= 0 total_weight= 1.167 rmsd (weighted)= 3.309 (unweighted)= 43.886 superimposing iter= 1 total_weight= 1891.616 rmsd (weighted)= 1.816 (unweighted)= 44.233 superimposing iter= 2 total_weight= 1055.963 rmsd (weighted)= 1.376 (unweighted)= 44.716 superimposing iter= 3 total_weight= 885.234 rmsd (weighted)= 1.126 (unweighted)= 45.306 superimposing iter= 4 total_weight= 997.187 rmsd (weighted)= 0.870 (unweighted)= 45.742 superimposing iter= 5 total_weight= 1027.267 rmsd (weighted)= 0.679 (unweighted)= 45.902 superimposing iter= 0 total_weight= 0.979 rmsd (weighted)= 1.497 (unweighted)= 40.830 superimposing iter= 1 total_weight= 2233.035 rmsd (weighted)= 0.682 (unweighted)= 41.000 superimposing iter= 2 total_weight= 1095.231 rmsd (weighted)= 0.470 (unweighted)= 41.080 superimposing iter= 3 total_weight= 770.881 rmsd (weighted)= 0.393 (unweighted)= 41.107 superimposing iter= 4 total_weight= 637.909 rmsd (weighted)= 0.363 (unweighted)= 41.120 superimposing iter= 5 total_weight= 583.478 rmsd (weighted)= 0.351 (unweighted)= 41.128 superimposing iter= 0 total_weight= 0.812 rmsd (weighted)= 1.136 (unweighted)= 37.924 superimposing iter= 1 total_weight= 2105.566 rmsd (weighted)= 0.481 (unweighted)= 37.918 superimposing iter= 2 total_weight= 976.188 rmsd (weighted)= 0.323 (unweighted)= 37.949 superimposing iter= 3 total_weight= 651.917 rmsd (weighted)= 0.267 (unweighted)= 37.967 superimposing iter= 4 total_weight= 567.655 rmsd (weighted)= 0.239 (unweighted)= 37.975 superimposing iter= 5 total_weight= 510.756 rmsd (weighted)= 0.225 (unweighted)= 37.979 superimposing iter= 0 total_weight= 1.240 rmsd (weighted)= 2.799 (unweighted)= 46.533 superimposing iter= 1 total_weight= 3062.522 rmsd (weighted)= 1.161 (unweighted)= 46.938 superimposing iter= 2 total_weight= 1412.508 rmsd (weighted)= 0.772 (unweighted)= 47.197 superimposing iter= 3 total_weight= 1104.719 rmsd (weighted)= 0.597 (unweighted)= 47.319 superimposing iter= 4 total_weight= 908.632 rmsd (weighted)= 0.519 (unweighted)= 47.355 superimposing iter= 5 total_weight= 778.044 rmsd (weighted)= 0.490 (unweighted)= 47.371 superimposing iter= 0 total_weight= 1.113 rmsd (weighted)= 2.218 (unweighted)= 50.934 superimposing iter= 1 total_weight= 2122.409 rmsd (weighted)= 1.056 (unweighted)= 50.751 superimposing iter= 2 total_weight= 1219.223 rmsd (weighted)= 0.721 (unweighted)= 50.635 superimposing iter= 3 total_weight= 914.256 rmsd (weighted)= 0.589 (unweighted)= 50.626 superimposing iter= 4 total_weight= 754.985 rmsd (weighted)= 0.535 (unweighted)= 50.651 superimposing iter= 5 total_weight= 688.304 rmsd (weighted)= 0.509 (unweighted)= 50.681 superimposing iter= 0 total_weight= 1.094 rmsd (weighted)= 3.615 (unweighted)= 66.021 superimposing iter= 1 total_weight= 2771.981 rmsd (weighted)= 1.331 (unweighted)= 66.385 superimposing iter= 2 total_weight= 1647.673 rmsd (weighted)= 0.769 (unweighted)= 66.360 superimposing iter= 3 total_weight= 936.571 rmsd (weighted)= 0.616 (unweighted)= 66.364 superimposing iter= 4 total_weight= 700.078 rmsd (weighted)= 0.573 (unweighted)= 66.364 superimposing iter= 5 total_weight= 642.361 rmsd (weighted)= 0.557 (unweighted)= 66.366 # command:# Printing sheets for alignments to T0459.undertaker-align.sheets # command: