LOOPP parallel driver v5.0 (06/13/08 15:45 EDT) with LOOPP v3.0 (compiled Jul 11 2008 17:20:20)
[NEWSABLE] [HSHFL] [ENE] [NEWALICHOICE]
This is HTML output, the other options are plain text, CASP AL and CASP TS formats.
If an error occured during execution it is logged in plain text version only,
there is no need to look for an error if this file ends with 'DONE' statement.
STARTING:Sat Aug 09 05:12:31 2008 EST
INPUT:
sim_min = 40.0% minimum sequence identity (%)
sim_max = 80.0% maximum sequence identity (%)
len_dif = 20.0% maximum length difference (% of query sequence length)
between query and homolog
nmax = 1 maximum number of homologous sequences (including query sequence)
maxout = 5 maximum number of outputted matches
strict = 0 all alignments will be accepted from LOOPP results
for homologs; they will be translated to query sequence
alignments using BLAST results
casp = 5 maximum number of outputted matches in CASP format
align = 'g' only corresponding global alignments will be reported
maxdiff = 50.0% only alignments differing no more than 50.0% from the query
sequence will be reported, or when reject=0, corresponding local
alignments will be reported
reject = 1 alignments shorter more than 50.0% from the query sequence
will be rejected
seccut = 0.00 structures with sec. str. score below seccut will be rejected
secdb = 1 type of secondary structure description: 1 - DSSB, 0 - phi/psi map
tasktb = 11111111111111111111 type of initial calculations
pdbcut = 60.0% pdb sequence identity threshold (%)
pdbstop = 0 stop if PDB structure with similarity above pdbcut found
domains = 0 query sequence will be decomposed into putative domains if =1
maxall = 300 maximum number of models evaluated in the second stage
refstr = 0 if equal to 1 rmsd distances between all hits and a reference structure
will be reported
maxpdb = 5 number of top PDB hits added to the second stage scoring
maxdyn = 5 number of dynamic domain entries from database added to the second stage scoring
beautify = 0 use pdb beautifier
rmsdtables = 1 compute rmsd tables between hits
local LOOPP/BLAST database will be used
input file T0402
--> 139 residues, sequence name: T0402
Database: T:\CBSU\blastdb\20080108\nr
-> 5 homolog sequences with sequence identity from 40.0% to 80.0% satisfying length constraints found
-> 0 representatives will be used in search (nmax=1 including query sequence)
Histogram of all homolog sequences found by BLAST (e-value cutoff 0.01, length constr.) by sequence identity:
| 00%-10% | 10%-20% | 20%-30% | 30%-40% | 40%-50% | 50%-60% | 60%-70% | 70%-80% | 80%-90% | 90%-100% |
| 0 | 0 | 9 | 22 | 5 | 0 | 0 | 0 | 1 | 5 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 1.71 | 4.17 | 0.89 | 5.19 |
2 | 1.71 | 0.00 | 4.03 | 1.64 | 4.97 |
3 | 4.17 | 4.03 | 0.00 | 4.24 | 4.85 |
4 | 0.89 | 1.64 | 4.24 | 0.00 | 5.24 |
5 | 5.19 | 4.97 | 4.85 | 5.24 | 0.00 |
Similarity table for hits: percentage of chain fitting below 3Å RMSD (Cells are shaded according to similarity starting at 30%)
1 | 2 | 3 | 4 | 5 | |
1 | 100.00 | 100.00 | 69.42 | 100.00 | 39.34 |
2 | 100.00 | 100.00 | 72.13 | 100.00 | 47.15 |
3 | 69.42 | 72.13 | 100.00 | 68.33 | 52.46 |
4 | 100.00 | 100.00 | 68.33 | 100.00 | 38.33 |
5 | 39.34 | 47.15 | 52.46 | 38.33 | 100.00 |
Similarity table for hits: percentage of chain fitting below 6Å RMSD (Cells are shaded according to similarity starting at 50%)
1 | 2 | 3 | 4 | 5 | |
1 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
2 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
3 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
4 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
5 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
ALIGNMENTS
--> hit 1 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 19.42% helical, 37.41% extended, 43.17% loops/other (query: 23.74% 41.01% 35.25%)
SCOP classification: [All beta proteins]/[Split barrel-like]
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
1W9A_A b.45.1.1 67.26.26.24 NONE -34.978 0 1 88.49% 21.95% OPTM -406.413 -261.100 2.456 0.752 0.658 0.822 0.930 22.450 -40.8 4.160 99.000 -104.5 7.630 86.000 -153.0 2.220 8.350 -22.8 2.470 5.490 -34.8 3.650 20.630 -16.5 9.590 21.780 -41.3 8.800 45.140 -47.0 16.070 22.860 -57.1 -30.000 57.000 -89.0 -30.000 29.000 -94.0 4.300 71.500 -48.0 10.560 71.000 -106.0 2.410 23.000 -39.0 3.900 21.000 -62.0 5.000 -11.0 -11.023 -63.4 -68.000 306.0 5.000 -11.0 0.380 -6.0 0.26 0.84
alignment source: OPTM
HHHHHHHH---EEEEEEE--- --EEEEEEEE--- -EEEEE------HHHHHH----EEEEEEE-----EEEEEEEEE
Query: 7 DKILAILEQHQVGVLTSVQGD-FPHARYMTFLHDG--LTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPGSAFLEINGLA 83
Sbjct: 8 DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADD-GWSYAVAEGTA 86
HHHHHHH---EEEEEEE-----EEEEEEE-EEE----EEEEEEE-------------EEEEEEE---- --EEEEEEE-E
EE-- -HHHHHHHHHHHHHHH----- ---EEEEEEE--EEEEEE---
Query: 84 SLEE-----DESIKERIWENISKDWFQGED--------SPSFVVIKIVPEQIRILNSDD 129
Sbjct: 87 QLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAVTDRRVLLTLPISHVYGLPPGR 145
E---------HHHHHHHHHHHHHH-----HHHHHH-----EEEEEEE--EEEEE----R
123 residues (88.49%) of query sequence aligned
--> hit 2 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 28.17% helical, 36.62% extended, 35.21% loops/other (query: 23.74% 41.01% 35.25%)
SCOP classification: [All beta proteins]/[Split barrel-like]
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
b.45.1.1.3_A b.45.1.1 67.26.26.24 NONE -35.021 0 1 90.65% 21.43% OPTM -373.267 -218.620 2.580 0.733 0.678 0.831 0.939 21.600 -43.2 4.800 94.500 -111.0 7.570 85.500 -148.5 1.380 3.280 -18.9 2.010 4.100 -28.5 3.830 18.080 -17.1 10.080 13.000 -32.4 9.350 44.550 -49.3 15.520 22.840 -56.7 -30.000 57.000 -92.0 -30.000 29.000 -99.0 4.440 79.000 -47.0 11.100 71.000 -105.0 3.980 39.000 -65.0 4.870 24.000 -81.0 5.000 -11.0 -11.817 -62.9 0.000 -9.3e+061 5.000 -11.0 0.724 -6.0 0.29 0.82
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHH---EEEEEEE--- --EEEEEEEE--- -EEEEE------HHHHHH----EEEEEEE-----EEEEEEE
Query: 5 LEDKILAILEQHQVGVLTSVQGD-FPHARYMTFLHDG--LTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPGSAFLEING 81
Sbjct: 6 FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDAD-DGWSYAVAEG 84
HHHHHHHHH---EEEEEEE-----EEEEEEE-EEE----EEEEEEE---HHHHHHHH--EEEEEEE--- ---EEEEEEE
EEEE-- -HHHHHHHHHHHHHHH------ --EEEEEEE--EEEEEE----
Query: 82 LASLEE-----DESIKERIWENISKDWFQGEDS---------PSFVVIKIVPEQIRILNSDDD 130
Sbjct: 85 TAQLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAMVTDRRVLLTLPISHVYGLPPGMR 147
-EE---------HHHHHHHHHHHHH------HHHHHHHHHH--EEEEEEE--EEEEE-----R
126 residues (90.65%) of query sequence aligned
--> hit 3 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 23.66% helical, 45.04% extended, 31.30% loops/other (query: 23.74% 41.01% 35.25%)
SCOP classification: [All beta proteins]/[Split barrel-like]
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
2HQ9_A b.45.1.1 67.26.26.24 NONE -35.029 0 1 87.77% 21.31% OPTM -479.642 -242.620 2.909 0.713 0.609 0.860 0.928 19.740 -40.1 4.380 73.000 -86.5 7.030 88.500 -143.5 -0.560 0.110 -9.3 1.790 4.020 -26.0 -0.410 -6.220 8.3 4.390 8.380 -21.5 6.730 39.510 -32.3 17.330 23.060 -54.7 -30.000 49.000 -83.0 -30.000 28.000 -95.0 8.050 121.500 -96.0 14.940 110.000 -150.0 4.390 42.000 -46.0 6.310 32.000 -75.0 5.000 -5.3 -6.787 -71.9 0.000 -9.3e+061 5.000 -4.5 0.041 -3.3 0.36 0.92
alignment source: OPTM
HHHHHHHHH---EEEEEEE-----EEEEEEEE----EEEEE------HHHHHH----EEEEEEE---- -EEEEEEEEE
Query: 6 EDKILAILEQHQVGVLTSVQGDFPHARYMTFLHDGLTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPG--SAFLEINGLA 83
Sbjct: 10 ALECTKVLTANRVGRLACAKDGQPYVVPLYYAYSDAHLYAFSP---GKKIEWRANPRVSVQVDEHGQGRGWKSVVVDGRY 86
HHHHHHHHH--EEEEEEEE--EEEEEEEE-EEE--EEEEE--- HHHH-----EEEEEEEEE-----EEEEEEEEEEE
EE--- HHHHHHHHHHHHHHH--------EEEEEEE--EEEEEE-
Query: 84 SLEED----ESIKERIWENISKDWFQGEDSPSFVVIKIVPEQIRILNS 127
Sbjct: 87 EELPDLIGHKLQRDHAWSVLSKHTDWWEAPHVFFRILIEQVSGREASE 134
E-------HHHHHHHHHHHHHHHHHH-----EEEEEEEEEEEEEE--E
122 residues (87.77%) of query sequence aligned
--> hit 4 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 21.74% helical, 39.13% extended, 39.13% loops/other (query: 23.74% 41.01% 35.25%)
SCOP classification: [All beta proteins]/[Split barrel-like]
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
1XXO_A b.45.1.1 67.26.26.24 NONE -35.032 0 1 86.33% 22.50% OPTM -347.139 -239.780 2.370 0.730 0.650 0.805 0.927 19.820 -38.2 4.850 106.000 -122.5 7.700 84.500 -153.0 1.110 0.210 -18.4 2.610 5.610 -28.7 4.600 17.940 -19.8 12.250 16.990 -37.2 8.860 45.580 -46.4 15.460 22.290 -53.1 -30.000 62.000 -85.0 -30.000 22.000 -88.0 4.170 70.000 -45.0 10.060 67.000 -104.0 2.970 41.000 -44.0 4.040 21.000 -63.0 5.000 -10.7 -11.692 -61.1 0.000 -9.3e+061 5.000 -10.7 0.716 -6.0 0.27 0.92
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHH---EEEEEEE--- --EEEEEEEE--- -EEEEE------HHHHHH----EEEEEEE-----EEEEEEEEE
Query: 7 DKILAILEQHQVGVLTSVQGD-FPHARYMTFLHDG--LTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPGSAFLEINGLA 83
Sbjct: 8 DKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADD-GWSYAVAEGTA 86
HHHHHHH---EEEEEEE-----EEEEEEE-EEE----EEEEEEE-------------EEEEEEE---- --EEEEEEE-E
EE-- -HHHHHHHHHHHHHHH----- ---EEEEEEE--EEEEEE
Query: 84 SLEE-----DESIKERIWENISKDWFQGED---------SPSFVVIKIVPEQIRILN 126
Sbjct: 87 QLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAMVTDRRVLLTLPISHVYGLP 143
E---------HHHHHHHHHHHHH------HHHHHHHHHH--EEEEEEEEEEEEEE-P
120 residues (86.33%) of query sequence aligned
--> hit 5 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 22.48% helical, 35.66% extended, 41.86% loops/other (query: 23.74% 41.01% 35.25%)
SCOP classification:
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
2RE7_A not_found 81.81.81.81 NONE -35.183 0 1 88.49% 18.70% OPTM -398.017 -282.510 3.471 0.662 0.521 0.864 0.909 22.260 -41.1 3.170 53.000 -92.5 5.170 37.000 -137.5 0.940 2.340 -11.4 1.080 3.700 -24.5 3.630 15.250 -10.2 7.110 13.490 -31.8 9.920 49.830 -41.4 17.720 30.610 -60.9 -30.000 50.000 -91.0 -30.000 37.000 -102.0 9.790 193.500 -155.0 20.040 121.000 -189.0 6.200 75.000 -57.0 8.980 39.000 -84.0 5.000 -13.0 -5.297 -57.0 0.000 -9.3e+061 5.000 -13.0 -0.959 -4.1 0.25 0.87
alignment source: OPTM
HHHHHHHHH---EEEEEEE-----EE EEEEEE----EEEEE------HHHHHH----EEEEEEE-----EEEEEEEEE
Query: 6 EDKILAILEQHQVGVLTSVQGDFPHA--RYMTFLHDGLTLYTPSGKELPKTEEVRRNPHVCVLIGYDSPGSAFLEINGLA 83
Sbjct: 7 IDKIQAVIKDVKFAISTSNKKGDIHAWPTTSEVNLDNKEIWFIGDKTSDVVKDIQDDARIGLTYATQDE-KNYVSISGDA 85
HHHHHHHHH-----EEE-----EEE-----EEE----EEEEEEE---HHHHHHHH--EEEEEEE----- -EEEEEEEEE
EE---HHHHHHHHHHHHHHH-- ------EEEEEEE--EEEEEE--
Query: 84 SLEEDESIKERIWENISKDWFQ-GEDSPSFVVIKIVPEQIRILNSD 128
Sbjct: 86 ELPTDKAKLDELWSPVYSAFFANGKEDANIQLIKVVPHGVECWLSG 131
----HHHHHHH--HHHHH----------EEEEEEEEEEEEEE---G
123 residues (88.49%) of query sequence aligned
DONE: Sat Aug 09 09:27:41 2008 EST