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:Fri Aug 15 02:30:33 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 T0453
--> 91 residues, sequence name: T0453
Database: T:\CBSU\blastdb\20080108\nr
-> 127 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 | 2 | 118 | 113 | 14 | 0 | 0 | 0 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 2.87 | 2.69 | 3.17 | 2.54 |
2 | 2.87 | 0.00 | 2.54 | 2.58 | 2.60 |
3 | 2.69 | 2.54 | 0.00 | 3.07 | 2.43 |
4 | 3.17 | 2.58 | 3.07 | 0.00 | 2.57 |
5 | 2.54 | 2.60 | 2.43 | 2.57 | 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 | 100.00 | 63.10 | 100.00 |
2 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
3 | 100.00 | 100.00 | 100.00 | 72.00 | 100.00 |
4 | 63.10 | 100.00 | 72.00 | 100.00 | 100.00 |
5 | 100.00 | 100.00 | 100.00 | 100.00 | 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: 24.71% helical, 22.35% extended, 52.94% loops/other (query: 21.98% 29.67% 48.35%)
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.
2NQW_A not_found 17.17.17.17 LOW -21.439 0 1 92.31% 29.41% OPTM -407.218 -235.090 3.342 0.809 0.716 0.968 0.979 21.450 -31.4 7.190 120.500 -121.5 9.670 73.500 -151.5 1.290 3.990 -6.6 2.560 3.290 -31.0 5.540 28.330 -15.5 10.130 18.710 -39.8 9.140 35.930 -37.6 17.580 22.430 -50.4 -30.000 37.000 -66.0 -30.000 22.000 -68.0 12.450 162.500 -141.0 17.750 133.000 -171.0 4.730 40.000 -30.0 5.320 23.000 -44.0 5.000 -16.5 -4.355 -40.6 0.000 -9.3e+061 5.000 -16.7 -0.108 -9.2 0.31 0.80
alignment source: OPTM
-EE----EEEEE----HHHHHHH---------------HHHHHHHHHHH--------EEEE--EEEEEEEE---EEEEEE
Query: 7 IVQREDGSWLVDGMVSLDRFREFFELEAPLPGEAGGNIHTLAGVMLYQLGRVPSVTDRFEWNGFSFEVVDMDRTRVDKIL 86
Sbjct: 6 FKVLGDGSYLFEGKTSLSDVRHYLDLPENAFGELGDEVDTLSGLFLEIKQELPHVGDTAVYEPFRFQVTQ-DKRRIIEIK 84
EE-----EEEE----HHHHHHHH-------HHHH-----HHHHHHHHH--------EEEE--EEEEE--- -----EEEE
EE---
Query: 87 VQRHH 91
Sbjct: 85 IFPFE 89
----E
84 residues (92.31%) 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: 9.76% helical, 24.39% extended, 65.85% loops/other (query: 21.98% 29.67% 48.35%)
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.
2PLS_A not_found 17.17.17.17 LOW -21.621 0 1 87.91% 41.67% OPTM -346.224 -249.530 4.549 0.726 0.706 0.931 0.942 23.330 -34.1 13.650 180.000 -219.5 18.910 177.500 -245.5 2.550 8.310 -9.8 -0.040 0.250 -26.4 6.930 35.180 -21.9 9.390 20.840 -40.8 10.180 30.520 -35.1 14.460 18.090 -45.4 -30.000 28.000 -59.0 -30.000 14.000 -62.0 21.160 310.000 -290.0 41.130 274.000 -312.0 4.710 38.000 -38.0 4.080 24.000 -47.0 5.000 -26.5 -9.410 -33.7 0.000 -9.3e+061 5.000 -26.5 -0.745 -16.0 0.36 0.65
alignment source: OPTM
EE----EEEEE----HHHHHHH---------------HHHHHHHHHHH--------EEEE--EEEEEEEE---EEEEEEE
Query: 8 VQREDGSWLVDGMVSLDRFREFFELEAPLPGEAGGNIHTLAGVMLYQLGRVPSVTDRFEWNGFSFEVVDMDRTRVDKILV 87
Sbjct: 346 VQREDGSWLLDGLIAVPELKDTLGLRA-VPEEEKGVYHTLSGIWL--LGRLPQTGDITFWENWRLEVID-DSKRIDKVLA 421
E-----EEEE----HHHHHHHH----- ----------------- --------EEEE--EEEEE--- -----EEEEE
E---
Query: 88 QRHH 91
Sbjct: 422 TKID 425
E--D
80 residues (87.91%) 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: 10.81% helical, 32.43% extended, 56.76% loops/other (query: 21.98% 29.67% 48.35%)
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.
2O3G_A not_found 17.17.17.17 LOW -21.649 0 1 79.12% 25.00% OPTM -260.106 -213.350 3.246 0.770 0.657 0.918 0.930 17.000 -27.5 4.850 102.500 -81.0 8.330 79.000 -140.5 3.460 8.390 -5.8 -0.250 -1.640 -25.5 5.970 25.620 -9.8 6.100 7.630 -30.4 9.880 27.010 -23.2 17.050 19.170 -43.0 -30.000 28.000 -51.0 -30.000 28.000 -61.0 13.980 183.000 -179.0 23.670 198.000 -238.0 2.550 16.000 -7.0 4.160 20.000 -42.0 5.000 -16.7 -5.013 -34.8 0.000 -9.3e+061 5.000 -18.7 0.114 -7.5 0.25 0.72
alignment source: OPTM
EEE----HHHHHHH---------------HHHHHHHHHHH--------EEEE--EEEEEEEE---EEEEEEEE---
Query: 16 LVDGMVSLDRFREFFELEAPLPGEAGGNIHTLAGVMLYQLGRVPSVTDRFEWNGFSFEVVDMDRTRVDKILVQRHH 91
Sbjct: 183 TVEGALEYVELAP--QLNLP-QQEEDADFHTVAGLIE-ELQTIPDVGDFADFHGWRFEVVEKEGQRIERVKITKLP 254
EE----HHHH--- ----- ---------HHHH--- ---------EEEE--EEEEEEEEE--EEEEEEEEE--P
72 residues (79.12%) 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: 20.48% helical, 16.87% extended, 62.65% loops/other (query: 21.98% 29.67% 48.35%)
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.
2P13_A not_found 17.17.17.17 LOW -21.724 0 1 92.31% 28.41% OPTM -335.785 -185.510 4.145 0.700 0.695 0.943 0.987 25.550 -33.3 10.000 176.500 -159.0 13.640 132.500 -177.0 3.480 11.080 -14.9 0.600 -0.120 -27.4 7.980 32.190 -22.6 6.380 14.030 -34.0 12.000 38.870 -39.9 15.670 19.130 -46.3 -30.000 34.000 -62.0 -30.000 12.000 -63.0 18.350 256.000 -252.0 34.510 228.000 -268.0 5.660 36.000 -37.0 5.580 20.000 -49.0 5.000 -20.7 -12.682 -29.8 0.000 -9.3e+061 5.000 -21.4 5.000 -10.1 0.61 0.71
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--HH-EE----EEEEE----HHHHHHH---------------HHHHHHHHHHH--------EEEE--EEEEEEEE---EE
Query: 3 EEDEIVQREDGSWLVDGMVSLDRFREFFELEAPLPGEAGGNIHTLAGVMLYQLGRVPSVTDRFEWNGFSFEVVDMDRTRV 82
Sbjct: 431 EKVVAEQQADGTWL-DGWISIRKASNLLEHDLVDEAERYS---TLGGYLLWQFGYIPAAGEQITVDGLIFEIVSVNKHNI 506
-------------- -----HHHHHHHH------------ -HHHHHHHHH--------EEEE--EEEEE--------
EEEEEE--
Query: 83 DKILVQRH 90
Sbjct: 507 GKVRVHRT 514
--EEEEE-
84 residues (92.31%) 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: 17.53% helical, 34.02% extended, 48.45% loops/other (query: 21.98% 29.67% 48.35%)
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.
2P3H_A not_found 17.17.17.17 LOW -21.918 0 1 90.11% 20.73% OPTM -353.365 -281.470 1.761 0.780 0.702 0.769 0.915 19.930 -29.9 2.500 42.000 -52.5 4.300 41.000 -102.0 0.340 -0.950 -5.9 0.790 2.300 -25.0 2.140 10.850 -2.6 3.800 3.750 -26.8 5.380 10.790 -21.6 12.180 14.880 -38.4 -30.000 13.000 -51.0 -30.000 8.000 -57.0 3.180 46.500 -41.0 8.810 64.000 -109.0 0.750 21.000 -13.0 1.710 11.000 -35.0 5.000 -11.5 -2.557 -73.7 0.000 -9.3e+061 5.000 -11.7 0.973 -3.7 0.34 0.82
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-EE----EEEEE----HHHHHHH---------------HHHHHHHHHHH--------EEEE--
Query: 7 IVQREDGSWLVDGMVSLDRFREFFELEAPLPGEAGGNIHTLAGVMLYQLGRVPSVTDRFEWNG----------------- 69
Sbjct: 7 ITETSPDKWLIDGDTPLDEVERAIGYELP-----EGDYETISGLLFDHANALLKTGDVIEIPLDFEPEDYLNNTSPTQRI 81
EEEE--EEEEE----HHHHHHHH------ -----HHHHHHHHH--------EEEEE-----------------EE
EEEEEEEE---EEEEEEEE
Query: 70 FSFEVVDMDRTRVDKILVQ 88
Sbjct: 82 LRITVLEVERNVPVKLALA 100
EEEEEEEE--EEEEEEEEE
82 residues (90.11%) of query sequence aligned
DONE: Fri Aug 15 03:38:36 2008 EST