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 09:49:30 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 T0455
--> 145 residues, sequence name: T0455
Database: T:\CBSU\blastdb\20080108\nr
-> 43 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 | 153 | 43 | 14 | 22 | 7 | 0 | 0 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 3.99 | 3.02 | 2.58 | 1.74 |
2 | 3.99 | 0.00 | 3.37 | 3.39 | 3.45 |
3 | 3.02 | 3.37 | 0.00 | 2.49 | 2.85 |
4 | 2.58 | 3.39 | 2.49 | 0.00 | 2.35 |
5 | 1.74 | 3.45 | 2.85 | 2.35 | 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 | 95.07 | 99.29 | 100.00 | 100.00 |
2 | 95.07 | 100.00 | 97.16 | 97.81 | 98.59 |
3 | 99.29 | 97.16 | 100.00 | 100.00 | 100.00 |
4 | 100.00 | 97.81 | 100.00 | 100.00 | 100.00 |
5 | 100.00 | 98.59 | 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: 17.53% helical, 43.51% extended, 38.96% loops/other (query: 22.07% 43.45% 34.48%)
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.
2OOI_A not_found 30.30.30.30 NONE -36.344 0 1 97.93% 26.76% OPTM -448.769 -361.430 6.549 0.634 0.598 0.894 0.988 40.540 -60.4 9.630 136.500 -190.5 14.690 107.000 -229.0 2.370 5.140 -19.1 3.260 9.550 -34.4 5.830 20.070 -17.7 15.370 35.610 -53.8 11.010 39.100 -52.8 30.390 55.920 -87.5 -30.000 61.000 -116.0 -30.000 50.000 -123.0 21.950 361.500 -357.5 44.910 351.000 -413.0 9.700 118.000 -116.0 16.190 69.000 -142.0 5.000 -30.4 0.857 -32.8 0.000 -9.3e+061 5.000 -30.5 -1.060 -14.2 0.77 0.91
alignment source: OPTM
--------EEEEEEEE---HHHHHH--------EEEEEEEEEE---EEEEEEE---HHHHHHHHHHHH---HHHHHHHH-
Query: 1 SQNRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKS 80
Sbjct: 84 SKSRMTSKVLVFKEMATPPKSVQDELQLNADDTVYYLERLRFVDDDVLCIEYSYYHKEIVKYLNDDIAKGSIFDYLESNM 163
---EEEEEEEEEEE----HHHHHH--------EEEEEEEEEE--EEEEEEEEEEEHHHH----HHHH---HHHHHHH---
---EEEEEEEEEEE---HHHHHH-------EEEEEEEEEE-----EEEEEEEEE---EEEEE
Query: 81 GHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFY 142
Sbjct: 164 KLRIGFSDIFFNVDKLTSSEASLLQLSTGEPCLRYHQTFYTMTGKPFDSSDIVFHYRHAQFY 225
--EEEEEEEEEEEE--HHHHHH-------EEEEEEEEEEE----EEEEEEEEEE-----EE-
142 residues (97.93%) 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: 14.69% helical, 46.15% extended, 39.16% loops/other (query: 22.07% 43.45% 34.48%)
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.
2IKK_A not_found 30.30.30.30 NONE -36.707 0 1 97.24% 22.54% OPTM -449.440 -247.650 5.517 0.584 0.573 0.922 0.935 30.110 -49.7 8.980 165.500 -189.0 11.930 135.000 -200.0 1.400 6.730 -19.5 1.200 1.090 -32.5 7.670 30.790 -33.8 13.310 28.450 -49.2 13.060 49.290 -68.2 24.600 44.650 -74.7 -30.000 55.000 -108.0 -30.000 42.000 -109.0 18.450 294.000 -321.5 34.130 269.000 -334.0 10.130 107.000 -107.0 13.380 60.000 -119.0 5.000 -30.5 -2.276 -37.4 0.000 -9.3e+061 5.000 -33.7 0.362 -12.7 0.75 0.80
alignment source: OPTM
--------EEEEEEEE---HHHHHH--------EEEEEEEEEE---EEEEEEE---HHHHHHHHHHHH---HHHHHHHH-
Query: 1 SQNRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKS 80
Sbjct: 84 TENLYFQHHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSHDILKQQY 163
EEEE---EEEEEEEEE--HHHHHHH------EEEEEEEEEE----EEEEEEEEEE-----------------HHHHHHH-
---EEEEEEEEEEE---HHHHHH-------EEEEEEEEEE-----EEEEEEEEE---EEEEE
Query: 81 GHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFY 142
Sbjct: 164 KVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLHT-NRVTFT 224
----EEEEEEEEEE--HHHHHHH------EEEEEEEEEEE---EEEEEEEE---- -EEEE-
141 residues (97.24%) 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: 17.61% helical, 43.66% extended, 38.73% loops/other (query: 22.07% 43.45% 34.48%)
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.
2P19_A not_found 30.30.30.30 NONE -36.709 0 1 96.55% 23.40% OPTM -504.066 -375.200 5.374 0.602 0.523 0.927 0.973 27.880 -49.0 7.710 106.500 -164.0 9.640 92.000 -172.0 2.280 5.950 -24.1 1.970 -1.040 -29.2 7.740 27.560 -31.2 9.120 11.180 -35.4 14.540 52.270 -69.3 23.600 42.160 -73.4 -30.000 61.000 -112.0 -30.000 44.000 -115.0 17.790 324.000 -324.0 33.210 288.000 -334.0 8.770 110.000 -71.0 12.820 57.000 -106.0 5.000 -30.2 -4.386 -34.4 0.000 -9.3e+061 5.000 -30.1 -1.328 -8.2 0.79 0.91
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--------EEEEEEEE---HHHHHH--------EEEEEEEEEE---EEEEEEE---HHHHHHHHHHHH---HHHHHHHH-
Query: 1 SQNRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKS 80
Sbjct: 3 NANLDPKTRVLEHRLLAASSAIAEKLGVSAGDEVLLIRRLRSTGDIPVAILENYLPPAF-NDVSLDELEKGGLYDALRSR 81
----EEEEEEEEEEEE--HHHHHHH------EEEEEEEEEEE--EEEEEEEEEE----- ---HHHHHH--HHHHHHH--
---EEEEEEEEEEE---HHHHHH-------EEEEEEEEEE-----EEEEEEEEE---EEEE
Query: 81 GHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEF 141
Sbjct: 82 GVVLKIANQKIGARRAVGEESTLLDIEDGGPLLTVERVALDNSGQVIELGSHCYRPDMYNF 142
----EEEEEEEEEE----HHHHH------EEEEEEEEEE-----EEEEEEEEE--------
140 residues (96.55%) 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: 18.98% helical, 40.88% extended, 40.15% loops/other (query: 22.07% 43.45% 34.48%)
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.
2OGG_A not_found 30.30.30.30 NONE -36.755 0 1 93.79% 21.17% OPTM -459.192 -273.170 4.784 0.625 0.552 0.939 0.979 22.830 -44.5 6.810 102.000 -140.5 8.580 89.500 -163.0 2.720 1.390 -23.9 4.290 4.830 -33.4 5.860 23.860 -27.4 10.840 28.910 -43.3 11.830 45.350 -59.6 23.940 43.180 -75.4 -30.000 52.000 -103.0 -30.000 39.000 -111.0 16.310 235.500 -267.0 32.560 221.000 -286.0 6.280 57.000 -57.0 9.200 34.000 -92.0 5.000 -25.4 -2.514 -30.6 0.000 -9.3e+061 5.000 -26.7 1.114 -7.7 0.31 0.89
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---EEEEEEEE---HHHHHH--------EEEEEEEEEE---EEEEEEE---HHHHHHHHHHHH---HHHHHHHH----EE
Query: 6 PSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIG 85
Sbjct: 95 TKTTVHKFGLEPPSELIQKQLRANLDDDIWEVIRSRKIDGEHVILDKDYFFRKHVPHLTKEICENSIYEYIEGELGLSIS 174
--EEEEEEEEE---HHHHHHH-------EEEEEEEEEE--EEEEEEEEEEE--------HHHH---HHHHHHHHH---EE
EEEEEEEEE---HHHHHH-------EEEEEEEEEE-----EEEEEEEEE---EEEEE
Query: 86 HSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFY 142
Sbjct: 175 YAQKEIVAEPCTDEDRELLDL-RGYDHVVVRNYVFLEDTSLFQYTESRHRLDKFRFV 230
EEEEEEE-----HHHHHH--- ------EEEEEEEE----EEEEEEEEE--------
136 residues (93.79%) 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: 11.36% helical, 30.00% extended, 58.64% loops/other (query: 22.07% 43.45% 34.48%)
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.
3BWG_A not_found 30.30.30.30 NONE -36.775 0 1 99.31% 25.52% OPTM -510.652 -334.840 5.128 0.639 0.566 0.639 0.967 32.650 -57.1 2.200 50.500 57.0 14.270 146.000 -240.5 0.260 -0.580 342.8 4.420 10.670 -36.5 1.940 -1.320 342.9 16.150 33.840 -53.9 0.860 11.300 193.3 27.350 45.280 -84.4 -30.000 31.000 -45.0 -30.000 40.000 -117.0 12.340 209.000 -64.0 41.730 316.000 -388.0 0.590 14.000 66.0 11.460 40.000 -117.0 5.000 -34.5 -2.074 -27.9 0.000 -9.3e+061 5.000 -34.5 0.041 -16.0 0.76 0.52
alignment source: OPTM
--------EEEEEEEE---HHHHHH--------EEEEEEEEEE---EEEEEEE---HHHHHHHHHHHH---HHHHHHHH-
Query: 1 SQNRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKS 80
Sbjct: 80 QGDFNVTSKVIELDVRKPTPEAAENLNIGDED-IYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGL 158
----EEEEEEEEEEE---HHHHHHH------E EEEEEEEEE--EEEEEEEEEEE--------HHHH---HHHHHHH---
---EEEEEEEEEEE---HHHHHH-------EEEEEEEEEE-----EEEEEEEEE---EEEEEEEE
Query: 81 GHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 145
Sbjct: 159 GLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQA 223
--EEEEEEEEEEEE--HHHHHHH------EEEEEEEEEEE----EEEEEEEEE------EE----
144 residues (99.31%) of query sequence aligned
DONE: Fri Aug 15 11:56:07 2008 EST