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:Thu Aug 07 06:31:48 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 = 200 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 T0391
--> 157 residues, sequence name: T0391
Database: T:\CBSU\blastdb\20080108\nr
-> 13 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 | 4 | 8 | 8 | 2 | 1 | 2 | 8 | 3 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 7.62 | 4.85 | 5.43 | 6.62 |
2 | 7.62 | 0.00 | 5.83 | 5.21 | 7.23 |
3 | 4.85 | 5.83 | 0.00 | 4.42 | 5.16 |
4 | 5.43 | 5.21 | 4.42 | 0.00 | 5.24 |
5 | 6.62 | 7.23 | 5.16 | 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 | 65.04 | 56.91 | 68.29 | 41.80 |
2 | 65.04 | 100.00 | 65.08 | 65.08 | 61.48 |
3 | 56.91 | 65.08 | 100.00 | 63.78 | 69.67 |
4 | 68.29 | 65.08 | 63.78 | 100.00 | 44.26 |
5 | 41.80 | 61.48 | 69.67 | 44.26 | 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 | 69.92 | 100.00 | 100.00 | 79.51 |
2 | 69.92 | 100.00 | 100.00 | 100.00 | 70.49 |
3 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
4 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
5 | 79.51 | 70.49 | 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: 0.00% helical, 46.60% extended, 53.40% loops/other (query: 1.27% 33.76% 64.97%)
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.
1VCK_A not_found 12.12.12.12 NONE -40.124 0 1 66.24% 19.51% OPTM -370.050 -318.940 1.857 0.514 0.659 0.820 0.966 12.930 -36.1 3.250 61.500 23.5 3.580 45.000 -101.0 1.510 -8.100 34.3 1.680 0.990 -37.7 1.250 -6.750 61.3 2.330 1.490 -29.4 2.940 1.530 24.6 2.180 -4.550 -37.8 -30.000 5.000 -40.0 -30.000 -1.000 -78.0 7.580 121.000 -30.0 20.520 134.000 -169.0 -0.160 12.000 58.0 2.950 10.000 -51.0 5.000 -16.2 -3.483 -41.7 31.000 128.0 5.000 -16.5 5.000 -3.2 0.42 0.72
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEEE-HH-------EEEEE---EEEEEE--- EEEEE--------------EEE-----EEEEEE----EEEE---
Query: 14 KYTSVCVGREEDIRKSERMTAVVHDREVVIFYHKG-EYHAMDIRCYHSGGPLHLGEIEDFNGQSCIVCPWHKYKITLATG 92
Sbjct: 4 IWLKVCAAS--DMQPGTIRRVNRVGAAPLAVYRVGDQFYATEDTCTHGIASLSEGTLDGD----VIECPFHGGAFNVCTG 77
-EEEEEE-- ------EEEEEE--EEEEEEEEE--EEEEEE-------------EEE-- EEE------EEE----
-EE--------------------EEEEEEEEEE--EEEEEE---
Query: 93 EGLYQSINPKDPSAKPKWCSKGVKQRIHTVKVDNGNIYVTLSKE 136
Sbjct: 78 MPASSP------------CT--VPLGVFEVEVKEGEVYVAGEKK 107
-EEE-- -- -------EEEE--EEEEE----
104 residues (66.24%) 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: 0.00% helical, 40.74% extended, 59.26% loops/other (query: 1.27% 33.76% 64.97%)
SCOP classification: [All beta proteins]/[ISP domain]
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.
1FQT_A b.33.1.1 130.14.14.8 NONE -40.155 0 1 68.79% 21.26% OPTM -429.823 -250.870 2.296 0.540 0.580 0.838 0.973 17.080 -38.5 4.310 79.000 -24.0 6.890 41.500 -122.0 1.780 10.070 24.4 1.840 3.770 -30.2 2.190 14.500 47.3 1.240 -2.280 -20.3 1.510 0.130 18.5 4.800 3.630 -43.8 -30.000 3.000 -49.0 -30.000 0.000 -79.0 11.310 159.000 -79.0 23.450 132.000 -169.0 1.960 22.000 34.0 2.890 15.000 -54.0 5.000 -15.7 -1.251 -36.1 7.000 167.0 5.000 -15.7 5.000 -4.4 0.43 0.83
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---EEEEEE-HH-------EEEEE---EEEEEE---EEEEE--------------EEE-----EEEEEE----EEEE---
Query: 13 KKYTSVCVGREEDIRKSERMTAVVHDREVVIFYHKGEYHAMDIRCYHSGGPLHLGEIEDFNGQSCIVCPWHKYKITLATG 92
Sbjct: 1 MKFTRVCDRR--DVPEGEALKVESGGTSVAIFNVDGELFATQDRCTHGDWSLSDGGYLEGD---VVECSLHMGKFCVRTG 75
---EEEEE-- ------EEEEEE--EEEEEEEE--EEEEEE---------------EE-- EEE------EEE----
-EE--------------------EEEEEEEEEE--EEEEEE------
Query: 93 EGLYQSINPKDPSAKPKWCSKGVKQRIHTVKVDNGNIYVTLSKEPFK 139
Sbjct: 76 -----------KVKSPPPCEA---LKIFPIRIEDNDVLVDFEAGYLA 108
-EEE------ -----EEEE--EEEE--------
108 residues (68.79%) 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: 0.00% helical, 37.96% extended, 62.04% loops/other (query: 1.27% 33.76% 64.97%)
SCOP classification: [All beta proteins]/[ISP domain]
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.33.1.1.4_A b.33.1.1 130.14.14.8 NONE -40.180 0 1 69.43% 23.26% OPTM -303.655 -273.550 2.320 0.523 0.676 0.805 0.948 13.960 -34.3 3.610 56.000 -19.5 3.560 49.000 -104.5 0.750 5.990 25.9 1.320 1.620 -30.7 2.260 11.320 41.7 3.950 6.260 -27.5 3.770 6.110 8.8 6.360 3.330 -48.3 -30.000 8.000 -54.0 -30.000 3.000 -77.0 11.790 147.000 -82.0 28.040 148.000 -183.0 0.060 13.000 43.0 3.440 18.000 -57.0 5.000 -3.2 -1.442 -30.5 0.000 -9.3e+061 5.000 -3.2 -0.036 -2.0 0.40 0.89
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEEE-HH-------EEEEE-- -EEEEEE-- -EEEEE--------------EEE-----EEEEEE----EEEE--
Query: 14 KYTSVCVGREEDIRKSERMTAVVHD-REVVIFYHK-GEYHAMDIRCYHSGGPLHLGEIEDFNGQSCIVCPWHKYKITLAT 91
Sbjct: 2 SFEKICSL--DDIWVGEMETFETSDGTEVLIVNSEEHGVKAYQAMCPHQEILLSEGSYEGG----VITCRAHLWTFNDGT 75
--EEEEE- ------EEEEEE-----EEEEEEE---EEEEEE-------------EEE-- EEE------EEE---
--EE--------------------EEEEEEEEEE--EEEEEE---------
Query: 92 GEGLYQSINPKDPSAKPKWCSKGVKQRIHTVKVDNGNIYVTLSKEPFKCDS 142
Sbjct: 76 GHGI----NPDD-----------AALAEYPVEVKGDDIYVST-KGILPNKA 110
---- ---- -------EEEE--EEEE-- --------
109 residues (69.43%) 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: 3.74% helical, 45.79% extended, 50.47% loops/other (query: 1.27% 33.76% 64.97%)
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.
2E4P_A not_found 12.12.12.12 NONE -40.258 0 1 68.79% 18.11% OPTM -393.684 -287.120 2.503 0.418 0.719 0.815 0.953 19.910 -37.8 5.110 94.000 -22.5 8.170 47.500 -131.0 1.170 0.450 32.5 1.180 0.620 -27.9 0.880 1.090 59.8 5.040 9.120 -28.6 1.280 1.050 25.8 4.350 5.200 -40.8 -30.000 4.000 -45.0 -30.000 2.000 -75.0 11.850 180.000 -97.0 26.830 161.000 -196.0 1.720 14.000 35.0 3.830 21.000 -58.0 5.000 -16.2 -2.883 -36.9 0.000 -9.3e+061 5.000 -16.2 -0.620 -3.5 0.32 0.71
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEEE-HH-------EEEEE---EEEEEE---EEEEE--------------EEE-----EEEEEE----EEEE----
Query: 14 KYTSVCVGREEDIRKSERMTAVVHDREVVIFYHKGEYHAMDIRCYHSGGPLHLGEIEDFNGQSCIVCPWHKYKITLATGE 93
Sbjct: 2 TFTKACSV--DEVPPGEALQVSHDAQKVAIFNVDGEFFATQDQCTHGEWSLSEGGYLDGD---VVECSLHMGKFCVRTG- 75
--EEEEE- -------EEEEEE--EEEEEEEE--EEEEEE---------HHHHEEEE-- EEEE-----EEE----
EE--------------------EEEEEEEEEE--EEEEEE-------
Query: 94 GLYQSINPKDPSAKPKWCSKGVKQRIHTVKVDNGNIYVTLSKEPFKC 140
Sbjct: 76 ----KVKSPPP------CEP---LKVYPIRIEGRDVLVDFSRAALHA 109
-EEE--- --- --EE-EEEE--EEEE---------
108 residues (68.79%) 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: 0.00% helical, 42.86% extended, 57.14% loops/other (query: 1.27% 33.76% 64.97%)
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.
3C0D_A not_found 12.12.12.12 NONE -40.262 0 1 67.52% 18.03% OPTM -322.722 -273.710 1.986 0.593 0.586 0.829 0.949 8.630 -31.3 2.710 6.000 9.5 3.570 37.000 -104.0 2.280 5.500 16.0 0.910 -0.560 -27.5 3.420 11.800 33.8 3.860 5.470 -27.6 6.040 11.880 5.2 5.080 7.900 -46.6 -30.000 5.000 -42.0 -30.000 5.000 -78.0 9.130 106.000 -52.0 17.480 116.000 -157.0 -0.040 8.000 66.0 4.990 11.000 -54.0 5.000 -8.0 1.125 -35.7 0.000 -9.3e+061 5.000 -8.0 1.041 -3.2 0.43 0.79
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-EEEEEE-HH-------EEEEE---EEEEEE-- -EEEEE--------------EEE-----EEEEEE----EEEE----
Query: 15 YTSVCVGREEDIRKSERMTAVVHDREVVIFYHK-GEYHAMDIRCYHSGGPLHLGEIEDFNGQSCIVCPWHKYKITLATGE 93
Sbjct: 4 LTKVKLCQLDDLP-FIGATVLIEGERVALFYIPDSGVYAVQDWDPIGKAYVSRGIVGDINGE-CVASPLYKQHFSLKSG- 80
--EEEEEE----- ---EEEEE--EEEEEEEE---EEEEEE-EE----EE----EE------ -EE------EE-----
EE--------------------EEEEEEEEEE--EEEEEE---
Query: 94 GLYQSINPKDPSAKPKWCSKGVKQRIHTVKVDNGNIYVTLSKE 136
Sbjct: 81 QCLE---------DEAHCLK-----TWRVTVDDNQVCYLAKEL 109
---- ------- EE-EEE---EEEEE----
106 residues (67.52%) of query sequence aligned
DONE: Thu Aug 07 10:08:15 2008 EST