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 14 13:05:01 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 T0451
--> 133 residues, sequence name: T0451
Database: T:\CBSU\blastdb\20080108\nr
-> 4 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 | 1 | 0 | 0 | 1 | 1 | 2 | 0 | 2 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.87 | 2.88 | 4.76 | 3.41 |
2 | 5.87 | 0.00 | 5.89 | 5.27 | 5.78 |
3 | 2.88 | 5.89 | 0.00 | 5.21 | 3.36 |
4 | 4.76 | 5.27 | 5.21 | 0.00 | 5.13 |
5 | 3.41 | 5.78 | 3.36 | 5.13 | 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 | 52.50 | 100.00 | 50.41 | 78.63 |
2 | 52.50 | 100.00 | 49.59 | 52.46 | 29.17 |
3 | 100.00 | 49.59 | 100.00 | 45.16 | 73.77 |
4 | 50.41 | 52.46 | 45.16 | 100.00 | 42.86 |
5 | 78.63 | 29.17 | 73.77 | 42.86 | 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: 31.71% helical, 45.53% extended, 22.76% loops/other (query: 30.08% 24.06% 45.86%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Cystatin-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.
1TUH_A d.17.4.11 76.31.23.1 NONE -33.390 0 1 90.98% 14.88% OPTM -549.002 -199.710 2.553 0.568 0.658 0.913 0.987 20.110 -36.5 2.120 54.000 -55.5 2.860 44.000 -96.5 0.070 -2.910 -17.0 0.520 2.450 -33.2 3.190 16.460 -13.9 5.240 13.820 -33.5 8.360 58.300 -43.5 19.650 33.770 -59.5 -30.000 80.000 -78.0 -30.000 40.000 -88.0 4.870 75.000 -71.0 8.110 65.000 -113.0 1.660 20.000 -44.0 4.880 25.000 -74.0 5.000 -0.2 1.551 -35.7 -57.000 212.0 5.000 -0.2 1.204 -1.0 0.24 0.54
alignment source: OPTM
-HHHHHHHHHHHHHHHH----HHHHHHHHH----EEEE- ---------HHHHHHHHHHHHHHH----EEEE--------
Query: 8 NTLKVAHQGFEFFTQGLATGEWQKFLDMLTEDFTFWFPM-GEFHGLNVGKERAKEFFTYVSESFHTGIQISSLDRVTSNE 86
Sbjct: 19 NEAEQNAETVRRGYAAFNSGDMKTLTELFDENASWHTPGRSRIAGDHKGREAIFAQFGRYGGETGGTFKAVLLHVLKSDD 98
-HHHHHHHHHHHHHHHHHH--HHHHHHHEEEEEEEEE-------EEEE-HHHHHHHHHHHHH------EEEEEEEEE---
-EEEEEE----EE-------EEEEEEEE----EEEEEEEE--
Query: 87 TTVVFEFRDEGLFLGKPYKNRVAVSFDVRGDKICSYREYFGS 128
Sbjct: 99 GRVIGIHRNTAERGGKRLDVGCCIVFEFKNGRVIDGREHFYD 140
--EEEEEEEEEEE--EEEEEEEEEEEEEE--EEEEEEEEE--
121 residues (90.98%) 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: 26.40% helical, 47.20% extended, 26.40% loops/other (query: 30.08% 24.06% 45.86%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Cystatin-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.
1TP6_A d.17.4.12 76.31.23.1 NONE -33.566 0 1 92.48% 16.26% OPTM -420.003 -288.250 1.934 0.572 0.587 0.932 0.954 17.990 -34.8 1.730 47.000 -43.0 1.400 25.500 -82.5 1.060 -1.280 -16.1 0.180 -0.540 -24.4 2.280 8.890 -5.4 2.780 3.380 -21.2 9.590 51.190 -39.8 15.520 27.190 -51.6 -30.000 85.000 -80.0 -30.000 44.000 -87.0 3.720 72.000 -31.0 3.420 24.000 -59.0 3.120 26.000 -49.0 5.030 22.000 -71.0 5.000 -1.4 3.258 -33.6 -44.000 166.0 5.000 -1.4 0.663 -1.1 0.16 0.46
alignment source: OPTM
HHHHHHHHHHHHHHHH----HHHHHHHHH----EEEE----------HHHHHHHHHHHHHHH---- EEEE--------
Query: 9 TLKVAHQGFEFFTQGLATGEWQKFLDMLTEDFTFWFPMGEFHGLNVGKERAKEFFTYVSESFHTGI--QISSLDRVTSNE 86
Sbjct: 5 YRREIHHAHVAIRDWLAGDSRADALDALMARFAEDFSMVTPHGVVLDKTALGELFRSKGGT-RPGLRIEIDGESLLASGV 83
HHHHHHHHHHHHHHHH------HHHHHH--EEEEEEEE-----EEEHHHHHHHHHHH---- ---EEEEEEEEEEEEE--
-EEEEEE----EE-------EEEEEEEE----EEEEEEEE-----
Query: 87 TTVVFEFRDEGLFLGKPYKNRVAVSFDVRGDKICSYREYFGSDGK 131
Sbjct: 84 DGATLAYREIQSDAAGRSERLSTVVLHRDDEGRLYWRHLQETFCG 128
EEEEEEEEEEEE--EEEEEEEEEEEEE-----EEEEEEEEEE--G
123 residues (92.48%) 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: 26.61% helical, 40.32% extended, 33.06% loops/other (query: 30.08% 24.06% 45.86%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Cystatin-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.
d.17.4.3.1_A d.17.4.3 76.31.23.5 NONE -33.624 0 1 92.48% 18.11% OPTM -457.883 -298.880 2.429 0.562 0.601 0.944 0.959 21.490 -34.6 5.470 81.500 -93.5 6.340 67.000 -115.0 0.420 4.630 -12.2 3.010 1.650 -28.6 1.580 9.210 -1.4 4.850 10.240 -25.4 8.760 48.010 -34.9 17.300 32.200 -54.2 -30.000 78.000 -83.0 -30.000 46.000 -89.0 7.640 99.000 -74.0 8.410 49.000 -88.0 2.730 14.000 -37.0 4.150 21.000 -59.0 5.000 -2.0 -1.965 -35.0 0.000 -9.3e+061 5.000 -2.0 5.000 5.0 0.34 0.61
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--HHHHHHHHHHHHHHHH----HHHHHHHHH----EEEE----------HHHHHHHHHHHHHHH----EEEE--------
Query: 7 DNTLKVAHQGFEFFTQGLATGEWQKFLDMLTEDFTFWFPMGEFHGLNVGKERAKEFFTYVSESFHTGIQISSLDRVTSNE 86
Sbjct: 1 MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVG--SEPRSGTAAIREFYA---NSLKLPLAVELTQEVRAVA 75
---HHHHHHHHHHHHHHHHH--HHHHH--EEEEEEEE---- ---EE-HHHHHHHHH HH-----EEEE----EEE-
-EEEEEE----EE-------EEEEEEEE--- -EEEEEEEE-------
Query: 87 TTVVFEFRDEGLFLGKPYKNRVAVSFDVRGD-KICSYREYFGSDGKSN 133
Sbjct: 76 NEAAFAFIVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHA 123
-EEEEEEEEEEEE--EEEEE--EEEEEE-----EEEEEEE-----EEE
123 residues (92.48%) 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: 27.50% helical, 53.33% extended, 19.17% loops/other (query: 30.08% 24.06% 45.86%)
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.
2R4I_A not_found 66.66.66.20 NONE -33.657 0 1 90.98% 14.52% OPTM -332.291 -263.560 1.409 0.557 0.571 0.923 0.945 11.570 -25.1 1.730 14.000 -32.0 1.160 5.000 -68.0 1.000 0.600 -7.9 1.060 3.950 -23.8 2.200 1.460 4.4 1.500 1.510 -16.2 8.370 45.090 -24.9 12.860 16.910 -38.3 -30.000 84.000 -67.0 -30.000 38.000 -75.0 2.200 24.000 -5.0 1.320 15.000 -48.0 3.430 31.000 -38.0 3.680 20.000 -64.0 5.000 -1.1 3.466 -37.7 0.000 -9.3e+061 5.000 -1.1 5.000 5.0 0.30 0.36
alignment source: OPTM
--HHHHHHHHHHHHHHHH----HHHHHHHHH----EEEE----------HHHHHHHHHHHHHHH----EEEE--------
Query: 7 DNTLKVAHQGFEFFTQGLATGEWQKFLDMLTEDFTFWFPMGEFHGLNVGKERAKEFFTYVSESFHTGIQISSLDRVTSNE 86
Sbjct: 3 GNQRDVILDCEKKLLTAIQNNDVESLEVLLHDDLLFIIPSGE----TVTKETDIAAYSS--GKIALRAVVPSDYIIRIIH 76
--HHHHH-HHHHHHHHHHHH--HHHHHHHEEEEEEEE----- EE-HHHHHHHHH- ---EEEEEEEEEEEEEEE-
-EEEEEE----EE--- ----EEEEEEEE----EEEEEEEE----
Query: 87 TTVVFEFRDEGLFLGK---PYKNRVAVSFDVRGDKICSYREYFGSDG 130
Sbjct: 77 DTVVVSVNIEIKGEYEHTLDNTFRYLRVWKLFDGNWKVIAGSCTAIG 123
-EEEEEEEEEEEEE---EEEEEEEEEEEEEEE--EEEEEEEEEEE--
121 residues (90.98%) 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: 22.73% helical, 40.91% extended, 36.36% loops/other (query: 30.08% 24.06% 45.86%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Cystatin-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.
2A15_A d.17.4.3 76.31.23.5 NONE -33.663 0 1 91.73% 17.21% OPTM -515.404 -272.590 2.059 0.524 0.660 0.868 0.944 15.440 -31.0 3.100 61.500 -63.5 2.130 28.000 -83.0 0.350 -4.540 -17.1 2.680 2.890 -28.5 2.360 12.710 -9.1 3.370 6.970 -21.8 8.020 48.520 -40.1 14.190 26.710 -51.3 -30.000 74.000 -81.0 -30.000 39.000 -88.0 3.580 60.500 -25.0 3.270 23.000 -61.0 2.920 0.000 -51.0 5.350 19.000 -75.0 5.000 -1.3 1.210 -39.4 0.000 -9.3e+061 5.000 -1.8 0.806 -0.0 0.22 0.52
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHHH----HHHHHHHHH----EEEE-------- --HHHHHHHHHHHHHHH----EEEE--------
Query: 12 VAHQGFEFFTQGLATGEWQKFLDMLTEDFTFWFPMGEFHGLN-----VGKERAKEFFTYVSESFHTGIQISSLDRVTSNE 86
Sbjct: 8 PALIASQSSWRCVQAHDREGWLALMADDVVIEDPIGKSVTNPDGSGIKGKEAVGAFFDTHIA--ANRLTVTCEETFPSSS 85
HHHHHHHHHHHHH---HHHHHH-EEEEEEEE--------------EE-HHHHHHHHHHH--- ---EEEEEEEEE----
- EEEEEE----EE-------EEEEEEEE---- EEEEEEEE-------
Query: 87 T-TVVFEFRDEGLFLGKPYKNRVAVSFDVRGDK---ICSYREYFGSDGKSN 133
Sbjct: 86 PDEIAHILVLHSEFDG-GFTSEVRGVFTYRVNKAGLITNMRGYWNLDMMTF 135
-EEEEEEEEEEEE--- EEEEEEEEEEEEE-----EEEEEEE------EEE
122 residues (91.73%) of query sequence aligned
DONE: Thu Aug 14 16:52:23 2008 EST