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 08 16:48:29 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 T0404
--> 110 residues, sequence name: T0404
Database: T:\CBSU\blastdb\20080108\nr
-> 9 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 | 8 | 8 | 0 | 1 | 4 | 4 | 0 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.95 | 7.91 | 13.44 | 6.47 |
2 | 5.95 | 0.00 | 4.51 | 14.07 | 3.78 |
3 | 7.91 | 4.51 | 0.00 | 12.77 | 4.13 |
4 | 13.44 | 14.07 | 12.77 | 0.00 | 13.90 |
5 | 6.47 | 3.78 | 4.13 | 13.90 | 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 | 47.42 | 40.91 | 36.84 | 45.65 |
2 | 47.42 | 100.00 | 49.44 | 35.06 | 52.69 |
3 | 40.91 | 49.44 | 100.00 | 34.62 | 47.78 |
4 | 36.84 | 35.06 | 34.62 | 100.00 | 34.18 |
5 | 45.65 | 52.69 | 47.78 | 34.18 | 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 | 48.86 | 42.11 | 53.26 |
2 | 100.00 | 100.00 | 100.00 | 38.96 | 100.00 |
3 | 48.86 | 100.00 | 100.00 | 41.03 | 100.00 |
4 | 42.11 | 38.96 | 41.03 | 100.00 | 40.51 |
5 | 53.26 | 100.00 | 100.00 | 40.51 | 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: 24.74% helical, 30.93% extended, 44.33% loops/other (query: 26.36% 28.18% 45.45%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Ferredoxin-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.
2CZ4_A d.58.5.1 97.54.12.6 GUESS -27.326 0 1 82.73% 28.87% OPTM -375.019 -255.580 4.486 0.655 0.520 0.887 0.905 14.830 -34.6 7.030 155.500 -134.0 13.870 106.000 -173.0 2.640 12.110 -9.8 1.410 3.100 -22.3 4.700 27.060 -8.9 11.830 21.970 -35.4 8.680 41.440 -35.2 20.630 22.460 -54.0 -30.000 21.000 -74.0 -30.000 15.000 -76.0 18.870 357.000 -319.0 39.410 325.000 -356.0 1.920 18.000 -15.0 1.970 3.000 -38.0 5.000 -35.1 -7.430 -40.1 0.000 -9.3e+061 5.000 -35.2 1.000 -9.7 0.31 0.91
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-EEEEEE-HHHHHHHHHHHHH-----EEEEE----------------------EEEEEEEE--HHHHHHHHHHHHHHHH-
Query: 6 NKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGGKGSRNVRSTGKPNTSDTDSNVKFEVLTENREMAEKIADQVAIKFFT 85
Sbjct: 7 KLVTIVAESLLEKRLVEEVKRLGAKGYTITPARGEGSRGIRSVDWEG-----QNIRLETIVS-EEVALRILQRLQEEYFP 80
EEEEEEE---HHHHHHHHHH------EEEEE---------------- EEEEEEEE-H HHHHHHHHHHHHH----
---EEEEEE-EEEE---
Query: 86 DYAGIIYICEAEVLYGR 102
Sbjct: 81 HYAVIAYVENVWVVRGE 97
---EEEEEEEEEE----
91 residues (82.73%) 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: 23.91% helical, 32.61% extended, 43.48% loops/other (query: 26.36% 28.18% 45.45%)
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.
2EG1_A not_found 74.74.74.28 GUESS -27.652 0 1 82.73% 21.90% OPTM -318.222 -158.750 1.022 0.604 0.353 0.775 0.851 9.200 -23.6 2.490 49.000 -61.5 2.170 15.500 -89.0 0.340 5.860 -2.7 -0.340 0.000 -20.0 2.280 10.370 -0.2 1.300 3.680 -18.9 6.160 26.080 -21.5 7.090 0.390 -32.7 -30.000 32.000 -53.0 -30.000 2.000 -58.0 2.860 79.000 -25.0 0.420 12.000 -48.0 -1.230 12.000 31.0 3.020 3.000 -29.0 5.000 -2.4 9.254 -55.4 0.000 -9.3e+061 5.000 -4.3 5.000 5.0 0.35 0.86
alignment source: OPTM
--EEEEEE-HHHHHHHHHHHHH-----EEEEE----------------------EEEEEEEE--HHHHHHHHHHHHHHHH
Query: 5 ANKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGGKGSRNVRSTGKPNTSDTDSNVKFEVLTENREMAEKIADQVAIKFF 84
Sbjct: 1 MKKIEAIIKPFKLDEVKDALVEIGIGGMTVTEVKGFD--------------FLPKVKIEVVVRDED-VEKVVETIVKTAQ 65
-EEEEEEE----HHHHHHHHHH------EEEEEEE-- -EEEEEEEEEE---- HHHHHHHHHHHH-
-- --EEEEEE-E EEE---EE-----
Query: 85 TD--YAGIIYICEA-EVLYGRTFCGPDG 109
Sbjct: 66 TGRVGDGKIFIIPVEDVIRIR--TGERG 91
-------EEEEEE-------- -----
91 residues (82.73%) 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: 27.91% helical, 46.51% extended, 25.58% loops/other (query: 26.36% 28.18% 45.45%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Ferredoxin-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.
1NZA_A d.58.5.2 97.54.12.4 GUESS -27.719 0 1 77.27% 12.22% OPTM -395.030 -174.730 1.039 0.724 0.251 0.793 0.904 0.710 -21.0 2.520 74.000 -41.0 2.000 4.500 -68.0 -0.800 2.580 -3.0 -0.800 -0.870 -18.4 0.070 6.380 6.5 -0.350 -0.850 -13.7 5.130 34.370 -21.5 9.540 4.430 -32.3 -30.000 22.000 -58.0 -30.000 1.000 -60.0 1.460 51.000 8.0 -0.120 -1.000 -33.0 0.600 16.000 1.0 2.280 -1.000 -36.0 5.000 5.0 1.742 -53.9 56.000 163.0 5.000 5.0 1.079 0.7 0.44 0.60
alignment source: OPTM
---EEEEEE- HHHHHHHHHHHHH-----EEEEE----------------------EEEEEEEE--HHHHHHHHHHHHHH
Query: 4 RANKLVIVTE-KVLLKKVAKIIEEAGATGYTVVDTGGKGSRNVRSTGKPNTSDTDSNVKFEVLTENREMAEKIADQVAIK 82
Sbjct: 1 MEEVVLITVPSEEVARTIAKALVEERLAACVNIVPGLTSIYRWQ-----GEVVEDQELLLLVKTTTH-AFPKLKERVKAL 74
-EEEEEEEE--HHHHHHHHHHHHH-----EEEEEEEEEEEEE-- --EEEEEEEEEEEEEE-- -HHHHHHHHHHH
HH----EEEEE
Query: 83 FFTDYAGIIYI 93
Sbjct: 75 HPYTVPEIVAL 85
-------EEEE
85 residues (77.27%) 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: 30.67% helical, 37.33% extended, 32.00% loops/other (query: 26.36% 28.18% 45.45%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Ferredoxin-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.58.18.6.3_A d.58.18.6 97.54.9.2 GUESS -27.745 0 1 59.09% 16.46% OPTM -173.267 -76.730 0.381 0.533 0.267 0.768 0.797 3.310 -20.1 0.850 -6.500 24.0 3.770 13.000 -78.5 0.650 1.240 17.8 -0.630 -0.260 -17.4 0.860 -1.440 31.2 -0.090 -4.870 -14.5 0.980 -15.690 23.7 4.010 -0.990 -22.9 -30.000 1.000 -31.0 -30.000 2.000 -47.0 0.030 -25.000 58.0 -0.440 -16.000 -32.0 1.980 14.000 37.0 1.310 7.000 -27.0 5.000 -0.9 9.615 -51.5 0.000 -9.3e+061 5.000 -0.9 5.000 5.0 0.52 0.73
alignment source: OPTM
----EEEEEE-HHHHHHHHHHHHH-----EEEEE----------------------EEEEEEEE- -HHHHHHHHHHHHH
Query: 3 KRANKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGGKGSRNVRSTGKPNTSDTDSNVKFEVLTE-NREMAEKIADQVAI 81
Sbjct: 2 RRILSVLLENESGALSRVIGLFSQRGY--------------NIESLTVAPTDD-PTLSRMTIQTVGDEKVLEQIEKQLHK 66
-EEEEEEEE----HHHHHHHHHH---- ---EEEEEE--- --EEEEEEEE---HHHHHHHHHHHHH
65 residues (59.09%) 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, 0.00% extended, 100.00% loops/other (query: 26.36% 28.18% 45.45%)
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.
2J9D_E not_found 74.74.74.28 GUESS -27.745 0 1 86.36% 23.16% OPTM -350.372 -150.520 1.257 0.719 0.393 0.787 0.905 11.200 -28.3 4.470 99.000 -109.0 4.240 26.500 -119.0 1.310 3.950 -18.0 -0.650 -0.230 -20.5 3.120 12.220 -15.4 2.670 5.640 -21.5 2.260 4.070 -29.7 1.820 4.310 -31.2 -30.000 0.000 -50.0 -30.000 0.000 -50.0 3.840 117.000 -64.0 4.520 42.000 -83.0 2.230 25.000 4.0 2.880 4.000 -31.0 5.000 -5.5 2.870 -50.7 0.000 -9.3e+061 5.000 -5.5 5.000 -4.0 0.44 -0.09
alignment source: OPTM
----EEEEEE-HHHHHHHHHHHHH-----EEEEE--------- -------------EEEEEEEE--HHHHHHHHHHH
Query: 3 KRANKLVIVTEKVLLKKVAKIIEEAGATGYTVVDTGGKGSRNV---RSTGKPNTSDTDSNVKFEVLTENREMAEKIADQV 79
Sbjct: 3 GSMKKVEAIIRPEKLEIVKKALSDAGYVGMTVSEVKGRGVQGGIVERYRGREYIVDLIPKVKIELVVKEED-VDNVIDII 81
----------------------------------------------------------------------- --------
HHHHH- ---EEEEEE-EE
Query: 80 AIKFFT--DYAGIIYICEAE 97
Sbjct: 82 CENARTGNPGDGKIFVIPVE 101
--------------------
95 residues (86.36%) of query sequence aligned
DONE: Fri Aug 08 19:21:17 2008 EST