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:Sun Aug 17 04:04:12 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 T0464
--> 89 residues, sequence name: T0464
Database: T:\CBSU\blastdb\20080108\nr
-> 7 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 | 0 | 0 | 3 | 0 | 0 | 4 | 0 | 2 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 11.15 | 8.14 | 7.88 | 12.20 |
2 | 11.15 | 0.00 | 5.09 | 6.10 | 12.36 |
3 | 8.14 | 5.09 | 0.00 | 6.05 | 12.36 |
4 | 7.88 | 6.10 | 6.05 | 0.00 | 12.13 |
5 | 12.20 | 12.36 | 12.36 | 12.13 | 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 | 28.95 | 64.71 | 58.82 | 32.65 |
2 | 28.95 | 100.00 | 71.70 | 90.57 | 26.98 |
3 | 64.71 | 71.70 | 100.00 | 75.93 | 35.71 |
4 | 58.82 | 90.57 | 75.93 | 100.00 | 40.48 |
5 | 32.65 | 26.98 | 35.71 | 40.48 | 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 | 44.74 | 88.24 | 88.24 | 73.47 |
2 | 44.74 | 100.00 | 100.00 | 98.11 | 41.27 |
3 | 88.24 | 100.00 | 100.00 | 98.15 | 64.29 |
4 | 88.24 | 98.11 | 98.15 | 100.00 | 61.90 |
5 | 73.47 | 41.27 | 64.29 | 61.90 | 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: 45.76% helical, 0.00% extended, 54.24% loops/other (query: 20.22% 11.24% 68.54%)
SCOP classification: [All alpha proteins]/[DNA/RNA-binding 3-helical bundle]
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.
a.4.5.32.2_A a.4.5.32 4.1.1.1 LOW -22.044 0 1 55.06% 28.57% OPTM -41.843 -89.560 0.394 0.564 0.190 0.615 0.735 4.920 -15.6 1.370 14.000 -9.5 1.320 11.000 -65.0 -0.760 -0.410 21.3 -1.420 -0.200 -9.9 -0.500 -4.520 30.2 -1.230 -0.180 -9.0 2.060 1.180 11.1 3.710 4.270 -23.0 -30.000 1.000 -17.0 -30.000 4.000 -42.0 2.630 41.000 -10.0 3.080 17.000 -64.0 0.390 1.000 52.0 0.030 -1.000 -19.0 5.000 5.0 1.992 -41.1 -17.000 143.0 5.000 5.0 5.000 5.0 0.62 0.26
alignment source: OPTM
HHHHHH---------- ------HHHHHHHHHH-----------------
Query: 3 RKLLHLLCSPDTRQPL-------SLLESKGLEALNKAIASGTVQRADGSIQNQSLH 51
Sbjct: 30 KKIIKILQN-DGKAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALG 84
HHHHHH--- ----HHHHHHH-------HHHHHHHHHH-----------------G
49 residues (55.06%) 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, 28.33% extended, 71.67% loops/other (query: 20.22% 11.24% 68.54%)
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.
2JNY_A not_found 31.31.31.31 NONE -999.000 0 1 68.54% 21.62% OPTM -94.613 -89.440 1.043 0.329 0.174 0.718 0.852 3.820 -14.4 4.350 54.000 -54.0 3.730 44.500 -87.0 -0.150 -0.900 16.8 -0.070 -0.450 -9.6 4.400 8.390 13.4 5.490 7.850 -16.8 6.510 5.300 -1.0 6.160 2.330 -26.3 -30.000 4.000 -24.0 -30.000 0.000 -44.0 5.370 85.500 -52.5 6.880 54.000 -79.0 -0.680 -4.000 70.0 0.640 0.000 -16.0 5.000 -7.5 -10.881 -58.6 0.000 -9.3e+061 5.000 -7.4 0.681 -5.1 0.36 0.25
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-----------HHHHHHHHHH-------------------EE-----EEEEE----EEE--HH-----------
Query: 14 TRQPLSLLESKGLEALNKAIASGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLPEEAIATIQIANFP 87
Sbjct: 1 MSLDPQLLEV------------LACPKDKGPLRYLESEQLLVNERLNLAYRIDDGIPVLLIDEA-TEWTPNNLE 61
---------- ----------EEE----EEEE----EEEEEE--EE------- EE-------
61 residues (68.54%) 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: 7.46% helical, 25.37% extended, 67.16% loops/other (query: 20.22% 11.24% 68.54%)
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.
2JR6_A not_found 31.31.31.31 NONE -999.000 0 1 60.67% 20.37% OPTM -75.384 -54.010 0.920 0.492 0.148 0.641 0.767 0.010 -13.3 2.780 25.000 -31.0 3.690 28.000 -79.0 -0.290 -1.710 8.9 0.380 0.420 -15.5 3.050 5.530 8.7 1.610 0.320 -15.1 4.470 4.890 -7.0 3.710 -0.620 -24.3 -30.000 -4.000 -30.0 -30.000 -7.000 -43.0 4.370 59.000 -39.0 6.120 50.000 -79.0 0.420 4.000 36.0 2.750 5.000 -26.0 5.000 -7.7 -5.024 -51.9 0.000 -9.3e+061 5.000 -7.7 5.000 -3.2 0.45 0.46
alignment source: OPTM
-------------------EE-----EEEEE----EEE-- HH------------
Query: 35 SGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLP-------EEAIATIQIANFPD 88
Sbjct: 8 ILVCPVTKGRLEYHQDKQELWSRQAKLAYPIKDGIPYMLENEARPLSEEELKALEHHHHHH 68
----------EEE----EEEE----EEEEEE--EE-------EE--HHHHH---------H
54 residues (60.67%) 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: 0.00% helical, 26.09% extended, 73.91% loops/other (query: 20.22% 11.24% 68.54%)
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.
2JS4_A not_found 31.31.31.31 NONE -999.000 0 1 61.80% 18.18% OPTM -76.223 -59.420 0.863 0.555 0.176 0.719 0.904 2.880 -14.3 1.130 -2.500 -29.5 3.060 27.000 -86.0 -0.100 -1.100 8.9 0.070 0.570 -9.6 1.880 4.240 9.2 4.610 6.060 -15.0 1.640 -2.430 -6.4 4.540 1.260 -26.9 -30.000 -6.000 -33.0 -30.000 -6.000 -42.0 4.270 47.000 -44.0 5.950 45.000 -77.0 0.660 3.000 70.0 1.470 1.000 -19.0 5.000 -5.0 -9.044 -62.8 0.000 -9.3e+061 5.000 -5.0 5.000 -1.2 0.39 0.30
alignment source: OPTM
-------------------EE-----EEEEE----EEE--HH-------------
Query: 35 SGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLPEEAIATIQIANFPDK 89
Sbjct: 8 ILVCPVCKGRLEFQRAQAELVCNADRLAFPVRDGVPIMLEAEARSLDAEAPAQPS 62
---------EEEE----EEEE----EEEEEE--EE-------EE-----------
55 residues (61.80%) 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: 20.83% helical, 10.42% extended, 68.75% loops/other (query: 20.22% 11.24% 68.54%)
SCOP classification: [Alpha and beta proteins (a+b)]/[DUSP-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.
1W6V_A d.324.1.1 14.1.1.1 NONE -999.000 0 1 83.15% 18.92% OPTM -95.158 -72.050 0.795 0.563 0.299 0.524 0.798 4.000 -16.6 1.490 30.000 16.0 0.760 -0.500 -54.5 -0.080 0.450 55.6 -1.270 -2.220 -15.3 -0.350 2.560 69.0 2.080 4.180 -15.1 3.310 13.770 22.8 5.660 6.700 -32.8 -30.000 13.000 -42.0 -30.000 1.000 -56.0 1.330 15.000 55.0 5.370 32.000 -57.0 2.000 11.000 5.0 1.460 7.000 -36.0 5.000 0.8 -0.253 -84.2 0.000 -9.3e+061 5.000 0.9 1.114 0.0 0.54 0.97
alignment source: OPTM
HHHHHH------- ---------HHHHHHHHHH----------------- --EE-----EEEE E----EEE--
Query: 3 RKLLHLLCSPDTR-QPLSLLESKGLEALNKAIASGTVQRADGSIQNQSLH----EALITRDRKQVFR---IEDSIPVLLP 74
Sbjct: 14 SDIATLLKTSLRKGDTWYLVDSRWFKQWKKYVGFDSWDKYQMGDQNVYPGPIDNSGLLKDGDAQSLKEHLIDELDYILLP 93
HHHHHH--------EEEEEEHHHHHHHHHHH-------------------------------------------EEEE-H
HH
Query: 75 EE 76
Sbjct: 94 TE 95
HH
74 residues (83.15%) of query sequence aligned
DONE: Sun Aug 17 05:17:11 2008 EST