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 06:44:45 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 T0396
--> 105 residues, sequence name: T0396
Database: T:\CBSU\blastdb\20080108\nr
-> 0 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 | 25 | 5 | 0 | 0 | 0 | 0 | 0 | 9 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 1.21 | 0.67 | 7.55 | 12.90 |
2 | 1.21 | 0.00 | 2.27 | 7.69 | 14.45 |
3 | 0.67 | 2.27 | 0.00 | 7.53 | 14.06 |
4 | 7.55 | 7.69 | 7.53 | 0.00 | 9.86 |
5 | 12.90 | 14.45 | 14.06 | 9.86 | 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 | 100.00 | 100.00 | 50.00 | 23.91 |
2 | 100.00 | 100.00 | 100.00 | 45.83 | 23.71 |
3 | 100.00 | 100.00 | 100.00 | 45.83 | 23.23 |
4 | 50.00 | 45.83 | 45.83 | 100.00 | 34.72 |
5 | 23.91 | 23.71 | 23.23 | 34.72 | 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 | 88.57 | 44.57 |
2 | 100.00 | 100.00 | 100.00 | 83.33 | 42.27 |
3 | 100.00 | 100.00 | 100.00 | 84.72 | 42.42 |
4 | 88.57 | 83.33 | 84.72 | 100.00 | 63.89 |
5 | 44.57 | 42.27 | 42.42 | 63.89 | 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: 65.00% helical, 0.00% extended, 35.00% loops/other (query: 65.71% 0.00% 34.29%)
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.
2HJ3_A not_found 76.76.76.30 GUESS -25.620 0 1 87.62% 25.00% OPTM -530.532 -240.660 4.018 0.627 0.548 0.905 0.993 21.920 -41.4 7.450 117.500 -146.5 10.570 118.000 -174.0 4.190 10.920 -29.3 4.790 5.440 -35.3 10.860 35.080 -39.7 14.960 27.250 -47.7 13.500 31.810 -63.1 19.170 26.010 -68.7 -30.000 26.000 -88.0 -30.000 17.000 -91.0 12.470 193.000 -188.0 20.780 172.000 -218.0 3.690 46.000 -27.0 3.440 5.000 -47.0 5.000 -39.7 0.050 -48.5 0.000 -9.3e+061 5.000 -39.7 0.771 -10.5 0.46 0.99
alignment source: OPTM
-HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH--
Query: 7 GPKYWRSLHLYAIFFSDAPSWKEKYEAIQWILNFIESLPCTRCQHHAFSYLTKNPLTLNNSEDFQYWTFAFHNNVNNRLN 86
Sbjct: 15 GRATWTFLHTLAAQYPEKPTRQQKKDVKELMTILSRMYPCRECADHFKEILRSNPAQAGSQEEFSQWLCHVHNTVNRSLG 94
HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH---
------HHHHHH
Query: 87 KKIISWSEYKNI 98
Sbjct: 95 KLVFPCERVDAR 106
-------HHHH-
92 residues (87.62%) 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: 61.54% helical, 0.00% extended, 38.46% loops/other (query: 65.71% 0.00% 34.29%)
SCOP classification: [All alpha proteins]/[Four-helical up-and-down 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.
1JR8_A a.24.15.1 84.5.2.2 GUESS -25.654 0 1 92.38% 24.74% OPTM -364.728 -216.680 3.523 0.624 0.595 0.910 0.984 22.710 -42.2 7.230 134.500 -136.0 10.490 106.000 -162.0 1.290 10.280 -24.9 4.770 -0.030 -34.0 6.970 33.920 -33.9 12.460 22.920 -46.5 10.560 31.880 -60.7 18.150 22.970 -68.4 -30.000 25.000 -91.0 -30.000 18.000 -91.0 9.120 144.500 -133.0 15.050 119.000 -162.0 5.680 65.000 -51.0 8.190 21.000 -68.0 5.000 -36.0 0.532 -47.6 -12.000 150.0 5.000 -36.5 5.000 -9.3 0.42 0.92
alignment source: OPTM
-HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH--
Query: 7 GPKYWRSLHLYAIFFSDAPSWKEKYEAIQWILNFIESLPCTRCQHHAFSYLTKNPLTLNNSEDFQYWTFAFHNNVNNRLN 86
Sbjct: 15 GRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLK 94
HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH---
------HHHHHHHH---
Query: 87 KKIISWSEYKNIYEQSI 103
Sbjct: 95 KDIYDCATILEDYDCGC 111
-------HHHH-----C
97 residues (92.38%) 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: 59.09% helical, 0.00% extended, 40.91% loops/other (query: 65.71% 0.00% 34.29%)
SCOP classification: [All alpha proteins]/[Four-helical up-and-down 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.
1OQC_A a.24.15.1 84.5.2.2 GUESS -25.848 0 1 94.29% 22.22% OPTM -469.858 -222.920 3.818 0.611 0.515 0.876 0.989 19.970 -42.6 6.410 86.500 -125.0 9.080 96.000 -155.0 4.230 11.940 -31.9 5.920 7.380 -38.3 9.210 30.210 -39.5 15.910 29.170 -50.0 12.950 25.360 -64.5 20.200 24.920 -71.8 -30.000 18.000 -94.0 -30.000 18.000 -97.0 9.190 166.000 -139.0 16.950 136.000 -179.0 4.290 53.000 -44.0 6.120 12.000 -66.0 5.000 -40.5 2.771 -49.0 -3.000 134.0 5.000 -40.7 -0.155 -9.5 0.40 0.87
alignment source: OPTM
-HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH--
Query: 7 GPKYWRSLHLYAIFFSDAPSWKEKYEAIQWILNFIESLPCTRCQHHAFSYLTKNPLTLNNSEDFQYWTFAFHNNVNNRLN 86
Sbjct: 23 GRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLG 102
HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH---
------HHHHHHHH-----
Query: 87 KKIISWSEYKNIYEQSILK 105
Sbjct: 103 KPDFDCSRVDERWRDGWKD 121
-------HHHHH-------
99 residues (94.29%) 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: 70.00% helical, 0.00% extended, 30.00% loops/other (query: 65.71% 0.00% 34.29%)
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.
2IP6_A not_found 76.76.76.30 GUESS -25.988 0 1 68.57% 9.72% OPTM -330.306 -150.960 0.800 0.596 0.603 0.766 0.916 0.470 -21.2 0.890 7.000 -9.5 -0.220 3.000 -46.0 1.160 -0.400 -6.2 1.590 3.630 -28.9 1.200 -0.340 6.9 0.920 2.080 -20.2 5.670 2.930 -23.4 4.090 -1.660 -40.4 -30.000 4.000 -57.0 -30.000 -7.000 -67.0 -0.240 -12.000 26.0 -1.920 -6.000 -20.0 0.770 11.000 -1.0 2.280 2.000 -39.0 5.000 1.1 1.223 -34.4 0.000 -9.3e+061 5.000 1.1 1.176 1.0 0.56 0.91
alignment source: OPTM
HHHHHHHHHHHHHHH- --HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH--------HHHHHHHH
Query: 29 EKYEAIQWILNFIESL-------PCTRCQHHAFSYLTKNPLTLNNSEDFQYWTFAFHNNVNNRLNKKIISWSEYKNIYE 100
Sbjct: 9 IKQQALDLFTRLQFLLQKHDTIEPYQYVLDILETGISKTKHNQQTPERQARVVYNKIASQALVDKLHFT--AEENKVLA 85
HHHHHHHHHHHHHH----------HHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH------H HHHHHHHH
72 residues (68.57%) 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: 58.65% helical, 0.00% extended, 41.35% loops/other (query: 65.71% 0.00% 34.29%)
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.
2H7B_A not_found 76.76.76.30 NONE -999.000 0 1 98.10% 13.33% OPTM -281.981 -191.140 1.310 0.474 0.350 0.950 0.950 6.320 -20.9 2.370 43.000 -51.0 0.130 3.000 -58.0 0.500 0.030 -21.5 1.450 0.570 -28.1 2.100 8.180 -15.2 0.830 -4.850 -18.9 6.320 9.520 -47.5 8.520 9.960 -50.2 -30.000 12.000 -85.0 -30.000 14.000 -87.0 2.350 39.500 -13.0 -0.080 8.000 -34.0 1.920 18.000 -6.0 2.950 -1.000 -41.0 5.000 -0.8 1.473 -68.2 0.000 -9.3e+061 5.000 -0.8 5.000 5.0 0.79 0.86
alignment source: OPTM
-------HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHH
Query: 1 GSMLHWGPKYWRSLHLYAIFFSDAPSWKEKYEAIQWILNFIESLPCTRCQHHAFSYLTKNPLTLNNSEDFQYWTFAFHNN 80
Sbjct: 3 GSARQLSK--LKRFLTTLQQFGNDISPEIGERVRTLVLGLVNSTLTIEEFHSKLQEATNFPLRPFVIPFLKANLPLLQRE 80
-------H HHHHHHHHHH-HHHH-HHHHHHHHHHHHHHH-----HHHHHHHHHHH---------HHHHH--HHHHHHH
HHHH--------HHHHHHHH-----
Query: 81 VNNRLNKKIISWSEYKNIYEQSILK 105
Sbjct: 81 LLHAARLAKQNPAQYLAQHEQLLLD 105
HHHH---------HHHH--------
103 residues (98.10%) of query sequence aligned
DONE: Fri Aug 08 09:03:45 2008 EST