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 01:23:57 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 T0429
--> 178 residues, sequence name: T0429
Database: T:\CBSU\blastdb\20080108\nr
-> 25 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 | 1 | 2 | 5 | 18 | 0 | 6 | 8 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 18.54 | 16.75 | 17.64 | 15.25 |
2 | 18.54 | 0.00 | 19.49 | 15.37 | 16.92 |
3 | 16.75 | 19.49 | 0.00 | 15.36 | 18.68 |
4 | 17.64 | 15.37 | 15.36 | 0.00 | 14.24 |
5 | 15.25 | 16.92 | 18.68 | 14.24 | 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 | 11.59 | 11.61 | 8.75 | 12.27 |
2 | 11.59 | 100.00 | 9.68 | 10.00 | 9.82 |
3 | 11.61 | 9.68 | 100.00 | 11.61 | 10.97 |
4 | 8.75 | 10.00 | 11.61 | 100.00 | 10.00 |
5 | 12.27 | 9.82 | 10.97 | 10.00 | 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 | 21.34 | 23.23 | 25.00 | 19.63 |
2 | 21.34 | 100.00 | 16.13 | 27.50 | 17.79 |
3 | 23.23 | 16.13 | 100.00 | 27.74 | 16.77 |
4 | 25.00 | 27.50 | 27.74 | 100.00 | 19.38 |
5 | 19.63 | 17.79 | 16.77 | 19.38 | 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, 51.83% extended, 48.17% loops/other (query: 5.62% 34.83% 59.55%)
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.
2QF4_A not_found 30.30.30.30 NONE -999.000 0 1 91.57% 9.76% OPTM -130.731 -171.870 1.015 0.407 0.441 0.842 0.871 4.190 -30.2 0.700 14.000 -19.0 -0.740 9.000 -54.0 3.130 7.490 -24.7 0.670 1.420 -34.1 3.920 17.400 -11.2 2.790 12.080 -28.8 5.810 7.780 -53.1 7.300 8.410 -60.5 -30.000 3.000 -107.0 -30.000 5.000 -112.0 3.720 64.000 -11.0 3.270 16.000 -55.0 1.280 28.000 -34.0 0.190 6.000 -53.0 5.000 -0.0 -0.953 -26.6 0.000 -9.3e+061 5.000 -0.0 1.491 -0.0 0.50 0.55
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-----------------------EEEEE-- EEEE------EEEEEEEEEE--- -------------
Query: 3 HHHHHSSGRENLYFQGMWDETELGLYKVNE-------YVDARDTNMGAWFEAQVVRVTRK-------APSRDEPCSSTSR 68
Sbjct: 108 LQATKTLAADVIMRSPVSWKQELTLDAGRSKGASENMLAIANG-----GLIGSVSKVEENSTIVNLLTNTENADKISVKI 182
---EEEEEEEEEEE-------EEEE------------EEEE-- EEEEEEEEE----EEEEE----------EEEE
------EEEEEEE-------EEEE------HHHHHH---------EEEEEEE---------EEEEEEEEEE-------EE
Query: 69 PALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTAREL 148
Sbjct: 183 QHGSTTIYGIIIGYDK-ENDVLKISQLN---------SNSDISAGDKVTTGGLGNFNVADIPVGEVVATTHSTDYLTREV 252
EE--EEEEEEEEEEE- ---EEEEE--- ---------EEEEE-------EEEEEEEEEEEE--------EE
EEEEEE--------EEEE
Query: 149 YANVVLGDDSLNDCRIIF 166
Sbjct: 253 TVKLSADTHNVDVIELVG 270
EEEE--------EEEEEE
163 residues (91.57%) 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: 7.10% helical, 36.69% extended, 56.21% loops/other (query: 5.62% 34.83% 59.55%)
SCOP classification: [All beta proteins]/[Prealbumin-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.
1XPN_A b.3.7.1 163.2.1.1 NONE -999.000 0 1 93.26% 13.25% OPTM -108.287 -197.830 0.891 0.398 0.131 0.684 0.699 9.150 -33.0 3.120 78.500 -77.0 3.800 27.500 -120.0 -0.380 4.720 -14.3 -1.350 -1.040 -26.4 2.300 9.210 -6.0 2.800 6.780 -25.0 2.940 8.430 -40.3 7.780 14.670 -60.0 -30.000 12.000 -94.0 -30.000 9.000 -101.0 2.920 80.000 -23.0 4.500 6.000 -68.0 0.290 18.000 41.0 -0.040 -1.000 -35.0 5.000 0.2 -1.295 -31.6 -97.000 214.0 5.000 0.2 0.792 0.8 0.73 0.93
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-------------------------EEEEE--EEEE------EEEEEEEEEE----------------------EEEEEE
Query: 1 MHHHHHHSSGRENLYFQGMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVK 80
Sbjct: 3 SHHHHHHSSGLVPRGSHMASNPNDLPDFPEHEYAATQQVG-GGVINGDLYLTSASGAIQKG-----------TNTKVALE 70
---------------------------------------- --EEEEE-EE-----EE--- -EEEEEEE
E-- -----EEEE---- --HHHHHH---------EEEEEEE---------EEEEEEEEEE----
Query: 81 YDD------YPENGVVQMNSRD-------VRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETR---- 143
Sbjct: 71 PATSYMKAYYAKFGNLDAAKRDPDVQPPVLDPRRATYVREATTDQN----GRFDFDHIPNGTYYISSELTWSAQSDGKTI 146
---HHHHHHHH---EE----------------HHHH-EEEEE---- EEEE-----EEEEEEEEEEEEEEE--EEEE
---EEEEEEEE--------EEEE
Query: 144 -TARELYANVVLGDDSLNDCRIIF 166
Sbjct: 147 TEGGTVTKLVTVSGS--QPQKVLL 168
EEEEEEEEEEE---- -EEEEE-
166 residues (93.26%) 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: 4.11% helical, 31.51% extended, 64.38% loops/other (query: 5.62% 34.83% 59.55%)
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.
2ENP_A not_found 30.30.30.30 NONE -999.000 0 1 82.58% 9.03% OPTM -133.409 -240.680 0.851 0.429 0.150 0.848 0.892 6.980 -31.0 0.720 17.000 -10.0 -1.620 2.000 -57.0 1.280 1.860 -2.1 -0.090 -0.000 -31.5 1.580 8.600 16.4 0.650 2.240 -22.9 5.950 5.870 -28.3 5.740 3.750 -53.0 -30.000 3.000 -94.0 -30.000 7.000 -110.0 0.410 -14.500 41.0 1.570 18.000 -51.0 3.680 40.000 42.0 4.160 5.000 -39.0 5.000 0.7 -1.625 -36.9 0.000 -9.3e+061 5.000 0.7 0.380 0.6 0.39 0.90
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-------------------EEEEE--EEEE------EEEEEEEEEE----------------------EEEEEEE-----
Query: 7 HSSGRENLYFQGMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPE 86
Sbjct: 1 GSSGSSG-------SKYQLGMLHFSTQYDLLHN----HLTVRVIEARDLPPPISHD-GSRQDMAHSNPYVKICLLPDQKN 68
------- ------EEEEEEEEE---- EEEEEEEEEE--------- -----------EEEEEEE-----
--EEEE------HHHHHH-------- -EEEEEEE---------EEEEEEEEEE-------EEEEEEEE-----
Query: 87 NGVVQMNSRDVRARARTIIKWQDLEV-------GQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSL 159
Sbjct: 69 S--KQTGVKRKTQKP-VFEERYTFEIPFLEAQRRTLLLTVVDFDKFSRHCVIGKVSVPLCEVDLVKGGHWWKALIPSGPS 145
- EE---------- ------EE---HHHHHH-EEEEEEE-----------EEEEEE-----------EEE--------
--
Query: 160 ND 161
Sbjct: 146 SG 147
--
147 residues (82.58%) 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, 42.65% extended, 57.35% loops/other (query: 5.62% 34.83% 59.55%)
SCOP classification: [All beta proteins]/[C2 domain-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.
1WFM_A b.7.1.2 163.8.8.5 NONE -999.000 0 1 75.84% 12.21% OPTM -254.004 -409.260 0.792 0.400 0.468 0.744 0.917 8.420 -33.2 0.850 13.500 15.0 -0.670 -15.500 -52.5 1.950 3.200 7.9 1.200 4.710 -28.6 2.690 13.550 27.7 1.730 3.180 -19.8 3.080 1.780 -7.2 3.730 4.250 -48.8 -30.000 -2.000 -78.0 -30.000 10.000 -101.0 0.260 -7.000 51.0 3.160 26.000 -59.0 1.510 18.000 33.0 0.970 2.000 -49.0 5.000 0.3 -3.830 -34.3 37.000 80.0 5.000 0.3 1.041 0.5 0.35 0.73
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-------------------EEEEE--EEEE------EEEEEEEEEE----------------------EEEEEEE-----
Query: 7 HSSGRENLYFQGMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPE 86
Sbjct: 1 GSSGSS-----GSWNQAP----KLHYCLDYDCQKA----ELFVTRLEAVTSNHDGGC----------DCYVQGSVANRTG 57
------ ------- EEEEEEEEE---- EEEEEEEEEE-------- -EEEEEEEEE--E
--EEEE------HHHHHH---------EEEEEEE---------EEEEEEEEEE-------EEEEEEEE--------EEEE
Query: 87 NGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIF 166
Sbjct: 58 SVEAQTALKKRQLH----TTWEEG-----LVLPLAEEELPT-ATLTLTLRTCDRFSRHSVAGELRLGLDGTSVPLGAAQW 127
EEEEE--------- EE---- EEEE-------- -EEEEEEEE----------EEEEEE-----------EE
HHHHEEE-----
Query: 167 VDEVFKIERPGE 178
Sbjct: 128 ----GELKTSGP 135
EE------
135 residues (75.84%) 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, 50.00% extended, 50.00% loops/other (query: 5.62% 34.83% 59.55%)
SCOP classification: [All beta proteins]/[Nucleoplasmin-like/VP (viral coat and capsid proteins)]
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.
1M06_G b.121.5.1 163.4.2.2 NONE -999.000 0 1 91.57% 9.82% OPTM -209.383 -159.540 0.783 0.363 0.436 0.720 0.814 -2.660 -29.9 0.930 2.500 -12.0 -0.390 -16.000 -53.5 1.940 5.660 -27.1 0.510 3.230 -35.5 1.960 6.080 -6.4 0.050 1.420 -25.5 2.870 1.020 -45.1 4.690 -1.040 -55.6 -30.000 -4.000 -106.0 -30.000 1.000 -115.0 1.600 18.000 22.0 0.370 5.000 -37.0 1.880 5.000 -36.0 -0.370 -19.000 -56.0 5.000 0.3 -3.664 -38.6 -18.000 88.0 5.000 0.3 -0.092 0.0 0.45 0.58
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----------------------EEEEE-- EEEE-- ----EEEEEEEEEE-------- ------------
Query: 4 HHHHSSGRENLYFQGMWDETELGLYKVNE--YVDARD----TNMGAWFEAQVVRVTRKAPSRD-----EPCSSTSRPALE 72
Sbjct: 1 MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCV 80
----------------EEEEEEEE-------EEE----------EEEEEEEEEE-------EEEEEEEE--------EEE
--EEEEEEE-- -----EEEE------HHHHHH---------EEEEEEE---------EEEEEEEEEE------ -EEE
Query: 73 EDVIYHVKYDD--YPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTA-RELY 149
Sbjct: 81 ISAGVNLSFAGTSYPIVGIVRFESASE--------QPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVF 152
EEEEEEEEE------EEEEEEEEE--- ---EEE----EEE-----EE---EEEEEEEEEEE--------EEE
EEEEE--------EEEE
Query: 150 ANVVLGDDSLNDCRIIF 166
Sbjct: 153 VGVICSSAKWTSGRVIG 169
EEEEEEE-----EEEEE
163 residues (91.57%) of query sequence aligned
DONE: Thu Aug 14 07:19:41 2008 EST