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 15 04:15:57 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 T0434
--> 205 residues, sequence name: T0434
Database: T:\CBSU\blastdb\20080108\nr
-> 12 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 | 20 | 3 | 5 | 1 | 3 | 4 | 15 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.90 | 12.03 | 14.46 | 14.18 |
2 | 5.90 | 0.00 | 11.59 | 13.16 | 12.88 |
3 | 12.03 | 11.59 | 0.00 | 11.97 | 9.00 |
4 | 14.46 | 13.16 | 11.97 | 0.00 | 9.55 |
5 | 14.18 | 12.88 | 9.00 | 9.55 | 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 | 93.10 | 24.50 | 24.18 | 30.07 |
2 | 93.10 | 100.00 | 23.97 | 23.29 | 31.51 |
3 | 24.50 | 23.97 | 100.00 | 33.73 | 32.54 |
4 | 24.18 | 23.29 | 33.73 | 100.00 | 69.11 |
5 | 30.07 | 31.51 | 32.54 | 69.11 | 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 | 78.81 | 78.43 | 81.05 |
2 | 100.00 | 100.00 | 78.77 | 41.10 | 82.88 |
3 | 78.81 | 78.77 | 100.00 | 77.51 | 78.11 |
4 | 78.43 | 41.10 | 77.51 | 100.00 | 84.82 |
5 | 81.05 | 82.88 | 78.11 | 84.82 | 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: 3.42% helical, 29.45% extended, 67.12% loops/other (query: 14.63% 21.95% 63.41%)
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.
2QPW_A not_found 45.45.45.45 NONE -53.087 0 1 71.22% 32.03% OPTM -332.489 -354.320 6.010 0.545 0.690 0.897 0.933 28.220 -54.3 11.270 240.500 -199.5 19.670 209.500 -306.5 3.550 10.320 18.8 1.090 -1.440 -31.9 15.500 53.220 2.4 15.920 33.000 -58.0 19.940 38.730 -27.5 20.000 34.790 -81.3 -30.000 13.000 -72.0 -30.000 5.000 -112.0 24.620 446.000 -373.0 58.060 447.000 -493.0 2.050 21.000 61.0 9.810 34.000 -96.0 5.000 -42.7 -4.016 -26.2 0.000 -9.3e+061 5.000 -42.7 -0.018 -19.4 0.57 0.63
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------------------ ------EEEEE------EEEEEE--------EEEEEE-----------------EEEE
Query: 45 NDHPWDSGADGGTSVQAE----ASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRI 120
Sbjct: 1 NQNTTEPVAATETLAEVPEHVLRGLPEEVRLFPSAVDKTRIGVWATKPILKGKKFGPFVGDKKKRSQVKNNV---YMWEV 77
------------------HHHHH-----EEEEE-------EEEEE--------EE-----EEE--------- -EEEE
E----EEEEEE--------HHHHH----------EEEEE---EEEEEEE-------EEEEE--HHHHHH--------
Query: 121 YSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGE 197
Sbjct: 78 YYPNLGWMCIDATDPEKGNWLRYVNWACSGEEQNLFPLEINRAIYYKTLKPIAPGEELLVWY--------NGEDNPE 146
EE---EEEEEE-------------EE--------EEEEEE--EEEEEE----------EE-- -------
146 residues (71.22%) 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: 8.97% helical, 27.56% extended, 63.46% loops/other (query: 14.63% 21.95% 63.41%)
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.
2JV0_A not_found 45.45.45.45 NONE -53.247 0 1 71.22% 32.88% OPTM -354.206 -301.910 5.721 0.412 0.755 0.859 0.952 28.620 -56.0 10.520 246.500 -222.5 20.010 217.000 -310.0 2.830 3.050 3.5 1.130 2.940 -50.3 12.080 45.370 -13.5 12.200 29.380 -65.8 19.820 35.920 -46.9 18.110 37.370 -84.6 -30.000 19.000 -94.0 -30.000 15.000 -120.0 23.120 421.000 -378.0 56.760 435.000 -472.0 2.510 21.000 26.0 6.300 15.000 -86.0 5.000 -44.0 -3.622 -25.2 0.000 -9.3e+061 5.000 -44.0 0.041 -19.7 0.51 0.77
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------------------- ------EEEEE------EEEEEE--------EEEEEE-----------------EEE
Query: 44 VNDHPWDSGADGGTSVQAE----ASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWR 119
Sbjct: 5 MDQNTTEPVAATETLAEVPEHVLRGLPEEVRLFPSAVDKTRIGVWATKPILKGKKFGPFVGDKKKRSQVKNNV---YMWE 81
------------------HHHH-------EEEE-------EEEE--------EEEEEE---EE---------- EEEE
EE----EEEEEE--------HHHHH----------EEEEE---EEEEEEE-------EEEEE-- HHHHHH
Query: 120 IYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYC------RDFAER 189
Sbjct: 82 VYYPNLGWMCIDATDPEKGNWLRYVNWACSGEEQNLFPLEINRAIYYKTLKPIAPGEELLVWYGEDNPEIAAAIEE 157
EE---EEEEEE-------------EE---------EEEEE--EEEEEE----------EE------HHHHHHHHHH
146 residues (71.22%) 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: 22.01% helical, 33.33% extended, 44.65% loops/other (query: 14.63% 21.95% 63.41%)
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.
1ZKK_A not_found 45.45.45.45 NONE -54.105 0 1 78.05% 11.24% OPTM -258.514 -230.370 1.560 0.407 0.368 0.833 0.877 11.410 -35.6 1.570 25.500 -24.5 2.110 39.500 -105.0 0.290 2.990 15.5 1.140 4.270 -44.4 0.750 13.500 41.1 2.970 8.900 -36.4 3.760 6.180 1.9 8.270 -1.270 -52.1 -30.000 -1.000 -65.0 -30.000 -6.000 -96.0 4.150 77.000 -18.0 10.750 72.000 -115.0 2.590 19.000 2.0 7.080 35.000 -83.0 5.000 -4.0 -1.472 -19.3 46.000 239.0 5.000 -4.0 1.322 -0.2 0.36 0.62
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--HHH-HHHHHHHHHHH-------------------------EEEEE------EEEEEE--------EEEEEE-----
Query: 27 DMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQAEASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYT-- 104
Sbjct: 193 KSKAELQSEERKRIDELIESGKEEG-------------------MKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEIT 253
--HHHHHHHHHHHHHHHHHH----- EEEEEE---EEEEEE--------EEEEE--EEEEHH
------------EEEEE----EEEEEE--------HHHHH----------EEEEE---EEEEEEE- ------EE
Query: 105 -----NDTVPKNANRKYFWRIYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIK-PIPANQEL 178
Sbjct: 254 DAKKREALYAQDPSTGCYMYYFQYLSKTYCVDAT-RETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEEL 332
HHHHHHHHH---------EEEEEE--EEEEEE-- ----------EE-----EEEEEEEE--EEEEEEEE----------
EEE-- HHHHHH------
Query: 179 LVWYC---RDFAERLHYPYP 195
Sbjct: 333 LYDYGDRSKASIEAHPWLKH 352
EE------HHHHHH------
160 residues (78.05%) 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: 7.54% helical, 25.63% extended, 66.83% loops/other (query: 14.63% 21.95% 63.41%)
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.
2O8J_A not_found 45.45.45.45 NONE -999.000 0 1 95.12% 14.87% OPTM -180.755 -248.720 1.798 0.367 0.419 0.717 0.755 15.240 -36.3 1.630 40.500 -49.0 1.080 9.000 -86.5 0.070 2.730 -26.9 1.400 3.130 -40.6 2.790 15.180 -11.8 2.070 3.760 -27.9 6.700 19.570 -67.2 6.850 17.010 -68.1 -30.000 16.000 -132.0 -30.000 15.000 -132.0 5.290 85.500 -52.5 12.390 84.000 -115.0 3.660 29.000 -67.0 3.350 14.000 -83.0 5.000 -9.7 -1.348 -29.4 0.000 -9.3e+061 5.000 -9.7 1.176 -1.5 0.60 0.78
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--------------------------HHH-HHHHHHHHHHH------------------ -------
Query: 3 SSHHHHHHSSGLVPRGSKMDMEDADMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQA-----------EASLPRN--- 68
Sbjct: 968 ITHLQHCTCVDDCS-SSNC-----------------LCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKN 1029
-------------- ---- HHHHH-----------------------EE--------------
EEEEE------EEEEEE--------EEEEEE-----------------EEEEE----EEEEEE--------H
Query: 69 --------LLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRIYSRGELHHFIDGFNEEKSNW 140
Sbjct: 1030 RVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDE---VYCIDARYYGNIS-- 1104
----------EEEEE-----EEEEE--------EEEE--EEEEEHHHHHH------EEEE-- -EEEEEEEEE---
HHHH----------EEEEE--- EEEEEEE-------EEEEE--HHHHHH--------
Query: 141 MRYVNPAHSPREQNLAACQNGM-----NIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGE 197
Sbjct: 1105 -RFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDYFTCQCGSE 1165
---EE-----EEEEEEE---------EEEEEE----------EE---HHHH----------
195 residues (95.12%) 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: 6.91% helical, 20.33% extended, 72.76% loops/other (query: 14.63% 21.95% 63.41%)
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.
2IGQ_A not_found 45.45.45.45 NONE -999.000 0 1 93.17% 15.71% OPTM -304.061 -167.880 1.759 0.402 0.564 0.735 0.788 16.710 -37.3 1.520 42.000 -41.5 1.360 26.000 -89.5 0.500 9.390 -23.5 1.100 0.560 -43.8 -0.080 0.340 8.9 1.410 -2.090 -31.3 3.230 7.060 -52.3 3.730 7.440 -58.6 -30.000 20.000 -129.0 -30.000 15.000 -129.0 5.780 65.500 -45.5 12.280 86.000 -118.0 2.640 56.000 -64.0 3.230 15.000 -81.0 5.000 -9.2 -2.226 -31.6 0.000 -9.3e+061 5.000 -9.2 1.633 -1.5 0.76 0.81
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----------------------HHH-HHHHHHHHHHH------- ------------
Query: 7 HHHHSSGLVPRGSKMDMEDADMTLWTEAEFEEKCTYIVNDHPWD------------------------SGADGGTSVQAE 62
Sbjct: 1021 IDRNITHLQYCVCIDDCSSSNC----------MCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQ 1090
---------------------H HHHH-----------------------EE-------------------
------EEEEE------EEEEEE--------EEEEEE-----------------EEEEE----EEEEEE--------HHH
Query: 63 ASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRIYSRGELHHFIDGFNEEKSNWMR 142
Sbjct: 1091 NGLRARLQLYRTRDMG--WGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLV-----YCIDARFYGNVS---R 1160
-----EEEEE-----E EEEE--------EEEE--EEEEEHHHHH-------EEE--E EEEEEEEE---- -
HH----------EEEEE--- EEEEEEE-------EEEEE--HHHHHH--------
Query: 143 YVNPAHSPREQNLAACQNGM-----NIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGE 197
Sbjct: 1161 FINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGSCRCGS 1220
-EE-----EEEEEEE---------EEEEEE----------EE---HHHHHHH--------
191 residues (93.17%) of query sequence aligned
DONE: Fri Aug 15 11:19:36 2008 EST