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:Sat Aug 09 03:41:16 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 T0401
--> 143 residues, sequence name: T0401
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 | 3 | 8 | 0 | 0 | 0 | 0 | 0 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 3.78 | 3.94 | 15.64 | 12.24 |
2 | 3.78 | 0.00 | 3.93 | 15.60 | 12.44 |
3 | 3.94 | 3.93 | 0.00 | 16.36 | 15.15 |
4 | 15.64 | 15.60 | 16.36 | 0.00 | 17.37 |
5 | 12.24 | 12.44 | 15.15 | 17.37 | 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 | 56.10 | 52.80 | 12.80 | 14.66 |
2 | 56.10 | 100.00 | 70.63 | 13.60 | 14.04 |
3 | 52.80 | 70.63 | 100.00 | 11.51 | 13.28 |
4 | 12.80 | 13.60 | 11.51 | 100.00 | 12.50 |
5 | 14.66 | 14.04 | 13.28 | 12.50 | 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 | 35.20 | 26.72 |
2 | 100.00 | 100.00 | 100.00 | 36.00 | 26.32 |
3 | 100.00 | 100.00 | 100.00 | 30.94 | 22.66 |
4 | 35.20 | 36.00 | 30.94 | 100.00 | 21.09 |
5 | 26.72 | 26.32 | 22.66 | 21.09 | 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: 31.61% helical, 17.42% extended, 50.97% loops/other (query: 37.06% 15.38% 47.55%)
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.
2ICG_A not_found 9.9.9.9 NONE -36.449 0 1 87.41% 21.60% OPTM -447.491 -271.370 1.548 0.611 0.551 0.746 0.925 13.190 -27.8 0.480 -7.000 -26.5 1.940 20.500 -94.0 0.800 8.780 -13.9 2.160 5.370 -35.8 0.260 9.370 7.3 0.380 -5.050 -25.5 4.310 16.160 -24.7 6.130 11.660 -41.3 -30.000 29.000 -78.0 -30.000 31.000 -89.0 2.900 58.000 -27.0 5.200 47.000 -82.0 2.850 17.000 -52.0 1.780 4.000 -68.0 5.000 -5.7 2.783 -30.0 0.000 -9.3e+061 5.000 -5.7 5.000 -0.3 0.25 0.85
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---------HHHHHHHHHH-----HHHHHHHHHHH-----------EEEE- HHHHHHHHH---HHHH--
Query: 7 KWYKKDGASSASIDDVEKLLNTTLPKQYKSFLLWSNGGEGKLGDNYIYIWA-----------IEDVIAYNHDYGIQKYLQ 75
Sbjct: 21 TFHASGTGTPELIKIYQDALGNEFPETYKLFLEKY--GTLTFNGVSFYGISKRGLSAASIPDVKFATEQARTFGD---IN 95
--------HHHHHHHHHHH-----HHHHHHHHH-- -EEE--EEE---------------HHHHHHHHHHH--- --
---EE-------EEEEE---- EEEEEE--------EEEE---HHHHHHHH----HH
Query: 76 KEYWAFGMDGDIGYILHLSDN-----SIYRVDLGDLDITSIKYIAPSFDDFLGKAIYLNFN 131
Sbjct: 96 KEIIKNSGYGSIFSIDTSIIGSEGEPVIVETNLSFKDNTEKKVVANSFGEFLLEEIELSLT 156
---EE-----EEEEEEEEE-----EEEEEE---HHHH---EEEE--HHHHHHHHHHHHHH-
125 residues (87.41%) 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: 32.06% helical, 16.03% extended, 51.91% loops/other (query: 37.06% 15.38% 47.55%)
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.
2PAG_A not_found 9.9.9.9 NONE -36.567 0 1 87.41% 14.29% OPTM -457.989 -288.850 1.554 0.604 0.518 0.831 0.870 14.130 -27.9 0.360 -4.000 -3.5 -0.190 -10.500 -53.0 0.280 0.410 -9.8 0.960 -0.680 -36.7 0.120 -3.250 9.7 1.210 -0.500 -28.5 1.200 7.930 -12.0 8.870 15.790 -44.6 -30.000 36.000 -71.0 -30.000 34.000 -89.0 2.530 34.000 -10.0 4.890 31.000 -64.0 1.790 18.000 -28.0 4.340 15.000 -67.0 5.000 -0.4 -0.172 -45.8 0.000 -9.3e+061 5.000 -0.5 0.826 -0.7 0.39 0.89
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHH----- ----HHHHHHHHHH-----HHHHHHHHHHH-----------EEEE- HHHHHHHHH---HHH
Query: 4 IESKWYKK----DGASSASIDDVEKLLNTTLPKQYKSFLLWSNGGEGKLGDNYIYIWA-------IEDVIAYNHDYGIQK 72
Sbjct: 8 LREANEPVPVPLELPDEDQLVEIEEQLFINIPFVFKEFLLTVSDVV--YGSLEPVTVTDPQSHTYLPEVCATAWDLG--- 82
HHH------------HHHHHHHHHHH-----HHHHHHHHHH----- ----------------HHHHHHHHHHH--
H-----EE-------EEEEE----EEEEEE--------EEEE---HHHHHHHH----
Query: 73 YLQKEYWAFGMDGDIGYILHLSDNSIYRVDLGDLDITSIKYIAPSFDDFLGKAIYLN 129
Sbjct: 83 -VPRELIPICQDGE-DYYCVEEDGTVLLWSA-----LVTEESWESVWHWARDVWLES 132
----EEEEEE--E EEEE-----EEEE--- EEEEEE--HHHHHHH-----S
125 residues (87.41%) 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: 32.67% helical, 21.33% extended, 46.00% loops/other (query: 37.06% 15.38% 47.55%)
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.
2PRV_A not_found 9.9.9.9 NONE -36.713 0 1 95.80% 19.29% OPTM -509.292 -331.050 2.483 0.613 0.541 0.797 0.857 17.360 -33.8 2.350 31.500 -79.5 3.920 54.000 -127.0 1.670 0.390 -26.7 0.610 -0.600 -33.2 2.110 0.530 -14.1 2.570 0.990 -28.5 6.390 18.470 -39.6 14.230 26.600 -58.4 -30.000 44.000 -89.0 -30.000 37.000 -95.0 4.910 52.000 -69.0 9.930 64.000 -128.0 4.830 36.000 -54.0 4.690 15.000 -71.0 5.000 -3.0 0.531 -27.7 0.000 -9.3e+061 5.000 -3.0 0.301 -1.8 0.42 0.79
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHH---------HHHHHHHHHH-----HHHHHHHHHHH-----------EEEE- HHHHHHHHH---HHHH----
Query: 4 IESKWYKKDGASSASIDDVEKLLNTTLPKQYKSFLLWSNGGEGKLGDNYIYIWA------IEDVIAYNHDYGIQKYLQKE 77
Sbjct: 15 NKQNAIFTEGASHENIGRIEENLQCDLPNSYKWFLEKYG--AGGLFGVLVLGYNFDHASVVNRTNEYKEHYG----LTDG 88
----EE-----HHHHHHHHHHH-----HHHHHHHHHH-- EEE--EEE--------HHHHHHHHHHHH--- ---E
-EE-------EEEEE-- --EEEEEE--------EEEE---HHHHHHHH----HHHHHHHH------
Query: 78 YWAFGMDGDIGYILHLS--DNSIYRVDLGDLDITSIKYIAPSFDDFLGKAIYLNFNKLQNVANNNLTT 143
Sbjct: 89 LVVIEDVDYFAYCLDTNKKDGECPVVEWDRV-IGYQDTVADSFIEFFYNK----IQEAKDDWDEDEDW 151
EEEEE---EEEEEE---------EEEEE--- EEEEEEE--HHHHHHHHH HHHHHHH-------
137 residues (95.80%) 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: 34.64% helical, 12.29% extended, 53.07% loops/other (query: 37.06% 15.38% 47.55%)
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.
2UVP_A not_found 9.9.9.9 NONE -999.000 0 1 97.20% 14.39% OPTM -322.623 -163.330 0.931 0.448 0.123 0.642 0.811 11.340 -25.1 0.670 5.000 -10.5 -1.390 -14.500 -68.5 0.410 -3.250 29.4 0.690 1.520 -33.5 1.360 2.900 49.2 0.420 1.070 -24.2 2.540 7.170 16.2 7.830 10.830 -45.8 -30.000 25.000 -75.0 -30.000 19.000 -89.0 1.260 -4.000 26.0 -1.570 -16.000 -36.0 2.870 11.000 -16.0 0.640 2.000 -51.0 5.000 0.4 3.397 -32.5 0.000 -9.3e+061 5.000 0.4 0.146 0.1 0.37 0.89
alignment source: OPTM
HH---------HHHH HHHHHH-- ---HHHHHHHHHHH-----------EEEE-H HHHH
Query: 5 ESKWYKKDGASSASI--DDVEKLLN--------TTLPKQYKSFLLWSNGGEGKLGDNYIYIWAI------------EDVI 62
Sbjct: 22 QSGWLELERSSYAKLIAQTISHVLNGGSLLVSADSSRHWFLNYILSNLNPKDLKERPLLSVIDFNASSFYPKNDANLSLA 101
----------HHHHHHHHHHHHH---EEEEEE----HHHHHHHHHHH------------EEE-----------HHHHHHH
HHHH---HHHH-----EE-- -----EEEEE----EEEEEE--------EEEE---HHHHHHHH----HH
Query: 63 AYNHDYGIQKYLQKEYWAFG-----------MDGDIGYILHLSDNSIYRVDLGDLDITSIKYIAPSFDDFLGKAIYLNFN 131
Sbjct: 102 TIEMTYQ-----NPMFWHVGKIENEGLKTILLSKIPSFLWLFEELKEDCLLLKEHD--------SLLDYKLLQLFKLFEN 168
HHHH--- EEEEEE-----HHHHHHH-----EEEEE--------EE------ -HHHHHHHHHHHHHHH
HHHHHH------
Query: 132 KLQNVANNNLTT 143
Sbjct: 169 ALFSVLYNKVTL 180
HHHHH------L
139 residues (97.20%) 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: 33.33% helical, 14.73% extended, 51.94% loops/other (query: 37.06% 15.38% 47.55%)
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.
2RIQ_A not_found 9.9.9.9 NONE -999.000 0 1 74.83% 10.16% OPTM -164.721 -189.390 0.760 0.359 0.207 0.683 0.718 6.040 -18.3 0.130 -6.500 -21.5 -1.210 -19.000 -53.0 1.380 -1.650 -19.1 0.760 0.290 -28.0 0.890 -2.650 -2.7 1.280 1.140 -19.8 5.130 19.180 -33.8 4.790 6.680 -38.1 -30.000 37.000 -76.0 -30.000 16.000 -77.0 2.150 11.000 -6.0 -0.490 0.000 -36.0 3.910 7.000 -8.0 2.700 13.000 -48.0 5.000 0.8 -1.004 -34.9 0.000 -9.3e+061 5.000 0.8 -1.538 0.1 0.28 0.91
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHH-----HHHHHHHHHHH-----------EEEE-HHHHHHHHH---HHHH-----EE-------EEEEE---
Query: 16 SASIDDVEKLLNTTLPKQYKSFLLWSNGGEGKLGDNYIYIWAIEDVIAYNHDYGIQKYLQKEYWAFGMDGDIGYILHLSD 95
Sbjct: 246 WNIKDELKKVCS---TNDLKELLIFNK---QQVPSG-------ESAILDRVADGMVFG-----ALLPCEECSGQLVFKSD 307
HHHHHHHHH--H HHHHHHHHH--- -----H HHHHHHHHHHHHH-E E---------EEEE--E
-EEEEEE--- -----EEEE---HHHHHHHH----HHHHHHHH------
Query: 96 NSIYRVDLGD-------LDITSIKYIAPSFDDFLGKAIYLNFNKLQNVANNNLTT 143
Sbjct: 308 AYYCTGDVTAWTKCMVKTQTPNRKEWVTPK----------EFREISYLKKLKVKK 352
EEE--EEE--EE---EE----EE-----HH HH-HHHHHH------
107 residues (74.83%) of query sequence aligned
DONE: Sat Aug 09 05:10:52 2008 EST