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 11:21:58 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 T0435
--> 151 residues, sequence name: T0435
Database: T:\CBSU\blastdb\20080108\nr
-> 14 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 | 22 | 114 | 11 | 0 | 3 | 0 | 4 | 18 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 6.84 | 5.87 | 13.51 | 13.22 |
2 | 6.84 | 0.00 | 7.18 | 12.62 | 12.98 |
3 | 5.87 | 7.18 | 0.00 | 4.71 | 4.14 |
4 | 13.51 | 12.62 | 4.71 | 0.00 | 4.46 |
5 | 13.22 | 12.98 | 4.14 | 4.46 | 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 | 84.78 | 36.97 | 32.37 | 31.88 |
2 | 84.78 | 100.00 | 32.00 | 29.71 | 33.33 |
3 | 36.97 | 32.00 | 100.00 | 63.03 | 36.43 |
4 | 32.37 | 29.71 | 63.03 | 100.00 | 54.35 |
5 | 31.88 | 33.33 | 36.43 | 54.35 | 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 | 97.83 | 100.00 | 89.93 | 90.58 |
2 | 97.83 | 100.00 | 96.80 | 89.86 | 88.89 |
3 | 100.00 | 96.80 | 100.00 | 100.00 | 100.00 |
4 | 89.93 | 89.86 | 100.00 | 100.00 | 100.00 |
5 | 90.58 | 88.89 | 100.00 | 100.00 | 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: 3.55% helical, 30.50% extended, 65.96% loops/other (query: 5.96% 31.13% 62.91%)
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 104.104.104.12 NONE -38.855 0 1 92.72% 27.86% OPTM -434.627 -353.720 5.556 0.602 0.660 0.884 0.927 25.830 -48.3 10.300 220.500 -243.0 14.140 187.500 -258.0 2.570 10.590 -32.2 1.230 4.870 -36.6 7.500 31.750 -37.5 8.810 15.490 -43.3 8.640 26.850 -64.6 11.240 24.670 -70.7 -30.000 15.000 -107.0 -30.000 7.000 -107.0 24.490 472.500 -430.5 47.560 395.000 -448.0 6.230 59.000 -51.0 7.610 37.000 -93.0 5.000 -41.7 -0.591 -35.3 0.000 -9.3e+061 5.000 -41.7 -1.432 -14.4 0.73 0.94
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------------------ ------EEEEE---- --EEEEE---------E-EEE--E---HHH-----------E
Query: 1 EHGPVTFVPDTPIESRAR----LSLPKQLVLRQSIVG-AEVGVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVNHIW 75
Sbjct: 1 NQNTTEPVAATETLAEVPEHVLRGLPEEVRLFPSAVDKTRIGVWATKPILKGKKFGPFVGDKKKRSQVKNNV-----YMW 75
------------------HHHHH-----EEEEE-------EEEEE--------EE-----EEE--------- -EE
EEEE----EEEEE----------EEE----------EEEEEE---EEEEEEEE-----EEEEE--
Query: 76 KIYHNGVLEFCIITTDENECNWMMFVRKARNREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYS 140
Sbjct: 76 EVYYPNLGWMCIDATDPEKGNWLRYVNWACSGEEQNLFPLEINRAIYYKTLKPIAPGEELLVWYN 140
EEEE---EEEEEE-------------EE--------EEEEEE--EEEEEE----------EE---
140 residues (92.72%) 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: 5.96% 31.13% 62.91%)
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 104.104.104.12 NONE -38.866 0 1 95.36% 27.78% OPTM -497.823 -400.290 5.658 0.492 0.606 0.802 0.898 26.630 -50.5 8.200 212.000 -209.5 14.950 176.500 -254.5 1.470 0.450 -29.0 -0.130 -2.420 -51.4 9.250 39.380 -39.7 9.090 20.670 -63.5 11.340 31.420 -65.0 14.020 29.660 -79.0 -30.000 23.000 -105.0 -30.000 19.000 -110.0 22.910 457.500 -396.0 48.610 392.000 -443.0 5.060 29.000 -44.0 6.910 23.000 -82.0 5.000 -43.0 -0.159 -34.6 0.000 -9.3e+061 5.000 -43.0 -0.921 -15.0 0.60 0.87
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----------------- -----EEEEE----- -EEEEE---------E-EEE--E---HHH---------
Query: 3 GPVTFVPDTPIESRARL---------SLPKQLVLRQSIVGA-EVGVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVN 72
Sbjct: 3 GSMDQNTTEPVAATETLAEVPEHVLRGLPEEVRLFPSAVDKTRIGVWATKPILKGKKFGPFVGDKKKR-----SQVKNNV 77
---------------------HHHH-------EEEE-------EEEE--------EEEEEE---EE-- -------
--EEEEE----EEEEE----------EEE----------EEEEEE---EEEEEEEE-----EEEEE-- HHHHHH
Query: 73 HIWKIYHNGVLEFCIITTDENECNWMMFVRKARNREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYS------RDYAQQ 146
Sbjct: 78 YMWEVYYPNLGWMCIDATDPEKGNWLRYVNWACSGEEQNLFPLEINRAIYYKTLKPIAPGEELLVWYGEDNPEIAAAIEE 157
-EEEEEE---EEEEEE-------------EE---------EEEEE--EEEEEE----------EE------HHHHHHHHH
144 residues (95.36%) 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: 10.69% helical, 33.33% extended, 55.97% loops/other (query: 5.96% 31.13% 62.91%)
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 104.104.104.12 NONE -39.104 0 1 86.09% 16.15% OPTM -408.289 -250.890 1.845 0.506 0.480 0.798 0.927 9.210 -33.1 2.410 45.500 -71.5 2.290 30.500 -92.5 -0.950 -0.640 -23.5 1.030 -1.830 -48.8 2.440 13.150 -17.4 2.570 4.830 -40.4 4.940 14.010 -46.6 7.440 9.260 -54.3 -30.000 4.000 -86.0 -30.000 9.000 -94.0 4.080 68.000 -40.0 5.980 19.000 -76.0 3.720 38.000 -55.0 5.180 28.000 -73.0 5.000 -6.2 2.331 -29.1 0.000 -9.3e+061 5.000 -6.2 -0.602 -1.0 0.43 0.86
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---EEEEE------EEEEE---------E-EEE--E---HHH-- ---------EEEEE----EEEEE---- ---
Query: 22 PKQLVLRQSIVGAEVGVWTGETIPVRTCFGPLIGQQSHSMEVAE-----WTDKAVNHIWKIYHNGVLEFCIITTDE-NEC 95
Sbjct: 214 KEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRL 293
---EEEEEE---EEEEEE--------EEEEE--EEEEHHHHHHHHHHH---------EEEEEE--EEEEEE---------
---EEE----------EEEEEE-- -EEEEEEEE-----EEEEE-- HHHHHH-----
Query: 96 NWMMFVRKARNREEQNLVAYPHDG--KIFFCTSQDIPPENELLFYYS---RDYAQQIGVPE 151
Sbjct: 294 GRLINHSKCGN---CQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLK 351
---EE-----E EEEEEEE--EEEEEEEE----------EE------HHHHHH------
130 residues (86.09%) 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: 3.07% helical, 17.24% extended, 79.69% loops/other (query: 5.96% 31.13% 62.91%)
SCOP classification: [All beta proteins]/[beta-clip]
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.
1MVH_A b.85.7.1 112.3.3.1 NONE -39.183 0 1 92.05% 18.71% OPTM -319.478 -253.160 1.691 0.560 0.745 0.814 0.881 15.310 -34.4 2.670 102.000 -73.0 2.760 40.000 -94.5 3.200 13.000 -37.5 1.630 2.030 -46.3 3.880 23.840 -25.2 2.340 4.710 -35.5 5.100 17.650 -56.8 6.090 7.920 -58.3 -30.000 9.000 -99.0 -30.000 8.000 -103.0 3.680 104.000 -31.5 6.730 40.000 -75.0 2.370 30.000 -37.0 3.220 17.000 -71.0 5.000 -9.0 -1.177 -34.5 0.000 -9.3e+061 5.000 -9.0 5.000 0.4 0.75 0.66
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-----------------------EEEEE------EEEEE---------E-EEE--E---HHH- ----------EEE
Query: 2 HGPVTFVPDTPIESRARLSLPKQLVLRQSIVGAEVGVWTGETIPVRTCFGPLIGQQSHSMEVA----EWTDKAVNHIWKI 77
Sbjct: 310 FCSCSMECPNRVVQRGR-TLP--LEIFKTK-EKGWGVRSLRFAPAGTFITCYLGEVITSAEAAKRDKNYDDDGITYLFDL 385
----------------- --E EEEE--- --EEEEE--------EEEE---EEEEHHHHHHHH----------EEEE-
EE-- --EEEEE----------EEE----------EEEEEE--- EEEEEEEE-----EEEEE--
Query: 78 YHNG-VLEFCIITTDENECNWMMFVRKARNREEQNLVAYPHDGK--------IFFCTSQDIPPENELLFYYS 140
Sbjct: 386 DMFDDASEYTVDAQNYGDVS-----RFFNHSCSPNIAIYSAVRNHGFRTIYDLAFFAIKDIQPLEELTFDYA 452
-------EEEE---EE---- --EE-----EEEEEEE---------EEEEEE----------EE----
139 residues (92.05%) 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: 7.09% helical, 34.04% extended, 58.87% loops/other (query: 5.96% 31.13% 62.91%)
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 104.104.104.12 NONE -39.373 0 1 92.72% 16.22% OPTM -412.679 -289.920 1.530 0.566 0.622 0.817 0.838 15.840 -33.7 1.980 73.500 -57.0 3.200 49.000 -106.5 0.870 3.060 -31.1 -0.010 -1.100 -35.4 0.140 4.030 -7.6 1.850 3.250 -25.5 0.730 -3.140 -39.3 6.540 11.830 -57.7 -30.000 -6.000 -89.0 -30.000 3.000 -100.0 2.670 48.000 -7.0 4.170 4.000 -67.0 0.890 13.000 -19.0 4.030 17.000 -67.0 5.000 -9.5 0.654 -34.4 0.000 -9.3e+061 5.000 -9.5 0.898 -0.1 0.48 0.92
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----------------------EEEEE------EEEEE---------E-EEE--E---HHH-----------EEEEE---
Query: 3 GPVTFVPDTPIESRARLSLPKQLVLRQSIVGAEVGVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVNHIWKIYHNGV 82
Sbjct: 1022 SCWRNCKNRVVQSGIKV----RLQLYRTA-KMGWGVRALQTIPQGTFICEYVGELISDAEADVREDD--SYLFDLDEV-- 1092
----------------- -EEEEE-- ---EEEEE--------EEEE--EEEEEHHHHHH---- --EEEE---
-EEEEE----------EEE----------EEEEEE-- -EEEEEEEE-----EEEEE--HHHHHH----
Query: 83 LEFCIITTDENECNWMMFVRKARNREEQNLVAYPHDG--------KIFFCTSQDIPPENELLFYYSRDYAQQIGVP 150
Sbjct: 1093 --YCIDARYYGNISRFINHLC-----DPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDYFTCQ 1161
EEEEEEEEE------EE-- ---EEEEEE----------EEEEEE----------EE---HHHH------
140 residues (92.72%) of query sequence aligned
DONE: Fri Aug 15 15:53:30 2008 EST