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:Mon Aug 11 14:21:40 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 T0415
--> 109 residues, sequence name: T0415
Database: T:\CBSU\blastdb\20080108\nr
-> 4 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 | 97 | 89 | 1 | 2 | 1 | 0 | 0 | 8 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 13.68 | 14.19 | 14.50 | 16.88 |
2 | 13.68 | 0.00 | 14.47 | 16.12 | 14.10 |
3 | 14.19 | 14.47 | 0.00 | 16.36 | 17.13 |
4 | 14.50 | 16.12 | 16.36 | 0.00 | 16.61 |
5 | 16.88 | 14.10 | 17.13 | 16.61 | 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 | 22.47 | 21.88 | 16.67 | 15.22 |
2 | 22.47 | 100.00 | 23.96 | 14.85 | 16.47 |
3 | 21.88 | 23.96 | 100.00 | 15.53 | 17.39 |
4 | 16.67 | 14.85 | 15.53 | 100.00 | 13.04 |
5 | 15.22 | 16.47 | 17.39 | 13.04 | 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 | 34.83 | 53.13 | 27.08 | 33.70 |
2 | 34.83 | 100.00 | 35.42 | 34.65 | 32.94 |
3 | 53.13 | 35.42 | 100.00 | 32.04 | 27.17 |
4 | 27.08 | 34.65 | 32.04 | 100.00 | 34.78 |
5 | 33.70 | 32.94 | 27.17 | 34.78 | 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: 7.22% helical, 51.55% extended, 41.24% loops/other (query: 26.61% 37.61% 35.78%)
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.
3BS1_A not_found 18.18.18.18 GUESS -26.873 0 1 85.32% 22.92% OPTM -355.946 -279.730 3.153 0.712 0.659 0.862 0.923 14.830 -32.6 5.830 90.000 -111.0 6.830 62.500 -130.5 0.790 0.680 -17.6 1.320 4.390 -47.1 4.760 15.410 -24.3 6.420 14.300 -53.1 7.250 15.760 -34.1 11.850 14.200 -51.8 -30.000 6.000 -56.0 -30.000 5.000 -64.0 10.670 147.000 -154.0 19.060 129.000 -172.0 6.730 56.000 -49.0 9.700 37.000 -74.0 5.000 -9.7 -5.253 -22.5 0.000 -9.3e+061 5.000 -9.7 5.000 -5.7 0.68 0.33
alignment source: OPTM
---EEEEE----EEEE----EEEEEE--- EEEEEE---EEEE---HHHHHHH-----EEEEE-HHEE-HHHHHHHH--
Query: 1 GKSVVTLKTTDGWIPVPFSKVMYLEAKDK--KTYVNAEELTGTHKYSLQEFEYLLPKDSFIRCHRSFIVNVNHIKAIYPD 78
Sbjct: 139 SVETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLD--DRFFRCHNSFVVNRHNIE---SI 213
--EEEEEE--EEEEEE---EEEEEE-----EEEEEE---EEEEE--HHHHHHH-- -EEEEE--EEEE---EEE EE
----EEEEE----EEEE-
Query: 79 THSTFLLSMDNGERVPVS 96
Sbjct: 214 DSKERIVYFKNKEHCYAS 231
----EEEE----EEE---
93 residues (85.32%) 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: 34.31% helical, 23.53% extended, 42.16% loops/other (query: 26.61% 37.61% 35.78%)
SCOP classification: [All alpha proteins]/[Putative DNA-binding domain]
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.
1SBX_A a.6.1.4 1.1.1.1 NONE -999.000 0 1 86.24% 9.80% OPTM -307.550 -222.340 1.096 0.494 0.167 0.815 0.822 8.380 -16.5 1.100 5.000 -18.5 1.560 12.000 -63.0 0.750 3.640 -7.8 -0.060 2.110 -25.6 1.370 8.750 1.1 3.590 4.270 -24.2 5.760 17.410 -21.8 8.150 11.180 -30.9 -30.000 40.000 -66.0 -30.000 28.000 -66.0 1.240 24.000 -1.0 1.510 10.000 -42.0 0.550 0.000 18.0 2.140 6.000 -30.0 5.000 5.0 -0.609 -53.0 37.000 148.0 5.000 5.0 5.000 5.0 0.27 0.56
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
E----EEEE----EEEEEE---EEEEEE---EEEE- --HHHHHHH-----E EEEE-HHEE-HHHHHHHH------EE
Query: 8 KTTDGWIPVPFSKVMYLEAKDKKTYVNAEELTGTHK-YSLQEFEYLLPKDSF--IRCHRSFIVNVNHIKAIYPDTHSTFL 84
Sbjct: 95 STERCETVLEGETISCFVVGGEKRLCLPQILNSVLRDFSLQQINAVCDELHIYCSRCT------ADQLEILKVGILP--- 165
---EEEEE--EEEEEEEE--EEEEEHHHHH--------HHHHHHHHHH-----EE--H HHHHHHH------
EEE----EEEE-HHHHHHHHHHHH-
Query: 85 LSMDNGERVPVSQSYASYFRKLLGF 109
Sbjct: 166 --FSAPSCGLITKTDAERLCNALLY 188
-----EEEEHHHHHHHHHHHH--
94 residues (86.24%) 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: 10.92% helical, 44.54% extended, 44.54% loops/other (query: 26.61% 37.61% 35.78%)
SCOP classification: [Alpha and beta proteins (a+b)]/[CYTH-like phosphatases]
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.
2FBL_A d.63.1.2 8.1.1.1 NONE -999.000 0 1 94.50% 17.48% OPTM -187.314 -162.310 0.951 0.502 0.130 0.511 0.683 6.610 -20.8 0.640 -30.000 8.0 -0.420 -8.500 -60.5 0.570 3.820 44.9 2.050 2.220 -28.2 0.710 2.090 61.5 1.880 -1.880 -20.4 4.930 22.440 23.0 7.670 10.260 -35.7 -30.000 29.000 -47.0 -30.000 14.000 -60.0 2.780 28.500 31.5 2.670 17.000 -53.0 4.390 30.000 -11.0 1.190 5.000 -40.0 5.000 -1.3 -3.081 -43.7 0.000 -9.3e+061 5.000 -0.7 -0.509 0.1 0.71 0.55
alignment source: OPTM
---EEEEE----EEEE-- --EEEEEE---EEEEEE---EEEE---HHHHHHH-- ---EEEEE-HHEE-HHHHHHHH-
Query: 1 GKSVVTLKTTDGWIPVPF-SKVMYLEAKDKKTYVNAEELTGTHKYSLQEFEYLLP--KDSFIRCHRSFIVNVNHIKAIYP 77
Sbjct: 15 DGELHAVPLRQGYLTTPTDSIELRLRQQGTEYFMTLKSQEYEIQIDVTQFEMLWPATEGRRVEKTRYSGKL--------P 86
---EEEEEEEEE--------EEEEEEE--EEEEEEE--EEEEEE-HHHHHHH-------EEEEEEEEEE-- -
-----EEEEE---- EEEE -HHHHHHH
Query: 78 DTHSTFLLSMDNGE-------RVPV-SQSYASYF 103
Sbjct: 87 D-GQLFELDVFAGHLSPLMLVEVEFLSEDAAQAF 119
- -EEEEEEE-------EEEEEEE--HHHHHH--
103 residues (94.50%) 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: 17.36% helical, 38.84% extended, 43.80% loops/other (query: 26.61% 37.61% 35.78%)
SCOP classification: [All beta proteins]/[Sm-like fold]
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.
1M5Q_A b.38.1.1 9.1.1.1 NONE -999.000 0 1 99.08% 14.81% OPTM -133.046 -145.300 0.817 0.418 0.104 0.413 0.416 5.400 -21.2 2.380 12.000 -44.0 1.980 8.500 -81.5 1.270 4.390 -13.4 -0.520 -0.210 -23.4 2.940 10.870 -5.8 1.460 -0.710 -19.1 4.330 14.120 -17.5 4.020 4.170 -28.3 -30.000 13.000 -51.0 -30.000 12.000 -58.0 1.600 14.000 -5.0 2.390 13.000 -62.0 0.910 9.000 -9.0 2.880 3.000 -37.0 5.000 1.3 3.104 -37.9 0.000 -9.3e+061 5.000 0.7 5.000 5.0 0.81 0.79
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---EEEEE---- EEEE--- -EEEEEE--- EEEEEE---EEEE--- HHHHHHH-----EEEE
Query: 1 GKSVVTLKTTDG------WIPVPFS-KVMYLEAKDK----KTYVNAEELTGTHKYS--------LQEFEYLLPKDSFIRC 61
Sbjct: 20 LGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIYRYIVHIDSTERRIDREFAKQAEKIFPGVKYIE- 98
--EEEEEE----EEEEEEEEE-----EEEEEEE-----EEEEEE----EEEEE--------HHHHHHHHH----EEE--
E-HHEE-HHHHHHHH------EEEEE----EEEE-H HHHHHHHHHHH
Query: 62 HRSFIVNVNHIKAIYPDTHSTFLLSMDNGERVPVSQ-------SYASYFRKLLG 108
Sbjct: 99 ------------------ETNVVLIGDK---VRVSEIGVEGVGPVAERAKRLFE 131
--EEEE---E EEE--EEE---HHHHHHHHHHHH
108 residues (99.08%) 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: 11.93% helical, 25.69% extended, 62.39% loops/other (query: 26.61% 37.61% 35.78%)
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.
2YUB_A not_found 18.18.18.18 NONE -999.000 0 1 84.40% 13.04% OPTM -143.623 -183.230 0.809 0.453 0.178 0.636 0.796 3.340 -16.3 1.780 -10.500 -46.5 1.120 0.000 -74.0 0.480 2.760 -14.4 1.750 3.760 -31.3 0.670 -3.340 -6.2 5.210 6.780 -31.3 3.770 11.790 -21.8 9.410 13.440 -41.2 -30.000 15.000 -48.0 -30.000 14.000 -61.0 1.040 -11.000 -3.0 0.410 3.000 -41.0 2.170 3.000 25.0 0.090 3.000 -30.0 5.000 0.2 -3.302 -46.6 0.000 -9.3e+061 5.000 0.2 5.000 5.0 0.75 0.47
alignment source: OPTM
---EEEEE---- EEEE----EEEEEE---EEEEEE---EEEE---HHHHHHH-----EEEEE-HHEE- HHHH
Query: 1 GKSVVTLKTTDG-----WIPVPFSKVMYLEAKDKKTYVNAEELTGTHKYSLQEFEYLLPKDSFIRCHRSFIVN---VNHI 72
Sbjct: 15 SVTLISMPATTECRRGFSVTVESAS------SNYATTVQVKEVNRMHIS--PNNRNAIHPGDRILEINGTPVRTLRVEEV 86
EEEEEE----------EEEEE---- ----EEEEEE-------- -HHHH------EEEE---------HHHHH
HHHH----- -EEEEE----E
Query: 73 KAIYPDTHS--TFLLSMDNGER 92
Sbjct: 87 EDAIKQTSQTLQLLIEHDPVPQ 108
HHHH-----EEEEEEE------
92 residues (84.40%) of query sequence aligned
DONE: Mon Aug 11 15:49:02 2008 EST