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:Wed Aug 06 22:46:48 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 T0389
--> 153 residues, sequence name: T0389
Database: T:\CBSU\blastdb\20080108\nr
-> 19 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 | 50 | 14 | 4 | 10 | 3 | 2 | 2 | 24 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.11 | 8.00 | 5.62 | 7.45 |
2 | 5.11 | 0.00 | 9.07 | 7.25 | 6.97 |
3 | 8.00 | 9.07 | 0.00 | 6.58 | 8.56 |
4 | 5.62 | 7.25 | 6.58 | 0.00 | 7.79 |
5 | 7.45 | 6.97 | 8.56 | 7.79 | 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 | 43.18 | 33.83 | 32.58 | 31.71 |
2 | 43.18 | 100.00 | 34.09 | 33.08 | 34.96 |
3 | 33.83 | 34.09 | 100.00 | 41.98 | 36.29 |
4 | 32.58 | 33.08 | 41.98 | 100.00 | 34.71 |
5 | 31.71 | 34.96 | 36.29 | 34.71 | 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 | 47.37 | 100.00 | 47.15 |
2 | 100.00 | 100.00 | 47.73 | 50.00 | 50.41 |
3 | 47.37 | 47.73 | 100.00 | 52.67 | 47.58 |
4 | 100.00 | 50.00 | 52.67 | 100.00 | 48.76 |
5 | 47.15 | 50.41 | 47.58 | 48.76 | 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: 39.69% helical, 16.03% extended, 44.27% loops/other (query: 33.33% 9.80% 56.86%)
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.
2OUC_A not_found 41.41.41.41 NONE -38.387 0 1 86.27% 29.10% OPTM -648.551 -334.790 6.015 0.656 0.830 0.918 0.931 30.180 -44.7 9.320 179.000 -183.5 16.250 189.000 -261.5 -0.710 -3.040 -5.0 0.500 0.510 -36.8 3.660 16.660 -7.8 13.640 35.410 -59.4 6.540 16.200 -29.2 19.960 35.260 -71.2 -30.000 26.000 -82.0 -30.000 30.000 -94.0 23.810 403.000 -387.0 53.150 402.000 -463.0 3.400 17.000 -29.0 9.370 32.000 -87.0 5.000 -37.4 -5.923 -27.1 0.000 -9.3e+061 5.000 -37.2 1.114 -17.3 0.31 0.75
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----HHHHHHHHH-----EEEEE---HHHHHH----------- HHHHHHHH------HHH----- HHHH-----
Query: 4 TQIVTERLVALLESGTEKVLLIDSRPFVEYNTSHILEAININC-SKLMKRRLQQDKVLITELIQHS-----AKHKVDIDC 77
Sbjct: 148 KIIYPNDLAKKMTKP----VIIDCRPFMEYNKSHIQGAVHINCADKISRRRLQQGKITVLDLISCREGKDSFKRIFSKE- 222
-EE-HHHHHHHHH-- EEEE---HHHHHHEEE---EE-----HHHHHHHH-----HHHHHH------HHHHHHH--
--EEEEEE-------------HHHHHHHHHH-----EEEE---HHHHHHHHHHH------
Query: 78 SQKVVVYDQSSQDVASLSSDCFLTVLLGKLEKSFNSVHLLAGGFAEFSRCFPGLCEGKST 137
Sbjct: 223 ---IIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLSSFKQNHENLCDNSKE 279
EEEE--------------HHHHHHHHHHH-----EEE--HHHHH-------EEE---
132 residues (86.27%) 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: 35.07% helical, 12.69% extended, 52.24% loops/other (query: 33.33% 9.80% 56.86%)
SCOP classification: [Alpha and beta proteins (a/b)]/[Rhodanese/Cell cycle control phosphatase]
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.
c.46.1.4.1_A c.46.1.4 24.12.12.2 NONE -38.754 0 1 86.27% 18.18% OPTM -561.980 -407.780 2.653 0.620 0.868 0.914 0.935 22.160 -37.7 1.930 19.500 -20.0 3.620 45.000 -91.0 -0.030 -1.410 -13.8 -0.710 -3.370 -34.3 1.160 -0.440 1.9 1.430 -1.050 -27.8 7.040 23.510 -34.2 10.680 19.850 -57.3 -30.000 17.000 -86.0 -30.000 29.000 -103.0 6.970 94.000 -50.0 14.900 70.000 -116.0 3.100 36.000 -34.0 8.090 29.000 -80.0 5.000 -7.2 -1.651 -28.5 0.000 -9.3e+061 5.000 -7.2 5.000 -1.2 0.36 0.91
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----HHHHHHHHH-----EEEEE---HHHHHH-----------HHHHHHHH------HHH---- -HHHH-------E
Query: 4 TQIVTERLVALLESGTEKVLLIDSRPFVEYNTSHILEAININCSKLMKRRLQQDKVLITELIQH---SAKHKVDIDCSQK 80
Sbjct: 181 GAITAKELYTMMTDKNISLIIMDARRMQDYQDSCILHSLSVP------EEAISPGVTASWIEAHLPDDSKDTWKKRGNVE 254
-EE-HHHHHHHHH-----EEEEE---HHHHHH------EE-- ---------HHHHHH---HHHHHHHH------
EEEEE-------------HHHHHHHHHH-- ---EEEE---HHHHHHHHHHH----
Query: 81 VVVYDQSSQDVASLSSDCFLTVLLGKLEKS------FNSVHLLAGGFAEFSRCFPGLCEGK 135
Sbjct: 255 YVVLLDWFSSAKDLQIGTTLRSLKDALFKWESKTVLRNEPLVLEGGYENWLLCYPQYTTNA 315
EEEEE-------------HHHHHHHHHH------------EEE--HHHHHHHH--------
132 residues (86.27%) 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: 42.45% helical, 18.87% extended, 38.68% loops/other (query: 33.33% 9.80% 56.86%)
SCOP classification: [Alpha and beta proteins (a/b)]/[Rhodanese/Cell cycle control phosphatase]
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.
1GMX_A c.46.1.3 24.12.12.2 NONE -39.012 0 1 67.97% 13.43% OPTM -554.095 -434.070 1.607 0.526 0.656 0.752 0.935 14.500 -27.2 2.300 68.000 8.5 0.610 11.500 -65.0 0.470 3.520 21.4 -0.680 0.560 -26.8 -0.070 2.010 47.2 1.770 5.600 -24.4 3.090 0.910 20.6 4.280 4.410 -33.9 -30.000 12.000 -48.0 -30.000 10.000 -66.0 6.870 122.000 -28.0 6.970 56.000 -86.0 2.230 17.000 28.0 4.790 22.000 -58.0 5.000 -4.4 -2.129 -31.3 -17.000 156.0 5.000 -4.4 5.000 -2.5 0.41 0.64
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-----HHHHHHHHH-----EEEEE---HHHHHH-----------HHHHHHHH------HHH-----HHHH-------EEE
Query: 3 GTQIVTERLVALLESGTEKVLLIDSRPFVEYNTSHILEAININCSKLMKRRLQQDKVLITELIQHSAKHKVDIDCSQKVV 82
Sbjct: 4 FECINVADAHQKLQEK--EAVLVDIRDPQSFAMGHAVQAFHLT-NDTLGAFMRDN------------------DFDTPVM 62
EEE-HHHHHHHHH--- -EEEE---HHHHHH-EE---EE--H HHHHHHHHH-- ----EEE
EEE-------------HHHHHHHHHH-----EEEE---HHHHHHHHHHH-----
Query: 83 VYDQSSQDVASLSSDCFLTVLLGKLEKSFNSVHLLAGGFAEFSRCFPGLCEGKS 136
Sbjct: 63 VMYHGNS---------SKGAAQYLLQQGYDVVYSIDGGFEAWQRQFPAEVAYGA 107
-----HH HHHHHHHHHH----EEEE--HHHHHHHH----EE---A
104 residues (67.97%) 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: 27.63% helical, 16.45% extended, 55.92% loops/other (query: 33.33% 9.80% 56.86%)
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.
2IFV_A not_found 41.41.41.41 NONE -39.259 0 1 91.50% 20.00% OPTM -637.917 -364.070 2.469 0.578 0.821 0.809 0.852 19.540 -35.0 4.480 108.500 -98.0 6.580 67.000 -122.0 1.610 9.190 -33.2 -0.220 -1.100 -36.1 2.260 18.930 -19.0 3.520 7.010 -33.4 2.270 12.740 -36.8 6.390 7.740 -51.1 -30.000 11.000 -86.0 -30.000 16.000 -92.0 7.690 127.500 -88.5 13.440 76.000 -116.0 2.510 36.000 -51.0 3.700 17.000 -73.0 5.000 -13.1 -1.313 -39.8 0.000 -9.3e+061 5.000 -13.1 0.672 -3.5 0.16 0.75
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--HHHHHHHHH---- -EEEEE---HHHHHH-----------HHHHHHHH------HHH-----HHHH-------EE
Query: 6 IVTERLVALLESGTE----KVLLIDSRPFVEYNTSHILEAININCSKLMKRRLQQDKVLITELIQHSAKHKVDIDCSQKV 81
Sbjct: 401 ISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSP------IAP-----CSLDKRVIL 469
-HHHHHHHH-------EEEEEEEE---HHHHH--EE---EE---HHHHHHHHH---- --- ----EEEEE
EEEE-------------HHHHHHHHHH-- ---EEEE---HHHHHHHHHHH-------------------
Query: 82 VVYDQSSQDVASLSSDCFLTVLLGKLEKS-------FNSVHLLAGGFAEFSRCFPGLCEGKSTLVPTCISQPAHHH 150
Sbjct: 470 IFHDEFSSE----RGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQ-DYRPMNHEAFKDEL 540
EE------H HHHHHHHHHHHHHH-----------EEEE--HHHHH-------EE--- -------------L
140 residues (91.50%) 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: 30.89% helical, 15.45% extended, 53.66% loops/other (query: 33.33% 9.80% 56.86%)
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.
2HHG_A not_found 41.41.41.41 NONE -39.395 0 1 69.28% 15.87% OPTM -493.752 -292.970 1.416 0.520 0.638 0.809 0.822 16.790 -31.5 -0.610 -17.500 23.5 2.920 15.500 -86.5 -0.700 -0.940 0.2 -0.430 1.380 -35.0 -0.620 -3.820 20.1 0.010 3.380 -25.4 1.890 0.980 -10.0 9.960 16.140 -51.4 -30.000 0.000 -71.0 -30.000 10.000 -87.0 1.340 55.000 37.0 8.590 53.000 -83.0 -1.300 -28.000 35.0 2.260 -6.000 -49.0 5.000 -0.2 -0.438 -38.4 0.000 -9.3e+061 5.000 -0.2 0.398 -1.8 0.73 0.84
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-------HHHHHHHHH-----EEEEE---HHHHHH-----------HHHHHHHH------HHH-----HHHH-------E
Query: 1 MIGTQIVTERLVALLESGTEKVLLIDSRPFVEYNTSHILEAININCSKLMKRRLQQDKVLITELIQHSAKHKVDIDCSQK 80
Sbjct: 19 SSIETLTTADAIALHKSGASDVVIVDIRDPREIERDGKIPG-SFSCTRGLEFWIDPQ--------SPYAKPIFQED--KK 87
--EEE-HHHHHHHHH-----EEEEE---HHHHHHH------ EE-----HHHH---- ----------- EE
EEEEE-------------HHHHHHHHHH-----EEEE---HHHHHH
Query: 81 VVVYDQSSQDVASLSSDCFLTVLLGKLEKSFNSVHLLAGGFAEFSR 126
Sbjct: 88 FVFYCA---------GGLRSALAAKTAQDGLKPVAHIEGGFGAWRD 124
EEE--- -HHHHHHHHHHH-----EEEE--HHHHHHH-
106 residues (69.28%) of query sequence aligned
DONE: Thu Aug 07 01:32:18 2008 EST