Job name:

1PV2 chain A

0bd36930-463b-4b83-9440-b2a391ec7324
Finished
Models Number of gaps:3 Gap lengths: 23, 9, 6
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Unknot -30387
Model 2 Unknot -30107
Model 3 Unknot -29945
Model 4 Unknot -29586
Model 5 Unknot -29364
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
None of the models is perfect? By clicking the button below you can download a .pdb file with the currently shown mix of models - for each gap at most one model can be selected. If none of them is checked, the gap will be left as is. Fourth and further gaps (sorted by size) can only come from one of the models.
Warning: JSmol may at times display gaps where there are none - due to some overlaps in models. This does not indicate presence of gaps in downloaded structure!
DOPE (Discrete Optimized Protein Energy) score per residue. The lower the score, the better.
Since DOPE is calculated against the neighbours of a given amino acid, the scores
can vary between unmoved segments of different models. See here for more information.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


1ONS

A

Unknot

99.28%

300.00%

300.00%

0.69

..Target: TSKNPQVDIAEDNAFFPSEYSLSQYTSPVSDLDGVDYPKPYRGKHKILVIAADERYLPTDNGKLFSTGNHPIETLLPLYHLHAAGFEFEVATISGLMTKFEYWAMPHKDEKVMPFFEQHKSLFRNPKKLADVVASLNADSEYAAIFVPGGHGALIGLPESQDVAAALQWAIKNDRFVISLCHGPAAFLALRHGDNPLNGYSICAFPDAADKQTPEIGYMPGHLTWYFGEELKKMGMNIINDDITGRVHKDRKLLTGDSPFAANALGKLAAQEMLAA--
Template: TSKNPQVDIAEDNAFFPSEYSLSQYTSPVSDLDGVDYPKPYRGKHKILVIAADERYLPTDNGKLFSTGNHPIETLLPLYHLHAAGFEFEVATISGLMTKFEYWAMPHKDEKVMPFFEQHKSLFRNPKKLADVVASLNADSEYAAIFVPGGHGALIGLPESQDVAAALQWAIKNDRFVISLCHGPAAFLALRHGDNPLNGYSICAFPDAADKQTPEIGYMPGHLTWYFGEELKKMGMNIINDDITGRVHKDRKLLTGDSPFAANALGKLAAQEMLAAYA

PDB
code
Chain Knot
type
Gap
coverage
Gap
identity
>Target_Sequence: gap

SLSQYTSPVSDLDGVDYPKPYRGKHKILV

1ONS A Unknot 100.00% 100.00%

SLSQYTSPVSDLDGVDYPKPYRGKHKILV

PDB
code
Chain Knot
type
Gap
coverage
Gap
identity
>Target_Sequence: gap

WAMPHKDEKVMPFFE

1ONS A Unknot 100.00% 100.00%

WAMPHKDEKVMPFFE

PDB
code
Chain Knot
type
Gap
coverage
Gap
identity
>Target_Sequence: gap

VASLNADSEYAA

1ONS A Unknot 100.00% 100.00%

VASLNADSEYAA


Sun Jul 23 14:55:25 2017	JOB CREATED : 0bd36930-463b-4b83-9440-b2a391ec7324
Sun Jul 23 15:33:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 15:33:02 2017	INFO : JOB STARTED AT: 2017-07-23 15:33:02.110398
Sun Jul 23 15:33:02 2017	INFO : METHOD: 1
Sun Jul 23 15:33:02 2017	INFO : Precalculated profile found...
Sun Jul 23 15:33:02 2017	INFO : Homologue pool found...
Sun Jul 23 15:33:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 15:38:03 2017	INFO : Starting homologue filtering...
Sun Jul 23 15:38:46 2017	INFO : Getting structures from PDB...
Sun Jul 23 15:38:49 2017	INFO : Creating modelling alignment...
Sun Jul 23 15:38:49 2017	INFO : Modelling...
Sun Jul 23 15:44:04 2017	INFO : Model 1 built
Sun Jul 23 15:44:04 2017	INFO : Validating Calpha distances...
Sun Jul 23 15:44:04 2017	INFO : Model 1 distances correct: True
Sun Jul 23 15:44:04 2017	INFO : Modelling...
Sun Jul 23 15:57:02 2017	INFO : Model 2 built
Sun Jul 23 15:57:02 2017	INFO : Validating Calpha distances...
Sun Jul 23 15:57:02 2017	INFO : Model 2 distances correct: True
Sun Jul 23 15:57:02 2017	INFO : Modelling...
Sun Jul 23 16:02:42 2017	INFO : Model 3 built
Sun Jul 23 16:02:42 2017	INFO : Validating Calpha distances...
Sun Jul 23 16:02:42 2017	INFO : Model 3 distances correct: True
Sun Jul 23 16:02:42 2017	INFO : Modelling...
Sun Jul 23 16:08:16 2017	INFO : Model 4 built
Sun Jul 23 16:08:16 2017	INFO : Validating Calpha distances...
Sun Jul 23 16:08:16 2017	INFO : Model 4 distances correct: True
Sun Jul 23 16:08:16 2017	INFO : Modelling...
Sun Jul 23 16:13:46 2017	INFO : Model 5 built
Sun Jul 23 16:13:46 2017	INFO : Validating Calpha distances...
Sun Jul 23 16:13:46 2017	INFO : Model 5 distances correct: True
Sun Jul 23 16:14:10 2017	INFO : Finished modelling
Sun Jul 23 16:14:10 2017	STATUS CHANGED : R -> P
Sun Jul 23 16:14:10 2017	INFO : Checking topology...
Sun Jul 23 16:17:18 2017	INFO : Knot matrices done...
Sun Jul 23 16:17:18 2017	INFO : No knots found...
Sun Jul 23 16:17:18 2017	INFO : No lassos found...
Sun Jul 23 16:17:18 2017	INFO : Finishing...
Sun Jul 23 16:17:19 2017	INFO : Job done
Sun Jul 23 16:17:19 2017	STATUS CHANGED : P -> F
Sun Jul 23 16:17:19 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling