Job name:

4MCB chain A

26530795-2932-496e-9eb1-be4097aae8b1
Finished
Models Number of gaps:1 Gap lengths: 14
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -21317
Model 2 Non-trivial -21304
Model 3 Non-trivial -21469
Model 4 Non-trivial -21216
Model 5 Non-trivial -21255
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
Provided protein had only one gap - thus there are no gap-filling combinations to be made.

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!
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Knot K +31 84-131 -- -- --
Model 2 Knot K +31 84-131 -- -- --
Model 3 Knot K +31 84-131 -- -- --
Model 4 Knot K +31 84-131 -- -- --
Model 5 Knot K +31 84-131 -- -- --
None
Topologies marked by an OK sign () are in accordance with the template topology.
Warning: Entanglement type is assigned automatically - for more complicated topologies there may be some disagreements with manually curated databases.
Model 1
Model 2
Model 3
Model 4
Model 5
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


4MCB

B

K +31

89.30%

100.00%

100.00%

0.79

..Target: MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTW------------------------LR
Template: MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAE

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

GVLGKQASAEEDSFADGLLD

4MCB B K +31 100.00% 100.00%

GVLGKQASAEEDSFADGLLD


Sun Jul 23 15:12:15 2017	JOB CREATED : 26530795-2932-496e-9eb1-be4097aae8b1
Mon Jul 24 03:12:02 2017	STATUS CHANGED : N -> R
Mon Jul 24 03:12:02 2017	INFO : JOB STARTED AT: 2017-07-24 03:12:02.431163
Mon Jul 24 03:12:02 2017	INFO : METHOD: 1
Mon Jul 24 03:12:02 2017	INFO : Precalculated profile found...
Mon Jul 24 03:12:02 2017	INFO : Homologue pool found...
Mon Jul 24 03:12:02 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 03:12:36 2017	INFO : Starting homologue filtering...
Mon Jul 24 03:13:10 2017	INFO : Getting structures from PDB...
Mon Jul 24 03:13:13 2017	INFO : Creating modelling alignment...
Mon Jul 24 03:13:13 2017	INFO : Modelling...
Mon Jul 24 03:15:46 2017	INFO : Model 1 built
Mon Jul 24 03:15:46 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:15:46 2017	INFO : Model 1 distances correct: True
Mon Jul 24 03:15:46 2017	INFO : Modelling...
Mon Jul 24 03:18:30 2017	INFO : Model 2 built
Mon Jul 24 03:18:30 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:18:30 2017	INFO : Model 2 distances correct: True
Mon Jul 24 03:18:30 2017	INFO : Modelling...
Mon Jul 24 03:21:08 2017	INFO : Model 3 built
Mon Jul 24 03:21:08 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:21:08 2017	INFO : Model 3 distances correct: True
Mon Jul 24 03:21:08 2017	INFO : Modelling...
Mon Jul 24 03:25:15 2017	INFO : Model 4 built
Mon Jul 24 03:25:15 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:25:15 2017	INFO : Model 4 distances correct: True
Mon Jul 24 03:25:15 2017	INFO : Modelling...
Mon Jul 24 03:28:00 2017	INFO : Model 5 built
Mon Jul 24 03:28:00 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:28:00 2017	INFO : Model 5 distances correct: True
Mon Jul 24 03:28:14 2017	INFO : Finished modelling
Mon Jul 24 03:28:14 2017	STATUS CHANGED : R -> P
Mon Jul 24 03:28:14 2017	INFO : Checking topology...
Mon Jul 24 03:33:02 2017	INFO : Knot matrices done...
Mon Jul 24 03:35:18 2017	INFO : Some knots found!
Mon Jul 24 03:35:18 2017	INFO : No lassos found...
Mon Jul 24 03:35:18 2017	INFO : Finishing...
Mon Jul 24 03:35:18 2017	INFO : Job done
Mon Jul 24 03:35:18 2017	STATUS CHANGED : P -> F
Mon Jul 24 03:35:18 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling