Job name:

4YVI chain A

1b6d5ecc-3caa-4d08-a36c-a54fb4240827
Finished
Electron density map:

Differential EDM:
Models Number of gaps:1 Gap lengths: 9
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -26312
Model 2 Non-trivial -26209
Model 3 Non-trivial -26185
Model 4 Non-trivial -26146
Model 5 Non-trivial -25824
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.

EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Knot K +31 85-132 -- -- --
Model 2 Knot K +31 85-132 -- -- --
Model 3 Knot K +31 85-132 -- -- --
Model 4 Knot K +31 85-132 -- -- --
Model 5 Knot K +31 85-132 -- -- --
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

100.00%

100.00%

100.00%

0.99

..Target: HMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Template: -MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAE---

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

GVLGKQASAEEDSFA

4MCB B K +31 100.00% 100.00%

GVLGKQASAEEDSFA


Sun Aug  6 23:40:48 2017	JOB CREATED : 1b6d5ecc-3caa-4d08-a36c-a54fb4240827
Sun Aug  6 23:41:02 2017	STATUS CHANGED : N -> R
Sun Aug  6 23:41:02 2017	INFO : JOB STARTED AT: 2017-08-06 23:41:02.656155
Sun Aug  6 23:41:02 2017	INFO : METHOD: 1
Sun Aug  6 23:41:02 2017	INFO : Precalculated profile found...
Sun Aug  6 23:41:02 2017	INFO : Homologue pool found...
Sun Aug  6 23:41:02 2017	INFO : Verifying structure sequences of homologues...
Sun Aug  6 23:42:24 2017	INFO : Starting homologue filtering...
Sun Aug  6 23:42:56 2017	INFO : Getting structures from PDB...
Sun Aug  6 23:42:59 2017	INFO : Creating modelling alignment...
Sun Aug  6 23:42:59 2017	INFO : Modelling...
Sun Aug  6 23:43:47 2017	INFO : Model 1 built
Sun Aug  6 23:43:47 2017	INFO : Validating Calpha distances...
Sun Aug  6 23:43:47 2017	INFO : Model 1 distances correct: True
Sun Aug  6 23:43:47 2017	INFO : Modelling...
Sun Aug  6 23:44:33 2017	INFO : Model 2 built
Sun Aug  6 23:44:33 2017	INFO : Validating Calpha distances...
Sun Aug  6 23:44:33 2017	INFO : Model 2 distances correct: True
Sun Aug  6 23:44:33 2017	INFO : Modelling...
Sun Aug  6 23:45:20 2017	INFO : Model 3 built
Sun Aug  6 23:45:20 2017	INFO : Validating Calpha distances...
Sun Aug  6 23:45:20 2017	INFO : Model 3 distances correct: True
Sun Aug  6 23:45:20 2017	INFO : Modelling...
Sun Aug  6 23:46:08 2017	INFO : Model 4 built
Sun Aug  6 23:46:08 2017	INFO : Validating Calpha distances...
Sun Aug  6 23:46:08 2017	INFO : Model 4 distances correct: True
Sun Aug  6 23:46:08 2017	INFO : Modelling...
Sun Aug  6 23:46:54 2017	INFO : Model 5 built
Sun Aug  6 23:46:54 2017	INFO : Validating Calpha distances...
Sun Aug  6 23:46:54 2017	INFO : Model 5 distances correct: True
Sun Aug  6 23:47:07 2017	INFO : Finished modelling
Sun Aug  6 23:47:07 2017	STATUS CHANGED : R -> P
Sun Aug  6 23:47:07 2017	INFO : Checking topology...
Sun Aug  6 23:53:52 2017	INFO : Knot matrices done...
Sun Aug  6 23:55:39 2017	INFO : Some knots found!
Sun Aug  6 23:55:39 2017	INFO : No lassos found...
Sun Aug  6 23:55:39 2017	INFO : Finishing...
Sun Aug  6 23:55:39 2017	INFO : Job done
Sun Aug  6 23:55:39 2017	STATUS CHANGED : P -> F
Sun Aug  6 23:55:39 2017	STATUS CHANGED : F -> F

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