GapRepairer

Models

Number of gaps:1

Gap lengths: 5

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Non-trivial	-64579	-1405
Model 2	Non-trivial	-64513	-1316
Model 3	Non-trivial	-64519	-1298
Model 4	Non-trivial	-64398	-1211
Model 5	Non-trivial	-64298	-1094
Colour the base model according to the B-factor (lowest to highest)				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.

Pro Tip: Since you provided a structure that contains some crystallographic information you can verify our models using the wwPDB service.
Validity report for the RCSB PDB structure you were repairing can be accessed here

EntanglementHelpKnotProtLassoProtLinkProt

Model	Type		Knot core	Slipknot	Lasso	Piercing	Show
			range	loop range	loop	position	in JSmol
Model 1	Slipknot	S 3₁	84-229	229-470	--	--
Model 2	Slipknot	S 3₁	84-229	229-470	--	--
Model 3	Slipknot	S 3₁	84-229	229-470	--	--
Model 4	Slipknot	S 3₁	84-229	229-470	--	--
Model 5	Slipknot	S 3₁	84-229	229-470	--	--
							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.

Knotting fingerprint thumbnails

Knot help

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.

Warning: No templates were used. Models were generated using de novo prediction. Possible reasons include: no homologues similar enough; homologues do not cover the gaps in the target; all gaps at most 2 amino acids long.

Download Files Models Similarity profile Modelling alignment Raw knot fingerprint matrices: Model_1 Model_2 Model_3 Model_4 Model_5

Job Log

Wed Oct 16 11:26:49 2019	JOB CREATED : 5287d3bc-4aed-46d2-beab-d468b7eab0cd
Wed Oct 16 11:27:01 2019	STATUS CHANGED : N -> R
Wed Oct 16 11:27:01 2019	INFO : JOB STARTED AT: 2019-10-16 11:27:01.821975
Wed Oct 16 11:27:01 2019	INFO : METHOD: 1
Wed Oct 16 11:27:01 2019	INFO : Building Profile...
Wed Oct 16 11:27:01 2019	INFO : --E-value set to 0.001--
Wed Oct 16 11:36:40 2019	INFO : Homologue pool found...
Wed Oct 16 11:36:40 2019	INFO : Verifying structure sequences of homologues...
Wed Oct 16 11:36:50 2019	INFO : Starting homologue filtering...
Wed Oct 16 11:36:58 2019	INFO : Getting structures from PDB...
Wed Oct 16 11:36:58 2019	INFO : Creating modelling alignment...
Wed Oct 16 11:36:58 2019	INFO : Modelling...
Wed Oct 16 11:38:26 2019	INFO : Model 1 built
Wed Oct 16 11:38:26 2019	INFO : Validating Calpha distances...
Wed Oct 16 11:38:26 2019	INFO : Model 1 distances correct: True
Wed Oct 16 11:38:26 2019	INFO : Modelling...
Wed Oct 16 11:39:50 2019	INFO : Model 2 built
Wed Oct 16 11:39:50 2019	INFO : Validating Calpha distances...
Wed Oct 16 11:39:50 2019	INFO : Model 2 distances correct: True
Wed Oct 16 11:39:50 2019	INFO : Modelling...
Wed Oct 16 11:41:17 2019	INFO : Model 3 built
Wed Oct 16 11:41:17 2019	INFO : Validating Calpha distances...
Wed Oct 16 11:41:17 2019	INFO : Model 3 distances correct: True
Wed Oct 16 11:41:17 2019	INFO : Modelling...
Wed Oct 16 11:42:38 2019	INFO : Model 4 built
Wed Oct 16 11:42:38 2019	INFO : Validating Calpha distances...
Wed Oct 16 11:42:38 2019	INFO : Model 4 distances correct: True
Wed Oct 16 11:42:38 2019	INFO : Modelling...
Wed Oct 16 11:45:01 2019	INFO : Model 5 built
Wed Oct 16 11:45:01 2019	INFO : Validating Calpha distances...
Wed Oct 16 11:45:01 2019	INFO : Model 5 distances correct: True
Wed Oct 16 11:45:29 2019	INFO : Finished modelling
Wed Oct 16 11:45:29 2019	STATUS CHANGED : R -> P
Wed Oct 16 11:45:38 2019	INFO : Finished edm surfaces: success
Wed Oct 16 11:45:38 2019	INFO : Checking topology...
Wed Oct 16 11:57:23 2019	INFO : Knot matrices done...
Wed Oct 16 11:58:53 2019	INFO : Some knots found!
Wed Oct 16 11:58:53 2019	INFO : No lassos found...
Wed Oct 16 11:58:53 2019	INFO : Finishing...
Wed Oct 16 11:58:53 2019	INFO : Job done
Wed Oct 16 11:58:53 2019	STATUS CHANGED : P -> F
Wed Oct 16 11:58:53 2019	STATUS CHANGED : F -> F

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