GapRepairer

Models

Number of gaps:0

Gap lengths:

Model	Entanglement	Average
		DOPE-HR
Model 1	Non-trivial	-89005
Model 2	Non-trivial	-88968
Model 3	Non-trivial	-89002
Model 4	Non-trivial	-89000
Model 5	Non-trivial	-88998
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 4₁3₁	38-255	255-289	--	--
Model 2	Slipknot	S 4₁3₁	38-255	255-289	--	--
Model 3	Slipknot	S 4₁3₁	38-255	255-289	--	--
Model 4	Slipknot	S 4₁3₁	38-255	255-289	--	--
Model 5	Slipknot	S 4₁3₁	38-255	255-289	--	--
							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

Fri Dec  1 09:48:37 2017	JOB CREATED : 32d1f47a-3482-4143-9c20-b542242f4b65
Sat Dec  2 01:48:02 2017	STATUS CHANGED : N -> R
Sat Dec  2 01:48:02 2017	INFO : JOB STARTED AT: 2017-12-02 01:48:02.923849
Sat Dec  2 01:48:02 2017	INFO : METHOD: 1
Sat Dec  2 01:48:03 2017	INFO : Precalculated profile found...
Sat Dec  2 01:48:03 2017	INFO : Homologue pool found...
Sat Dec  2 01:48:03 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 01:50:15 2017	INFO : Starting homologue filtering...
Sat Dec  2 01:51:23 2017	INFO : Getting structures from PDB...
Sat Dec  2 01:51:24 2017	INFO : Creating modelling alignment...
Sat Dec  2 01:51:24 2017	INFO : Modelling...
Sat Dec  2 01:52:17 2017	INFO : Model 1 built
Sat Dec  2 01:52:17 2017	INFO : Validating Calpha distances...
Sat Dec  2 01:52:17 2017	INFO : Model 1 distances correct: True
Sat Dec  2 01:52:17 2017	INFO : Modelling...
Sat Dec  2 01:53:09 2017	INFO : Model 2 built
Sat Dec  2 01:53:09 2017	INFO : Validating Calpha distances...
Sat Dec  2 01:53:09 2017	INFO : Model 2 distances correct: True
Sat Dec  2 01:53:09 2017	INFO : Modelling...
Sat Dec  2 01:53:55 2017	INFO : Model 3 built
Sat Dec  2 01:53:55 2017	INFO : Validating Calpha distances...
Sat Dec  2 01:53:55 2017	INFO : Model 3 distances correct: True
Sat Dec  2 01:53:55 2017	INFO : Modelling...
Sat Dec  2 01:54:44 2017	INFO : Model 4 built
Sat Dec  2 01:54:44 2017	INFO : Validating Calpha distances...
Sat Dec  2 01:54:44 2017	INFO : Model 4 distances correct: True
Sat Dec  2 01:54:44 2017	INFO : Modelling...
Sat Dec  2 01:55:33 2017	INFO : Model 5 built
Sat Dec  2 01:55:33 2017	INFO : Validating Calpha distances...
Sat Dec  2 01:55:33 2017	INFO : Model 5 distances correct: True
Sat Dec  2 01:56:43 2017	INFO : Finished modelling
Sat Dec  2 01:56:43 2017	STATUS CHANGED : R -> P
Sat Dec  2 01:56:43 2017	INFO : Checking topology...
Sat Dec  2 02:34:54 2017	INFO : Knot matrices done...
Sat Dec  2 02:38:03 2017	INFO : Some knots found!
Sat Dec  2 02:38:03 2017	INFO : No lassos found...
Sat Dec  2 02:38:03 2017	INFO : Finishing...
Sat Dec  2 02:38:03 2017	STATUS CHANGED : P -> E
Sat Dec  2 02:38:03 2017	ERROR : Error while finishing
Sat Dec  2 02:38:03 2017	STATUS CHANGED : E -> F

3GJD chain A