GapRepairer

Models

Number of gaps:1

Gap lengths: 6

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Non-trivial	-45331	-2164
Model 2	Non-trivial	-45511	-2152
Model 3	Non-trivial	-45631	-2091
Model 4	Non-trivial	-45443	-2087
Model 5	Non-trivial	-45262	-1996
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	Knot	K 3₁	24-164	--	--	--
Model 2	Knot	K 3₁	24-163	--	--	--
Model 3	Knot	K 3₁	24-164	--	--	--
Model 4	Knot	K 3₁	24-164	--	--	--
Model 5	Knot	K 3₁	24-164	--	--	--
							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

Tue Aug 27 18:27:52 2019	JOB CREATED : ad20894e-5bc1-41d3-b45c-417f36ddf8f6
Tue Aug 27 18:28:02 2019	STATUS CHANGED : N -> R
Tue Aug 27 18:28:02 2019	INFO : JOB STARTED AT: 2019-08-27 18:28:02.353405
Tue Aug 27 18:28:02 2019	INFO : METHOD: 2
Tue Aug 27 18:28:02 2019	INFO : Building Profile...
Tue Aug 27 18:28:02 2019	INFO : --E-value set to 0.001--
Tue Aug 27 18:32:33 2019	INFO : Homologue pool found...
Tue Aug 27 18:32:33 2019	ERROR : No homologues found using selected method. Maybe try specifying your own?
Tue Aug 27 18:32:33 2019	INFO : Proceeding using de novo modelling
Tue Aug 27 18:32:33 2019	INFO : Verifying structure sequences of homologues...
Tue Aug 27 18:32:33 2019	INFO : Getting structures from PDB...
Tue Aug 27 18:32:34 2019	INFO : Creating modelling alignment...
Tue Aug 27 18:32:34 2019	INFO : Modelling...
Tue Aug 27 18:43:29 2019	INFO : Model 1 built
Tue Aug 27 18:43:29 2019	INFO : Validating Calpha distances...
Tue Aug 27 18:43:29 2019	INFO : Model 1 distances correct: True
Tue Aug 27 18:43:29 2019	INFO : Modelling...
Tue Aug 27 19:08:50 2019	INFO : Model 2 built
Tue Aug 27 19:08:50 2019	INFO : Validating Calpha distances...
Tue Aug 27 19:08:50 2019	INFO : Model 2 distances correct: True
Tue Aug 27 19:08:50 2019	INFO : Modelling...
Tue Aug 27 19:26:51 2019	INFO : Model 3 built
Tue Aug 27 19:26:51 2019	INFO : Validating Calpha distances...
Tue Aug 27 19:26:51 2019	INFO : Model 3 distances correct: True
Tue Aug 27 19:26:51 2019	INFO : Modelling...
Tue Aug 27 19:44:52 2019	INFO : Model 4 built
Tue Aug 27 19:44:52 2019	INFO : Validating Calpha distances...
Tue Aug 27 19:44:52 2019	INFO : Model 4 distances correct: True
Tue Aug 27 19:44:52 2019	INFO : Modelling...
Tue Aug 27 20:09:52 2019	INFO : Model 5 built
Tue Aug 27 20:09:52 2019	INFO : Validating Calpha distances...
Tue Aug 27 20:09:52 2019	INFO : Model 5 distances correct: True
Tue Aug 27 20:10:20 2019	INFO : Finished modelling
Tue Aug 27 20:10:20 2019	STATUS CHANGED : R -> P
Tue Aug 27 20:10:50 2019	INFO : Finished edm surfaces: success
Tue Aug 27 20:10:50 2019	INFO : Checking topology...
Tue Aug 27 20:12:42 2019	INFO : Knot matrices done...
Tue Aug 27 20:13:57 2019	INFO : Some knots found!
Tue Aug 27 20:13:57 2019	INFO : No lassos found...
Tue Aug 27 20:13:57 2019	INFO : Finishing...
Tue Aug 27 20:13:57 2019	INFO : Job done
Tue Aug 27 20:13:57 2019	STATUS CHANGED : P -> F
Tue Aug 27 20:13:57 2019	STATUS CHANGED : F -> F

6OAW chain A