GapRepairer

Models

Number of gaps:6

Gap lengths: 95, 37, 11, 8, 4, 4

Model	Entanglement	Average	DOPE-HR (by gap length)			Smaller
		DOPE-HR	1st gap	2nd gap	3rd gap	gaps
Model 1	Non-trivial	-48072	-2326	-2418	-1354
Model 2	Non-trivial	-51202	-2285	-3108	-2049
Model 3	Non-trivial	-48251	-1904	-2328	-1528
Model 4	Non-trivial	-48561	-1903	-2589	-1982
						None
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

None of the models is perfect? By clicking the button below you can download a .pdb file with the currently shown mix of models - for each gap at most one model can be selected. If none of them is checked, the gap will be left as is. Fourth and further gaps (sorted by size) can only come from one of the models.

EntanglementHelpKnotProtLassoProtLinkProt

Model	Type		Knot core	Slipknot	Lasso	Piercing	Show
			range	loop range	loop	position	in JSmol
Model 1	Slipknot	S +3₁	90-279	279-553	--	--
	Lasso	L_-4N	--	--	97-314	-23,+33,-64,+89
Model 2	Slipknot	S 3₁	96-277	277-553	--	--
	Lasso	L_-4N	--	--	97-314	-21,+36,-64,+90
Model 3	Slipknot	S 3₁	93-278	278-553	--	--
	Lasso	L_-4N	--	--	97-314	-20,+34,-64,+92
Model 4	Slipknot	S 3₁	92-280	280-553	--	--
	Lasso	L_-4N	--	--	97-314	-20,+35,-64,+90
							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
Lasso thumbnails

Knot help

Lasso help

Model 1

Model 2

Model 3

Model 4

Model 1

Model 2

Model 3

Model 4

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

Job Log

Sun Jul 23 14:55:50 2017	JOB CREATED : 128d9d79-cfd4-416e-995d-ae01612e0036
Sun Jul 23 16:53:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 16:53:02 2017	INFO : JOB STARTED AT: 2017-07-23 16:53:02.203871
Sun Jul 23 16:53:02 2017	INFO : METHOD: 1
Sun Jul 23 16:53:02 2017	INFO : Precalculated profile found...
Sun Jul 23 16:53:02 2017	INFO : Homologue pool found...
Sun Jul 23 16:53:02 2017	ERROR : No homologues found using selected method. Maybe try specifying your own?
Sun Jul 23 16:53:02 2017	INFO : Proceeding using de novo modelling
Sun Jul 23 16:53:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 16:53:02 2017	INFO : Getting structures from PDB...
Sun Jul 23 16:53:02 2017	INFO : Creating modelling alignment...
Sun Jul 23 16:53:02 2017	INFO : Modelling...
Sun Jul 23 17:58:32 2017	INFO : Model 1 built
Sun Jul 23 17:58:32 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:58:32 2017	INFO : Model 1 distances correct: True
Sun Jul 23 17:58:32 2017	INFO : Modelling...
Sun Jul 23 19:37:56 2017	INFO : Model 2 built
Sun Jul 23 19:37:56 2017	INFO : Validating Calpha distances...
Sun Jul 23 19:37:56 2017	INFO : Model 2 distances correct: True
Sun Jul 23 19:37:56 2017	INFO : Modelling...
Sun Jul 23 21:49:50 2017	INFO : Model 3 built
Sun Jul 23 21:49:50 2017	INFO : Validating Calpha distances...
Sun Jul 23 21:49:50 2017	INFO : Model 3 distances correct: True
Sun Jul 23 21:49:50 2017	INFO : Modelling...
Sun Jul 23 23:53:26 2017	INFO : Model 4 built
Sun Jul 23 23:53:26 2017	INFO : Validating Calpha distances...
Sun Jul 23 23:53:26 2017	INFO : Model 4 distances correct: True
Sun Jul 23 23:53:26 2017	INFO : Modelling...
Sun Jul 23 23:53:43 2017	INFO : Model 5 creation failed - VTFM optimization failed. Possibly really bad templates were used?
Sun Jul 23 23:54:14 2017	INFO : Finished modelling
Sun Jul 23 23:54:14 2017	STATUS CHANGED : R -> P
Sun Jul 23 23:54:14 2017	INFO : Checking topology...
Mon Jul 24 00:51:22 2017	INFO : Knot matrices done...
Mon Jul 24 00:55:46 2017	INFO : Some knots found!
Mon Jul 24 00:57:13 2017	INFO : Some lassos found!
Mon Jul 24 00:57:13 2017	INFO : Finishing...
Mon Jul 24 00:57:14 2017	INFO : Job done
Mon Jul 24 00:57:14 2017	STATUS CHANGED : P -> F
Mon Jul 24 00:57:14 2017	STATUS CHANGED : F -> F

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