GapRepairer

Models

Number of gaps:1

Gap lengths: 8

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Unknot	-10630	-1481
Model 2	Unknot	-10629	-1467
Model 3	Unknot	-10626	-1457
Model 4	Unknot	-10591	-1432
Model 5	Unknot	-10458	-1290
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

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.

Templates (similarity across the whole protein) Help

PDB code	Chain	Entanglement type	Seq identity	Total gap coverage	Total gap identity	RMSD [Å]	Pairwise alignment to the target: gap
4HV0	D	Unknot	98.99%	100.00%	100.00%	0.50	..Target: XVTVEEEVYEFLKKKAKEEGTSVPAVIRKILKEYFGIEDRTRDYKRQDLEGSYIIVNGKKYYRINCKLEKRNEILVKLELKKRGTTLNRFLKEXIXIT- Template: XVTVEEEVYEFLKKKAKEEGTSVPAVIRKILKEYFGIEDRTRDYKRQDLEGSYIIVNGKKYYRINCKLEKRNEILVKLELKKRGTTLNRFLKEXIXITV

Templates (similarity to the largest gap - 8 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	RTRDYKRQDLEGSY
4HV0	D	Unknot	100.00%	100.00%	RTRDYKRQDLEGSY

Download Files Models Similarity profile Modelling alignment

Job Log

Tue Aug 27 18:38:46 2019	JOB CREATED : 634c0a3d-d2d8-464d-bc9d-b23737db7c00
Tue Aug 27 18:39:01 2019	STATUS CHANGED : N -> R
Tue Aug 27 18:39:01 2019	INFO : JOB STARTED AT: 2019-08-27 18:39:01.947358
Tue Aug 27 18:39:01 2019	INFO : METHOD: 1
Tue Aug 27 18:39:01 2019	INFO : Building Profile...
Tue Aug 27 18:39:01 2019	INFO : --E-value set to 0.001--
Tue Aug 27 18:41:21 2019	INFO : Homologue pool found...
Tue Aug 27 18:41:21 2019	INFO : Verifying structure sequences of homologues...
Tue Aug 27 18:41:25 2019	INFO : Starting homologue filtering...
Tue Aug 27 18:41:29 2019	INFO : Getting structures from PDB...
Tue Aug 27 18:41:31 2019	INFO : Creating modelling alignment...
Tue Aug 27 18:41:31 2019	INFO : Modelling...
Tue Aug 27 18:42:14 2019	INFO : Model 1 built
Tue Aug 27 18:42:14 2019	INFO : Validating Calpha distances...
Tue Aug 27 18:42:14 2019	INFO : Model 1 distances correct: True
Tue Aug 27 18:42:14 2019	INFO : Modelling...
Tue Aug 27 18:42:55 2019	INFO : Model 2 built
Tue Aug 27 18:42:55 2019	INFO : Validating Calpha distances...
Tue Aug 27 18:42:55 2019	INFO : Model 2 distances correct: True
Tue Aug 27 18:42:55 2019	INFO : Modelling...
Tue Aug 27 18:43:53 2019	INFO : Model 3 built
Tue Aug 27 18:43:53 2019	INFO : Validating Calpha distances...
Tue Aug 27 18:43:53 2019	INFO : Model 3 distances correct: True
Tue Aug 27 18:43:53 2019	INFO : Modelling...
Tue Aug 27 18:44:50 2019	INFO : Model 4 built
Tue Aug 27 18:44:50 2019	INFO : Validating Calpha distances...
Tue Aug 27 18:44:50 2019	INFO : Model 4 distances correct: True
Tue Aug 27 18:44:50 2019	INFO : Modelling...
Tue Aug 27 18:45:31 2019	INFO : Model 5 built
Tue Aug 27 18:45:31 2019	INFO : Validating Calpha distances...
Tue Aug 27 18:45:31 2019	INFO : Model 5 distances correct: True
Tue Aug 27 18:45:37 2019	INFO : Finished modelling
Tue Aug 27 18:45:37 2019	STATUS CHANGED : R -> P
Tue Aug 27 18:45:48 2019	INFO : Finished edm surfaces: success
Tue Aug 27 18:45:48 2019	INFO : Checking topology...
Tue Aug 27 18:45:55 2019	INFO : Knot matrices done...
Tue Aug 27 18:45:55 2019	INFO : No knots found...
Tue Aug 27 18:45:55 2019	INFO : No lassos found...
Tue Aug 27 18:45:55 2019	INFO : Finishing...
Tue Aug 27 18:45:55 2019	INFO : Job done
Tue Aug 27 18:45:55 2019	STATUS CHANGED : P -> F
Tue Aug 27 18:45:55 2019	STATUS CHANGED : F -> F

4HV0 chain A