GapRepairer

Models

Number of gaps:2

Gap lengths: 5, 4

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Err	-26209	-1242	-423
Model 2	Err	-26560	-1191	-826
Model 3	Unknot	-26336	-1170	-568
Model 4	Err	-26406	-1109	-605
Model 5	Err	-26302	-858	-754
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.

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
3OLL	A	Unknot	99.57%	200.00%	200.00%	0.92	..Target: DALSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL Template: -ALSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTAT--ADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVXDLLLEMLNAH--

Templates (similarity to the largest gap - 5 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	SMYPLVTATQD
3OLL	A	Unknot	100.00%	100.00%	SMYPLVTAT--

Templates (similarity to the 2nd largest gap - 4 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	KCKNVVPVYD
3OLL	A	Unknot	100.00%	100.00%	KCKNVVPVXD

Job Log

Sat Jun 30 15:05:23 2018	JOB CREATED : fef52860-c318-4685-83b4-ea9fd14bcc8d
Sat Jun 30 15:06:02 2018	STATUS CHANGED : N -> R
Sat Jun 30 15:06:02 2018	INFO : JOB STARTED AT: 2018-06-30 15:06:02.169303
Sat Jun 30 15:06:02 2018	INFO : METHOD: 1
Sat Jun 30 15:06:02 2018	INFO : Building Profile...
Sat Jun 30 15:06:02 2018	INFO : --E-value set to 0.001--
Sat Jun 30 15:18:46 2018	INFO : Homologue pool found...
Sat Jun 30 15:18:46 2018	INFO : Verifying structure sequences of homologues...
Sat Jun 30 16:00:48 2018	INFO : Starting homologue filtering...
Sat Jun 30 16:01:39 2018	INFO : Getting structures from PDB...
Sat Jun 30 16:01:43 2018	INFO : Creating modelling alignment...
Sat Jun 30 16:01:43 2018	INFO : Modelling...
Sat Jun 30 16:04:40 2018	INFO : Model 1 built
Sat Jun 30 16:04:40 2018	INFO : Validating Calpha distances...
Sat Jun 30 16:04:40 2018	INFO : Model 1 distances correct: True
Sat Jun 30 16:04:40 2018	INFO : Modelling...
Sat Jun 30 16:09:38 2018	INFO : Model 2 built
Sat Jun 30 16:09:38 2018	INFO : Validating Calpha distances...
Sat Jun 30 16:09:38 2018	INFO : Model 2 distances correct: True
Sat Jun 30 16:09:38 2018	INFO : Modelling...
Sat Jun 30 16:14:25 2018	INFO : Model 3 built
Sat Jun 30 16:14:25 2018	INFO : Validating Calpha distances...
Sat Jun 30 16:14:25 2018	INFO : Model 3 distances correct: True
Sat Jun 30 16:14:25 2018	INFO : Modelling...
Sat Jun 30 16:17:19 2018	INFO : Model 4 built
Sat Jun 30 16:17:19 2018	INFO : Validating Calpha distances...
Sat Jun 30 16:17:19 2018	INFO : Model 4 distances correct: True
Sat Jun 30 16:17:19 2018	INFO : Modelling...
Sat Jun 30 16:20:24 2018	INFO : Model 5 built
Sat Jun 30 16:20:24 2018	INFO : Validating Calpha distances...
Sat Jun 30 16:20:24 2018	INFO : Model 5 distances correct: True
Sat Jun 30 16:20:41 2018	INFO : Finished modelling
Sat Jun 30 16:20:41 2018	STATUS CHANGED : R -> P
Sat Jun 30 16:20:47 2018	INFO : Finished edm surfaces: success
Sat Jun 30 16:20:47 2018	INFO : Checking topology...
Sat Jun 30 16:20:48 2018	INFO : Knot matrices done...
Sat Jun 30 16:20:48 2018	INFO : No knots found...
Sat Jun 30 16:20:48 2018	INFO : No lassos found...
Sat Jun 30 16:20:48 2018	INFO : Finishing...
Sat Jun 30 16:20:49 2018	INFO : Job done
Sat Jun 30 16:20:49 2018	STATUS CHANGED : P -> F
Sat Jun 30 16:20:49 2018	STATUS CHANGED : F -> F

1NDE chain A