GapRepairer

Show only modeled chain

Models

Number of gaps:2

Gap lengths: 6, 5

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Err	-67380	-2277	-2372
Model 2	Err	-67349	-2185	-2445
Model 3	Err	-67442	-2084	-2540
Model 4	Err	-67369	-2053	-2578
Model 5	Unknot	-67313	-1980	-2562
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
3NK7	B	K +3₁	99.63%	200.00%	200.00%	0.65	..Target: SEFMTEPAIITNASDPAVQRIIDVTKHSRASIKTTLIEDTEPLMECIRAGVQFIEVYGSSGTPLDPALLDLCRQREIPVRLIDVSIVNQLFKAERKAKVFGIARVPRPARLADIAERGGDVVVLDGVKIVGNIGAIVRTSLALGAAGIVLVDSDLATIADRRLLRASRGYVFSLPVVLADREEAVSFLRDNDIALMVLDTDGDLGVKDLGDRADRMALVFGSEKGGPSGLFQEASAGTVSIPMLSSTESLNVSVSVGIALHERSARNFAVRRAAAQA Template: -------AIITNASDPAVQRIIDVTKHSRASIKTTLIEDTEPLMECIRAGVQFIEVYGSSGTPLDPALLDLCRQREIPVRLIDVSIVNQLFKAERKAKVFGIARVPRPARLADIAERGGDVVVLDGVKIVGNIGAIVRTSLALGAAGIVLVDSDLATIADRRLLRASRGYVFSLPVVLADREEAVSFLRDNDIALMVLDTDGDLGVKDLGDRADRMALVFGSEKGGPSGLFQEASAGTVSIPMLSSTESLNVSVSVGIALHERSARNFAVRR---AA

Templates (similarity to the largest gap - 6 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	QLFKAERKAKVF
3NK7	B	K +3₁	100.00%	100.00%	QLFKAERKAKVF

Templates (similarity to the 2nd largest gap - 5 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	KHSRASIKTTL
3NK7	B	K +3₁	100.00%	100.00%	KHSRASIKTTL

Job Log

Thu Mar 28 11:12:38 2019	JOB CREATED : 61f7a654-e40f-4585-a31a-f7465247be97
Thu Mar 28 11:13:02 2019	STATUS CHANGED : N -> R
Thu Mar 28 11:13:02 2019	INFO : JOB STARTED AT: 2019-03-28 11:13:02.445682
Thu Mar 28 11:13:02 2019	INFO : METHOD: 1
Thu Mar 28 11:13:02 2019	INFO : Precalculated profile found...
Thu Mar 28 11:13:02 2019	INFO : Homologue pool found...
Thu Mar 28 11:13:02 2019	INFO : Verifying structure sequences of homologues...
Thu Mar 28 11:14:51 2019	INFO : Starting homologue filtering...
Thu Mar 28 11:16:12 2019	INFO : Getting structures from PDB...
Thu Mar 28 11:16:16 2019	INFO : Creating modelling alignment...
Thu Mar 28 11:16:16 2019	INFO : Adding other chains
Thu Mar 28 11:16:16 2019	INFO : Modelling...
Thu Mar 28 11:21:46 2019	INFO : Model 1 built
Thu Mar 28 11:21:46 2019	INFO : Validating Calpha distances...
Thu Mar 28 11:21:46 2019	INFO : Model 1 distances correct: True
Thu Mar 28 11:21:46 2019	INFO : Modelling...
Thu Mar 28 11:25:03 2019	INFO : Model 2 built
Thu Mar 28 11:25:03 2019	INFO : Validating Calpha distances...
Thu Mar 28 11:25:03 2019	INFO : Model 2 distances correct: True
Thu Mar 28 11:25:03 2019	INFO : Modelling...
Thu Mar 28 11:28:16 2019	INFO : Model 3 built
Thu Mar 28 11:28:16 2019	INFO : Validating Calpha distances...
Thu Mar 28 11:28:16 2019	INFO : Model 3 distances correct: True
Thu Mar 28 11:28:16 2019	INFO : Modelling...
Thu Mar 28 11:31:28 2019	INFO : Model 4 built
Thu Mar 28 11:31:28 2019	INFO : Validating Calpha distances...
Thu Mar 28 11:31:28 2019	INFO : Model 4 distances correct: True
Thu Mar 28 11:31:28 2019	INFO : Modelling...
Thu Mar 28 11:34:39 2019	INFO : Model 5 built
Thu Mar 28 11:34:39 2019	INFO : Validating Calpha distances...
Thu Mar 28 11:34:39 2019	INFO : Model 5 distances correct: True
Thu Mar 28 11:35:13 2019	INFO : Finished modelling
Thu Mar 28 11:35:13 2019	STATUS CHANGED : R -> P
Thu Mar 28 11:35:51 2019	INFO : Finished edm surfaces: success
Thu Mar 28 11:35:51 2019	INFO : Checking topology...
Thu Mar 28 11:35:52 2019	INFO : Knot matrices done...
Thu Mar 28 11:35:52 2019	INFO : No knots found...
Thu Mar 28 11:35:52 2019	INFO : No lassos found...
Thu Mar 28 11:35:52 2019	INFO : Finishing...
Thu Mar 28 11:35:52 2019	INFO : Job done
Thu Mar 28 11:35:52 2019	STATUS CHANGED : P -> F
Thu Mar 28 11:35:52 2019	STATUS CHANGED : F -> F
Thu Mar 28 11:35:52 2019	ERROR : Error while preparing 'Mix&Match'' combinations

3NK6 chain A