GapRepairer

Models

Number of gaps:1

Gap lengths: 7

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Unknot	-10495	-1433
Model 2	Unknot	-10382	-1340
Model 3	Unknot	-10299	-1248
Model 4	Unknot	-10312	-1243
Model 5	Unknot	-10246	-1186
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
5ELI	A	Unknot	98.21%	100.00%	100.00%	0.89	..Target: HNTTVFQGVAGQSLQVSCPYDSMKHWGRHKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLA- Template: -NTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLAD

Templates (similarity to the largest gap - 7 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	SFLRRWNGSTAIT
5ELI	A	Unknot	100.00%	100.00%	SFLRRWNGSTAIT

Download Files Models Similarity profile Modelling alignment

Job Log

Fri Feb  8 14:28:10 2019	JOB CREATED : 6bd517e9-1a21-404e-9b50-badb2c152f97
Fri Feb  8 14:29:01 2019	STATUS CHANGED : N -> R
Fri Feb  8 14:29:01 2019	INFO : JOB STARTED AT: 2019-02-08 14:29:01.507870
Fri Feb  8 14:29:01 2019	INFO : METHOD: 1
Fri Feb  8 14:29:01 2019	INFO : Building Profile...
Fri Feb  8 14:29:01 2019	INFO : --E-value set to 0.001--
Fri Feb  8 14:35:12 2019	INFO : Homologue pool found...
Fri Feb  8 14:35:12 2019	INFO : Verifying structure sequences of homologues...
Fri Feb  8 20:54:29 2019	INFO : Starting homologue filtering...
Fri Feb  8 20:55:51 2019	INFO : Getting structures from PDB...
Fri Feb  8 20:55:54 2019	INFO : Creating modelling alignment...
Fri Feb  8 20:55:54 2019	INFO : Modelling...
Fri Feb  8 20:56:31 2019	INFO : Model 1 built
Fri Feb  8 20:56:31 2019	INFO : Validating Calpha distances...
Fri Feb  8 20:56:31 2019	INFO : Model 1 distances correct: True
Fri Feb  8 20:56:31 2019	INFO : Modelling...
Fri Feb  8 20:57:07 2019	INFO : Model 2 built
Fri Feb  8 20:57:07 2019	INFO : Validating Calpha distances...
Fri Feb  8 20:57:07 2019	INFO : Model 2 distances correct: True
Fri Feb  8 20:57:07 2019	INFO : Modelling...
Fri Feb  8 20:57:43 2019	INFO : Model 3 built
Fri Feb  8 20:57:43 2019	INFO : Validating Calpha distances...
Fri Feb  8 20:57:43 2019	INFO : Model 3 distances correct: True
Fri Feb  8 20:57:43 2019	INFO : Modelling...
Fri Feb  8 20:58:18 2019	INFO : Model 4 built
Fri Feb  8 20:58:18 2019	INFO : Validating Calpha distances...
Fri Feb  8 20:58:18 2019	INFO : Model 4 distances correct: True
Fri Feb  8 20:58:18 2019	INFO : Modelling...
Fri Feb  8 20:58:54 2019	INFO : Model 5 built
Fri Feb  8 20:58:54 2019	INFO : Validating Calpha distances...
Fri Feb  8 20:58:54 2019	INFO : Model 5 distances correct: True
Fri Feb  8 20:59:00 2019	INFO : Finished modelling
Fri Feb  8 20:59:00 2019	STATUS CHANGED : R -> P
Fri Feb  8 20:59:01 2019	INFO : Finished edm surfaces: no map
Fri Feb  8 20:59:01 2019	INFO : Checking topology...
Fri Feb  8 20:59:12 2019	INFO : Knot matrices done...
Fri Feb  8 20:59:12 2019	INFO : No knots found...
Fri Feb  8 20:59:12 2019	INFO : No lassos found...
Fri Feb  8 20:59:12 2019	INFO : Finishing...
Fri Feb  8 20:59:12 2019	INFO : Job done
Fri Feb  8 20:59:12 2019	STATUS CHANGED : P -> F
Fri Feb  8 20:59:12 2019	STATUS CHANGED : F -> F

5UD8 chain A