GapRepairer

Models

Number of gaps:1

Gap lengths: 12

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Err	-37720	-2575
Model 2	Err	-37494	-2508
Model 3	Unknot	-37370	-2354
Model 4	Err	-37360	-2209
Model 5	Err	-37140	-2089
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
3ADU	B	Unknot	100.00%	100.00%	100.00%	0.76	..Target: ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY Template: ESADLRALAKHLYDSYIKSFPLTKAKARAILTG----KSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTET--SLHPLLQEI----Y

Templates (similarity to the largest gap - 12 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	KIKFKHITPLQEQSKEVA
3ADU	B	Unknot	100.00%	100.00%	KIKFKHITPLQEQSKEVA

Download Files Models Similarity profile Modelling alignment

Job Log

Sun Apr  7 11:38:18 2019	JOB CREATED : 75049a51-a97b-43f0-970f-b9cd6c10cd8c
Sun Apr  7 11:39:01 2019	STATUS CHANGED : N -> R
Sun Apr  7 11:39:01 2019	INFO : JOB STARTED AT: 2019-04-07 11:39:01.978497
Sun Apr  7 11:39:01 2019	INFO : METHOD: 1
Sun Apr  7 11:39:02 2019	INFO : Building Profile...
Sun Apr  7 11:39:02 2019	INFO : --E-value set to 0.001--
Sun Apr  7 11:47:56 2019	INFO : Homologue pool found...
Sun Apr  7 11:47:56 2019	INFO : Verifying structure sequences of homologues...
Sun Apr  7 12:49:09 2019	INFO : Starting homologue filtering...
Sun Apr  7 12:50:34 2019	INFO : Getting structures from PDB...
Sun Apr  7 12:50:38 2019	INFO : Creating modelling alignment...
Sun Apr  7 12:50:38 2019	INFO : Modelling...
Sun Apr  7 12:54:39 2019	INFO : Model 1 built
Sun Apr  7 12:54:39 2019	INFO : Validating Calpha distances...
Sun Apr  7 12:54:39 2019	INFO : Model 1 distances correct: True
Sun Apr  7 12:54:39 2019	INFO : Modelling...
Sun Apr  7 12:58:43 2019	INFO : Model 2 built
Sun Apr  7 12:58:43 2019	INFO : Validating Calpha distances...
Sun Apr  7 12:58:43 2019	INFO : Model 2 distances correct: True
Sun Apr  7 12:58:43 2019	INFO : Modelling...
Sun Apr  7 13:02:41 2019	INFO : Model 3 built
Sun Apr  7 13:02:41 2019	INFO : Validating Calpha distances...
Sun Apr  7 13:02:41 2019	INFO : Model 3 distances correct: True
Sun Apr  7 13:02:41 2019	INFO : Modelling...
Sun Apr  7 13:06:39 2019	INFO : Model 4 built
Sun Apr  7 13:06:39 2019	INFO : Validating Calpha distances...
Sun Apr  7 13:06:39 2019	INFO : Model 4 distances correct: True
Sun Apr  7 13:06:39 2019	INFO : Modelling...
Sun Apr  7 13:10:44 2019	INFO : Model 5 built
Sun Apr  7 13:10:44 2019	INFO : Validating Calpha distances...
Sun Apr  7 13:10:44 2019	INFO : Model 5 distances correct: True
Sun Apr  7 13:11:01 2019	INFO : Finished modelling
Sun Apr  7 13:11:01 2019	STATUS CHANGED : R -> P
Sun Apr  7 13:11:10 2019	INFO : Finished edm surfaces: success
Sun Apr  7 13:11:10 2019	INFO : Checking topology...
Sun Apr  7 13:11:10 2019	INFO : Knot matrices done...
Sun Apr  7 13:11:10 2019	INFO : No knots found...
Sun Apr  7 13:11:10 2019	INFO : No lassos found...
Sun Apr  7 13:11:10 2019	INFO : Finishing...
Sun Apr  7 13:11:11 2019	INFO : Job done
Sun Apr  7 13:11:11 2019	STATUS CHANGED : P -> F
Sun Apr  7 13:11:11 2019	STATUS CHANGED : F -> F

4XUM chain A