GapRepairer

Models

Number of gaps:1

Gap lengths: 8

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Unknot	-38805	-1816
Model 2	Unknot	-38704	-1806
Model 3	Unknot	-38689	-1690
Model 4	Unknot	-38569	-1657
Model 5	Unknot	-38630	-1568
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%	0.78	..Target: ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY Template: ESADLRALAKHLYDSYIKSFPLTKAKARAILTG----KSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTET--SLHPLLQEI----Y

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

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

Download Files Models Similarity profile Modelling alignment

Job Log

Wed Feb  6 19:52:39 2019	JOB CREATED : 7eb05464-2018-4026-8f15-448e7a9287f5
Wed Feb  6 19:53:02 2019	STATUS CHANGED : N -> R
Wed Feb  6 19:53:02 2019	INFO : JOB STARTED AT: 2019-02-06 19:53:02.228594
Wed Feb  6 19:53:02 2019	INFO : METHOD: 1
Wed Feb  6 19:53:02 2019	INFO : Building Profile...
Wed Feb  6 19:53:02 2019	INFO : --E-value set to 0.001--
Wed Feb  6 20:02:00 2019	INFO : Homologue pool found...
Wed Feb  6 20:02:00 2019	INFO : Verifying structure sequences of homologues...
Wed Feb  6 21:11:06 2019	INFO : Starting homologue filtering...
Wed Feb  6 21:12:32 2019	INFO : Getting structures from PDB...
Wed Feb  6 21:12:36 2019	INFO : Creating modelling alignment...
Wed Feb  6 21:12:36 2019	INFO : Modelling...
Wed Feb  6 21:16:00 2019	INFO : Model 1 built
Wed Feb  6 21:16:00 2019	INFO : Validating Calpha distances...
Wed Feb  6 21:16:00 2019	INFO : Model 1 distances correct: True
Wed Feb  6 21:16:00 2019	INFO : Modelling...
Wed Feb  6 21:19:20 2019	INFO : Model 2 built
Wed Feb  6 21:19:20 2019	INFO : Validating Calpha distances...
Wed Feb  6 21:19:20 2019	INFO : Model 2 distances correct: True
Wed Feb  6 21:19:20 2019	INFO : Modelling...
Wed Feb  6 21:25:06 2019	INFO : Model 3 built
Wed Feb  6 21:25:06 2019	INFO : Validating Calpha distances...
Wed Feb  6 21:25:06 2019	INFO : Model 3 distances correct: True
Wed Feb  6 21:25:06 2019	INFO : Modelling...
Wed Feb  6 21:28:27 2019	INFO : Model 4 built
Wed Feb  6 21:28:27 2019	INFO : Validating Calpha distances...
Wed Feb  6 21:28:27 2019	INFO : Model 4 distances correct: True
Wed Feb  6 21:28:27 2019	INFO : Modelling...
Wed Feb  6 21:34:04 2019	INFO : Model 5 built
Wed Feb  6 21:34:04 2019	INFO : Validating Calpha distances...
Wed Feb  6 21:34:04 2019	INFO : Model 5 distances correct: True
Wed Feb  6 21:34:22 2019	INFO : Finished modelling
Wed Feb  6 21:34:22 2019	STATUS CHANGED : R -> P
Wed Feb  6 21:34:32 2019	INFO : Finished edm surfaces: success
Wed Feb  6 21:34:32 2019	INFO : Checking topology...
Wed Feb  6 21:35:04 2019	INFO : Knot matrices done...
Wed Feb  6 21:35:04 2019	INFO : No knots found...
Wed Feb  6 21:35:04 2019	INFO : No lassos found...
Wed Feb  6 21:35:04 2019	INFO : Finishing...
Wed Feb  6 21:35:05 2019	INFO : Job done
Wed Feb  6 21:35:05 2019	STATUS CHANGED : P -> F
Wed Feb  6 21:35:05 2019	STATUS CHANGED : F -> F

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