GapRepairer

Models

Number of gaps:2

Gap lengths: 7, 5

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Unknot	-36974	-1976	-1688
Model 2	Err	-36662	-1945	-1537
Model 3	Err	-36804	-1916	-1651
Model 4	Err	-36498	-1874	-1403
Model 5	Err	-36618	-1851	-1458
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
3ADW	A	Unknot	98.18%	200.00%	200.00%	0.71	..Target: -----SADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDL Template: QLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDL

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

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	HITPLQEQSKEVA
3ADW	A	Unknot	100.00%	100.00%	HITPLQEQSKEVA

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

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	LTGKTTDKSPF
3ADW	A	Unknot	100.00%	100.00%	LTGKTTDKSPF

Job Log

Tue Jun 25 15:21:51 2019	JOB CREATED : 31c65e8b-8df7-4d4e-bc61-ac915d61597a
Tue Jun 25 15:22:02 2019	STATUS CHANGED : N -> R
Tue Jun 25 15:22:02 2019	INFO : JOB STARTED AT: 2019-06-25 15:22:02.483284
Tue Jun 25 15:22:02 2019	INFO : METHOD: 1
Tue Jun 25 15:22:02 2019	INFO : Building Profile...
Tue Jun 25 15:22:02 2019	INFO : --E-value set to 0.001--
Tue Jun 25 15:31:28 2019	INFO : Homologue pool found...
Tue Jun 25 15:31:28 2019	INFO : Verifying structure sequences of homologues...
Tue Jun 25 16:36:25 2019	INFO : Starting homologue filtering...
Tue Jun 25 16:38:34 2019	INFO : Getting structures from PDB...
Tue Jun 25 16:38:37 2019	INFO : Creating modelling alignment...
Tue Jun 25 16:38:37 2019	INFO : Modelling...
Tue Jun 25 16:42:48 2019	INFO : Model 1 built
Tue Jun 25 16:42:48 2019	INFO : Validating Calpha distances...
Tue Jun 25 16:42:48 2019	INFO : Model 1 distances correct: True
Tue Jun 25 16:42:48 2019	INFO : Modelling...
Tue Jun 25 16:49:34 2019	INFO : Model 2 built
Tue Jun 25 16:49:34 2019	INFO : Validating Calpha distances...
Tue Jun 25 16:49:34 2019	INFO : Model 2 distances correct: True
Tue Jun 25 16:49:34 2019	INFO : Modelling...
Tue Jun 25 16:53:39 2019	INFO : Model 3 built
Tue Jun 25 16:53:39 2019	INFO : Validating Calpha distances...
Tue Jun 25 16:53:39 2019	INFO : Model 3 distances correct: True
Tue Jun 25 16:53:39 2019	INFO : Modelling...
Tue Jun 25 16:57:52 2019	INFO : Model 4 built
Tue Jun 25 16:57:52 2019	INFO : Validating Calpha distances...
Tue Jun 25 16:57:52 2019	INFO : Model 4 distances correct: True
Tue Jun 25 16:57:52 2019	INFO : Modelling...
Tue Jun 25 17:01:53 2019	INFO : Model 5 built
Tue Jun 25 17:01:53 2019	INFO : Validating Calpha distances...
Tue Jun 25 17:01:53 2019	INFO : Model 5 distances correct: True
Tue Jun 25 17:02:11 2019	INFO : Finished modelling
Tue Jun 25 17:02:11 2019	STATUS CHANGED : R -> P
Tue Jun 25 17:02:17 2019	INFO : Finished edm surfaces: success
Tue Jun 25 17:02:17 2019	INFO : Checking topology...
Tue Jun 25 17:02:18 2019	INFO : Knot matrices done...
Tue Jun 25 17:02:18 2019	INFO : No knots found...
Tue Jun 25 17:02:18 2019	INFO : No lassos found...
Tue Jun 25 17:02:18 2019	INFO : Finishing...
Tue Jun 25 17:02:18 2019	INFO : Job done
Tue Jun 25 17:02:18 2019	STATUS CHANGED : P -> F
Tue Jun 25 17:02:18 2019	STATUS CHANGED : F -> F

3S9S chain A