GapRepairer

Models

Number of gaps:2

Gap lengths: 5, 4

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Unknot	-37087	-1587	-1754
Model 2	Unknot	-37268	-1564	-1962
Model 3	Unknot	-37223	-1536	-1961
Model 4	Unknot	-36873	-1534	-1586
Model 5	Unknot	-37276	-1492	-2080
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
3C1X	A	Unknot	93.79%	200.00%	200.00%	0.83	..Target: ---IDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG-------------- Template: TVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADF---------------------LPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNATYVNVK

Templates (similarity to the largest gap - 5 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	LLDNDGKKIHC
3C1X	A	Unknot	100.00%	100.00%	LLDNDGKKIHC

Templates (similarity to the 2nd largest gap - 4 aa)

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	LNRITDIGEV
3C1X	A	Unknot	100.00%	100.00%	LNRITDIGEV

Job Log

Fri Feb  7 09:34:08 2020	JOB CREATED : a840602e-43f6-42f4-8c9c-f65d7d2e1a93
Fri Feb  7 09:35:02 2020	STATUS CHANGED : N -> R
Fri Feb  7 09:35:02 2020	INFO : JOB STARTED AT: 2020-02-07 09:35:02.036714
Fri Feb  7 09:35:02 2020	INFO : METHOD: 2
Fri Feb  7 09:35:02 2020	INFO : Building Profile...
Fri Feb  7 09:35:02 2020	INFO : --E-value set to 0.001--
Fri Feb  7 09:51:01 2020	INFO : Homologue pool found...
Fri Feb  7 09:51:01 2020	INFO : Verifying structure sequences of homologues...
Fri Feb  7 12:34:51 2020	INFO : Starting homologue filtering...
Fri Feb  7 12:35:15 2020	INFO : Getting structures from PDB...
Fri Feb  7 12:35:18 2020	INFO : Creating modelling alignment...
Fri Feb  7 12:35:18 2020	INFO : Modelling...
Fri Feb  7 12:38:19 2020	INFO : Model 1 built
Fri Feb  7 12:38:19 2020	INFO : Validating Calpha distances...
Fri Feb  7 12:38:19 2020	INFO : Model 1 distances correct: True
Fri Feb  7 12:38:19 2020	INFO : Modelling...
Fri Feb  7 12:40:20 2020	INFO : Model 2 built
Fri Feb  7 12:40:20 2020	INFO : Validating Calpha distances...
Fri Feb  7 12:40:20 2020	INFO : Model 2 distances correct: True
Fri Feb  7 12:40:20 2020	INFO : Modelling...
Fri Feb  7 12:42:15 2020	INFO : Model 3 built
Fri Feb  7 12:42:15 2020	INFO : Validating Calpha distances...
Fri Feb  7 12:42:15 2020	INFO : Model 3 distances correct: True
Fri Feb  7 12:42:15 2020	INFO : Modelling...
Fri Feb  7 12:44:08 2020	INFO : Model 4 built
Fri Feb  7 12:44:08 2020	INFO : Validating Calpha distances...
Fri Feb  7 12:44:08 2020	INFO : Model 4 distances correct: True
Fri Feb  7 12:44:08 2020	INFO : Modelling...
Fri Feb  7 12:46:51 2020	INFO : Model 5 built
Fri Feb  7 12:46:51 2020	INFO : Validating Calpha distances...
Fri Feb  7 12:46:51 2020	INFO : Model 5 distances correct: True
Fri Feb  7 12:47:10 2020	INFO : Finished modelling
Fri Feb  7 12:47:10 2020	STATUS CHANGED : R -> P
Fri Feb  7 12:47:21 2020	INFO : Finished edm surfaces: success
Fri Feb  7 12:47:21 2020	INFO : Checking topology...
Fri Feb  7 12:47:52 2020	INFO : Knot matrices done...
Fri Feb  7 12:47:52 2020	INFO : No knots found...
Fri Feb  7 12:47:52 2020	INFO : No lassos found...
Fri Feb  7 12:47:52 2020	INFO : Finishing...
Fri Feb  7 12:47:53 2020	INFO : Job done
Fri Feb  7 12:47:53 2020	STATUS CHANGED : P -> F
Fri Feb  7 12:47:53 2020	STATUS CHANGED : F -> F

4DEI chain A