GapRepairer

Models

Number of gaps:1

Gap lengths: 9

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Unknot	-10572	-2320
Model 2	Unknot	-10575	-2266
Model 3	Unknot	-10446	-2211
Model 4	Unknot	-10302	-2136
Model 5	Unknot	-10189	-2001
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
5B8C	C	Unknot	98.28%	100.00%	100.00%	0.81	..Target: --NPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTE Template: SWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTE

Templates (similarity to the largest gap - 9 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	FPEDRSQPGQDSRFR
5B8C	C	Unknot	100.00%	100.00%	FPEDRSQPGQDSRFR

Job Log

Tue Feb 25 16:28:13 2020	JOB CREATED : 39e57d27-a87f-49c5-a039-b6ecce7f74b0
Tue Feb 25 16:29:02 2020	STATUS CHANGED : N -> R
Tue Feb 25 16:29:02 2020	INFO : JOB STARTED AT: 2020-02-25 16:29:02.254768
Tue Feb 25 16:29:02 2020	INFO : METHOD: 1
Tue Feb 25 16:29:02 2020	INFO : Building Profile...
Tue Feb 25 16:29:02 2020	INFO : --E-value set to 1.0--
Tue Feb 25 16:36:34 2020	INFO : Homologue pool found...
Tue Feb 25 16:36:34 2020	INFO : Verifying structure sequences of homologues...
Tue Feb 25 21:36:39 2020	INFO : Starting homologue filtering...
Tue Feb 25 21:36:59 2020	INFO : Getting structures from PDB...
Tue Feb 25 21:37:02 2020	INFO : Creating modelling alignment...
Tue Feb 25 21:37:02 2020	INFO : Modelling...
Tue Feb 25 21:38:51 2020	INFO : Model 1 built
Tue Feb 25 21:38:51 2020	INFO : Validating Calpha distances...
Tue Feb 25 21:38:51 2020	INFO : Model 1 distances correct: True
Tue Feb 25 21:38:51 2020	INFO : Modelling...
Tue Feb 25 21:40:39 2020	INFO : Model 2 built
Tue Feb 25 21:40:39 2020	INFO : Validating Calpha distances...
Tue Feb 25 21:40:39 2020	INFO : Model 2 distances correct: True
Tue Feb 25 21:40:39 2020	INFO : Modelling...
Tue Feb 25 21:42:30 2020	INFO : Model 3 built
Tue Feb 25 21:42:30 2020	INFO : Validating Calpha distances...
Tue Feb 25 21:42:30 2020	INFO : Model 3 distances correct: True
Tue Feb 25 21:42:30 2020	INFO : Modelling...
Tue Feb 25 21:44:12 2020	INFO : Model 4 built
Tue Feb 25 21:44:12 2020	INFO : Validating Calpha distances...
Tue Feb 25 21:44:12 2020	INFO : Model 4 distances correct: True
Tue Feb 25 21:44:12 2020	INFO : Modelling...
Tue Feb 25 21:46:40 2020	INFO : Model 5 built
Tue Feb 25 21:46:40 2020	INFO : Validating Calpha distances...
Tue Feb 25 21:46:40 2020	INFO : Model 5 distances correct: True
Tue Feb 25 21:46:48 2020	INFO : Finished modelling
Tue Feb 25 21:46:48 2020	STATUS CHANGED : R -> P
Tue Feb 25 21:46:55 2020	INFO : Finished edm surfaces: success
Tue Feb 25 21:46:55 2020	INFO : Checking topology...
Tue Feb 25 21:47:04 2020	INFO : Knot matrices done...
Tue Feb 25 21:47:04 2020	INFO : No knots found...
Tue Feb 25 21:47:04 2020	INFO : No lassos found...
Tue Feb 25 21:47:04 2020	INFO : Finishing...
Tue Feb 25 21:47:05 2020	INFO : Job done
Tue Feb 25 21:47:05 2020	STATUS CHANGED : P -> F
Tue Feb 25 21:47:05 2020	STATUS CHANGED : F -> F

4ZQK chain B