GapRepairer

Models

Number of gaps:1

Gap lengths: 4

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap
Model 1	Unknot	-35958	-926
Model 2	Unknot	-35576	-919
Model 3	Unknot	-35713	-881
Model 4	Unknot	-35434	-878
Model 5	Unknot	-35434	-819
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
4F0I	A	Unknot	100.00%	100.00%	100.00%	0.75	..Target: SDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLD Template: ---CVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLP--DKMLVAVKALK----SARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPV---

Templates (similarity to the largest gap - 4 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	AKLLAGGEDV
4F0I	A	Unknot	100.00%	100.00%	AKLLAGGEDV

Download Files Models Similarity profile Modelling alignment

Job Log

Thu Dec  6 16:34:08 2018	JOB CREATED : 3e7a562b-3082-4774-8ec9-b9092a5978f8
Thu Dec  6 16:35:02 2018	STATUS CHANGED : N -> R
Thu Dec  6 16:35:02 2018	INFO : JOB STARTED AT: 2018-12-06 16:35:02.305851
Thu Dec  6 16:35:02 2018	INFO : METHOD: 1
Thu Dec  6 16:35:02 2018	INFO : Building Profile...
Thu Dec  6 16:35:02 2018	INFO : --E-value set to 0.001--
Thu Dec  6 16:44:47 2018	INFO : Homologue pool found...
Thu Dec  6 16:44:47 2018	INFO : Verifying structure sequences of homologues...
Thu Dec  6 20:03:05 2018	INFO : Starting homologue filtering...
Thu Dec  6 20:04:29 2018	INFO : Getting structures from PDB...
Thu Dec  6 20:04:34 2018	INFO : Creating modelling alignment...
Thu Dec  6 20:04:34 2018	INFO : Modelling...
Thu Dec  6 20:08:34 2018	INFO : Model 1 built
Thu Dec  6 20:08:34 2018	INFO : Validating Calpha distances...
Thu Dec  6 20:08:34 2018	INFO : Model 1 distances correct: True
Thu Dec  6 20:08:34 2018	INFO : Modelling...
Thu Dec  6 20:12:01 2018	INFO : Model 2 built
Thu Dec  6 20:12:01 2018	INFO : Validating Calpha distances...
Thu Dec  6 20:12:01 2018	INFO : Model 2 distances correct: True
Thu Dec  6 20:12:01 2018	INFO : Modelling...
Thu Dec  6 20:15:28 2018	INFO : Model 3 built
Thu Dec  6 20:15:28 2018	INFO : Validating Calpha distances...
Thu Dec  6 20:15:28 2018	INFO : Model 3 distances correct: True
Thu Dec  6 20:15:28 2018	INFO : Modelling...
Thu Dec  6 20:18:47 2018	INFO : Model 4 built
Thu Dec  6 20:18:47 2018	INFO : Validating Calpha distances...
Thu Dec  6 20:18:47 2018	INFO : Model 4 distances correct: True
Thu Dec  6 20:18:47 2018	INFO : Modelling...
Thu Dec  6 20:22:14 2018	INFO : Model 5 built
Thu Dec  6 20:22:14 2018	INFO : Validating Calpha distances...
Thu Dec  6 20:22:14 2018	INFO : Model 5 distances correct: True
Thu Dec  6 20:22:33 2018	INFO : Finished modelling
Thu Dec  6 20:22:33 2018	STATUS CHANGED : R -> P
Thu Dec  6 20:22:40 2018	INFO : Finished edm surfaces: success
Thu Dec  6 20:22:40 2018	INFO : Checking topology...
Thu Dec  6 20:23:16 2018	INFO : Knot matrices done...
Thu Dec  6 20:23:16 2018	INFO : No knots found...
Thu Dec  6 20:23:16 2018	INFO : No lassos found...
Thu Dec  6 20:23:16 2018	INFO : Finishing...
Thu Dec  6 20:23:17 2018	INFO : Job done
Thu Dec  6 20:23:17 2018	STATUS CHANGED : P -> F
Thu Dec  6 20:23:17 2018	STATUS CHANGED : F -> F

4GT5 chain A