GapRepairer

Models

Number of gaps:2

Gap lengths: 16, 4

Model	Entanglement	Average	DOPE-HR (by gap length)
		DOPE-HR	1st gap	2nd gap
Model 1	Unknot	-34593	-1526	-1592
Model 2	Unknot	-34407	-1517	-1416
Model 3	Unknot	-34547	-1439	-1633
Model 4	Unknot	-33937	-1434	-1029
Model 5	Unknot	-34411	-1339	-1595
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
1HYN	P	S -3₁	99.66%	200.00%	200.00%	0.88	..Target: -VYVELQELVMDEKNQELRWMEAARWVQLEENLGENGAWGRPHLSHLTFWSLLELRRVFTKGTVLLDLQETSLAGVANQLLDRFIFEDQIRPQDREELLRALLLKHSHAGELEALGGVKPAVLTRSGDPSQPLLPQHSSLETQLFCEQGDGGTEGHSPSGILEKIPPDSEATLVLVGRADFLEQPVLGFVRLQEAAELEAVELPVPIRFLFVLLGPEAPHIDYTQLGRAAATLMSERVFRIDAYMAQSRGELLHSLEGFLDCSLVLPPTDAPSEQALLSLVPVQRELLRRRYQSS Template: KVYVELQELVMDEKNQELRWMEAARWVQLEENLGENGAWGRPHLSHLTFWSLLELRRVFTKGTVLLDLQETSLAGVANQLLDRFIFEDQIRPQDREELLRALLLKHSHAGELEALGGVKPAVLTRSGDPSQPLLPQHSSLETQLFCEQGDGGTEGHSPSGILEKIPPDSEATLVLVGRADFLEQPVLGFVRLQEAAELEAVELPVPIRFLFVLLGPEAPHIDYTQLGRAAATLMSERVFRIDAYMAQSRGELLHSLEGFLDCSLVLPPTDAPSEQALLSLVPVQRELLRRRYQ--

Templates (similarity to the largest gap - 16 aa) Help

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	FCEQGDGGTEGHSPSGILEKIP
1HYN	P	S -3₁	100.00%	100.00%	FCEQGDGGTEGHSPSGILEKIP

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

PDB code	Chain	Knot type	Gap coverage	Gap identity	>Target_Sequence: gap	LTRSGDPSQP
1HYN	P	S -3₁	100.00%	100.00%	LTRSGDPSQP

Job Log

Fri Dec  1 09:52:18 2017	JOB CREATED : cf1797fc-03cb-45c7-ae1d-ff505385cd3c
Sat Dec  2 06:07:01 2017	STATUS CHANGED : N -> R
Sat Dec  2 06:07:02 2017	INFO : JOB STARTED AT: 2017-12-02 06:07:02.000283
Sat Dec  2 06:07:02 2017	INFO : METHOD: 1
Sat Dec  2 06:07:02 2017	INFO : Precalculated profile found...
Sat Dec  2 06:07:02 2017	INFO : Homologue pool found...
Sat Dec  2 06:07:02 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 06:07:17 2017	INFO : Starting homologue filtering...
Sat Dec  2 06:07:25 2017	INFO : Getting structures from PDB...
Sat Dec  2 06:07:32 2017	INFO : Creating modelling alignment...
Sat Dec  2 06:07:32 2017	INFO : Modelling...
Sat Dec  2 06:12:01 2017	INFO : Model 1 built
Sat Dec  2 06:12:01 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:12:01 2017	INFO : Model 1 distances correct: True
Sat Dec  2 06:12:01 2017	INFO : Modelling...
Sat Dec  2 06:16:20 2017	INFO : Model 2 built
Sat Dec  2 06:16:20 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:16:20 2017	INFO : Model 2 distances correct: True
Sat Dec  2 06:16:20 2017	INFO : Modelling...
Sat Dec  2 06:20:26 2017	INFO : Model 3 built
Sat Dec  2 06:20:26 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:20:26 2017	INFO : Model 3 distances correct: True
Sat Dec  2 06:20:26 2017	INFO : Modelling...
Sat Dec  2 06:24:39 2017	INFO : Model 4 built
Sat Dec  2 06:24:39 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:24:39 2017	INFO : Model 4 distances correct: True
Sat Dec  2 06:24:39 2017	INFO : Modelling...
Sat Dec  2 06:29:03 2017	INFO : Model 5 built
Sat Dec  2 06:29:03 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:29:03 2017	INFO : Model 5 distances correct: True
Sat Dec  2 06:29:37 2017	INFO : Finished modelling
Sat Dec  2 06:29:37 2017	STATUS CHANGED : R -> P
Sat Dec  2 06:29:37 2017	INFO : Checking topology...
Sat Dec  2 06:30:50 2017	INFO : Knot matrices done...
Sat Dec  2 06:32:08 2017	INFO : No knots found...
Sat Dec  2 06:32:08 2017	INFO : No lassos found...
Sat Dec  2 06:32:08 2017	INFO : Finishing...
Sat Dec  2 06:32:08 2017	STATUS CHANGED : P -> E
Sat Dec  2 06:32:08 2017	ERROR : Error while finishing
Sat Dec  2 06:32:08 2017	STATUS CHANGED : E -> F

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