Job name:

1ERE chain A

28e13629-db62-4467-ad89-f6d2f8b86601
Finished
Electron density map:

Differential EDM:
Models Number of gaps:2 Gap lengths: 7, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Unknot -30799
Model 2 Err -30952
Model 3 Err -30680
Model 4 Err -30596
Model 5 Err -30197
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.
Help
PDB
code		 Chain Entanglement
type		 Seq
identity		 Total gap
coverage		 Total gap
identity		 RMSD [Å] Pairwise alignment to the target: gap


1A52
A
Unknot
99.58%
200.00%
200.00%
0.62

..Target: SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHR
Template: -LALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHERLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEML----
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YSEYDPTRPFSEA
1A52 A Unknot 100.00% 100.00%

YSEYDPTRPFSEA
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YTFLSSTLKS
1A52 A Unknot 100.00% 100.00%

YTFLSSTLKS

Models
Similarity profile
Modelling alignment

Sat May  4 21:35:51 2019	JOB CREATED : 28e13629-db62-4467-ad89-f6d2f8b86601
Sat May  4 21:36:01 2019	STATUS CHANGED : N -> R
Sat May  4 21:36:01 2019	INFO : JOB STARTED AT: 2019-05-04 21:36:01.865285
Sat May  4 21:36:01 2019	INFO : METHOD: 1
Sat May  4 21:36:01 2019	INFO : Building Profile...
Sat May  4 21:36:01 2019	INFO : --E-value set to 0.001--
Sat May  4 21:46:49 2019	INFO : Homologue pool found...
Sat May  4 21:46:49 2019	INFO : Verifying structure sequences of homologues...
Sat May  4 22:40:46 2019	INFO : Starting homologue filtering...
Sat May  4 22:42:12 2019	INFO : Getting structures from PDB...
Sat May  4 22:42:15 2019	INFO : Creating modelling alignment...
Sat May  4 22:42:15 2019	INFO : Modelling...
Sat May  4 22:47:42 2019	INFO : Model 1 built
Sat May  4 22:47:42 2019	INFO : Validating Calpha distances...
Sat May  4 22:47:42 2019	INFO : Model 1 distances correct: True
Sat May  4 22:47:42 2019	INFO : Modelling...
Sat May  4 22:53:14 2019	INFO : Model 2 built
Sat May  4 22:53:14 2019	INFO : Validating Calpha distances...
Sat May  4 22:53:14 2019	INFO : Model 2 distances correct: True
Sat May  4 22:53:14 2019	INFO : Modelling...
Sat May  4 22:57:22 2019	INFO : Model 3 built
Sat May  4 22:57:22 2019	INFO : Validating Calpha distances...
Sat May  4 22:57:22 2019	INFO : Model 3 distances correct: True
Sat May  4 22:57:22 2019	INFO : Modelling...
Sat May  4 22:59:41 2019	INFO : Model 4 built
Sat May  4 22:59:41 2019	INFO : Validating Calpha distances...
Sat May  4 22:59:41 2019	INFO : Model 4 distances correct: True
Sat May  4 22:59:41 2019	INFO : Modelling...
Sat May  4 23:02:03 2019	INFO : Model 5 built
Sat May  4 23:02:03 2019	INFO : Validating Calpha distances...
Sat May  4 23:02:03 2019	INFO : Model 5 distances correct: True
Sat May  4 23:02:20 2019	INFO : Finished modelling
Sat May  4 23:02:20 2019	STATUS CHANGED : R -> P
Sat May  4 23:02:26 2019	INFO : Finished edm surfaces: success
Sat May  4 23:02:26 2019	INFO : Checking topology...
Sat May  4 23:02:26 2019	INFO : Knot matrices done...
Sat May  4 23:02:26 2019	INFO : No knots found...
Sat May  4 23:02:26 2019	INFO : No lassos found...
Sat May  4 23:02:26 2019	INFO : Finishing...
Sat May  4 23:02:27 2019	INFO : Job done
Sat May  4 23:02:27 2019	STATUS CHANGED : P -> F
Sat May  4 23:02:27 2019	STATUS CHANGED : F -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling