Job name:

1XKK chain A

b0375d32-0a90-4287-91c7-dc4ec6ced65d
Finished
Electron density map:

Differential EDM:
Models Number of gaps:5 Gap lengths: 9, 8, 6, 5, 5
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Unknot -37507

Model 2 Unknot -37438

Model 3 Unknot -37300

Model 4 Unknot -37486

Model 5 Unknot -37810

None
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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


5CNN
B
Unknot
99.01%
422.22%
422.22%
0.77

..Target: --ALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLI
Template: NQALLRQLKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLG-----------KVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDAD----

5CZH
A
Unknot
97.43%
450.00%
437.50%
0.83

..Target: ------ALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLI
Template: GEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPD------------EEDMDDVVDADEYLI
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

EEKEYHAEGGKVPIK
5CNN B Unknot 22.22% 22.22%

----------KVPIK
5CZH A Unknot 100.00% 100.00%

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

ERMHLPSPTDSNFY
5CNN B Unknot 100.00% 100.00%

ERMHLPSPTDSNFY
5CZH A Unknot 37.50% 50.00%

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

MDEEDMDDVVDA
5CNN B Unknot 100.00% 100.00%

MDEEDMDDVVDA
5CZH A Unknot 100.00% 100.00%

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

WIPEGEKVKIP
5CNN B Unknot 100.00% 100.00%

WIPEGEKVKIP
5CZH A Unknot 100.00% 100.00%

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

LREATSPKANK
5CNN B Unknot 100.00% 100.00%

LREATSPKANK
5CZH A Unknot 100.00% 100.00%

LREATSPKANK

Models
Similarity profile
Modelling alignment

Thu Dec 28 15:55:46 2017	JOB CREATED : b0375d32-0a90-4287-91c7-dc4ec6ced65d
Thu Dec 28 15:56:01 2017	STATUS CHANGED : N -> R
Thu Dec 28 15:56:01 2017	INFO : JOB STARTED AT: 2017-12-28 15:56:01.955556
Thu Dec 28 15:56:01 2017	INFO : METHOD: 1
Thu Dec 28 15:56:02 2017	INFO : Building Profile...
Thu Dec 28 15:56:02 2017	INFO : --E-value set to 0.001--
Thu Dec 28 16:07:13 2017	INFO : Homologue pool found...
Thu Dec 28 16:07:13 2017	INFO : Verifying structure sequences of homologues...
Thu Dec 28 18:27:05 2017	INFO : Starting homologue filtering...
Thu Dec 28 18:27:40 2017	INFO : Getting structures from PDB...
Thu Dec 28 18:27:46 2017	INFO : Creating modelling alignment...
Thu Dec 28 18:27:46 2017	INFO : Modelling...
Thu Dec 28 18:43:49 2017	INFO : Model 1 built
Thu Dec 28 18:43:49 2017	INFO : Validating Calpha distances...
Thu Dec 28 18:43:50 2017	INFO : Model 1 distances correct: True
Thu Dec 28 18:43:50 2017	INFO : Modelling...
Thu Dec 28 18:55:31 2017	INFO : Model 2 built
Thu Dec 28 18:55:31 2017	INFO : Validating Calpha distances...
Thu Dec 28 18:55:31 2017	INFO : Model 2 distances correct: True
Thu Dec 28 18:55:31 2017	INFO : Modelling...
Thu Dec 28 19:14:34 2017	INFO : Model 3 built
Thu Dec 28 19:14:34 2017	INFO : Validating Calpha distances...
Thu Dec 28 19:14:34 2017	INFO : Model 3 distances correct: True
Thu Dec 28 19:14:34 2017	INFO : Modelling...
Thu Dec 28 19:30:07 2017	INFO : Model 4 built
Thu Dec 28 19:30:07 2017	INFO : Validating Calpha distances...
Thu Dec 28 19:30:07 2017	INFO : Model 4 distances correct: True
Thu Dec 28 19:30:07 2017	INFO : Modelling...
Thu Dec 28 19:40:55 2017	INFO : Model 5 built
Thu Dec 28 19:40:55 2017	INFO : Validating Calpha distances...
Thu Dec 28 19:40:55 2017	INFO : Model 5 distances correct: True
Thu Dec 28 19:41:18 2017	INFO : Finished modelling
Thu Dec 28 19:41:18 2017	STATUS CHANGED : R -> P
Thu Dec 28 19:41:18 2017	INFO : Checking topology...
Thu Dec 28 19:41:57 2017	INFO : Knot matrices done...
Thu Dec 28 19:41:57 2017	INFO : No knots found...
Thu Dec 28 19:41:57 2017	INFO : No lassos found...
Thu Dec 28 19:41:57 2017	INFO : Finishing...
Thu Dec 28 19:41:57 2017	STATUS CHANGED : P -> E
Thu Dec 28 19:41:57 2017	ERROR : Error while finishing
Thu Dec 28 19:41:57 2017	STATUS CHANGED : E -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling