Job name:

6BNS chain A

339a5cbe-1d14-4278-9401-32cd77af58e0
Finished
Electron density map:

Differential EDM:
Models Number of gaps:3 Gap lengths: 15, 13, 7
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Unknot -38378
Model 2 Unknot -38837
Model 3 Unknot -38659
Model 4 Unknot -38682
Model 5 Unknot -38177
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


4S0T
B
Unknot
100.00%
153.33%
153.33%
0.82

..Target: GLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGSSGGSGGSSHSSLTERHKILHRLLQE
Template: GLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVL-------ESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGI----------------------------
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

PGVLSSGCELPESLQAPSREE
4S0T B Unknot 53.33% 53.33%

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

GITGSSGGSGGSSHSSLTE
4S0T B Unknot 0.00% 0.00%

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

CLEDTAGGFQQLL
4S0T B Unknot 100.00% 100.00%

CLEDTAGGFQQLL

Models
Similarity profile
Modelling alignment

Fri Jan 31 19:30:13 2020	JOB CREATED : 339a5cbe-1d14-4278-9401-32cd77af58e0
Fri Jan 31 19:31:01 2020	STATUS CHANGED : N -> R
Fri Jan 31 19:31:01 2020	INFO : JOB STARTED AT: 2020-01-31 19:31:01.705579
Fri Jan 31 19:31:01 2020	INFO : METHOD: 1
Fri Jan 31 19:31:01 2020	INFO : Building Profile...
Fri Jan 31 19:31:01 2020	INFO : --E-value set to 1.0--
Fri Jan 31 19:41:10 2020	INFO : Homologue pool found...
Fri Jan 31 19:41:10 2020	INFO : Verifying structure sequences of homologues...
Fri Jan 31 20:29:28 2020	INFO : Starting homologue filtering...
Fri Jan 31 20:29:52 2020	INFO : Getting structures from PDB...
Fri Jan 31 20:29:55 2020	INFO : Creating modelling alignment...
Fri Jan 31 20:29:55 2020	INFO : Modelling...
Fri Jan 31 20:38:26 2020	INFO : Model 1 built
Fri Jan 31 20:38:26 2020	INFO : Validating Calpha distances...
Fri Jan 31 20:38:26 2020	INFO : Model 1 distances correct: True
Fri Jan 31 20:38:26 2020	INFO : Modelling...
Fri Jan 31 20:59:15 2020	INFO : Model 2 built
Fri Jan 31 20:59:15 2020	INFO : Validating Calpha distances...
Fri Jan 31 20:59:15 2020	INFO : Model 2 distances correct: True
Fri Jan 31 20:59:15 2020	INFO : Modelling...
Fri Jan 31 21:07:57 2020	INFO : Model 3 built
Fri Jan 31 21:07:57 2020	INFO : Validating Calpha distances...
Fri Jan 31 21:07:57 2020	INFO : Model 3 distances correct: True
Fri Jan 31 21:07:57 2020	INFO : Modelling...
Fri Jan 31 21:16:48 2020	INFO : Model 4 built
Fri Jan 31 21:16:48 2020	INFO : Validating Calpha distances...
Fri Jan 31 21:16:48 2020	INFO : Model 4 distances correct: True
Fri Jan 31 21:16:48 2020	INFO : Modelling...
Fri Jan 31 21:25:37 2020	INFO : Model 5 built
Fri Jan 31 21:25:37 2020	INFO : Validating Calpha distances...
Fri Jan 31 21:25:37 2020	INFO : Model 5 distances correct: True
Fri Jan 31 21:25:57 2020	INFO : Finished modelling
Fri Jan 31 21:25:57 2020	STATUS CHANGED : R -> P
Fri Jan 31 21:26:12 2020	INFO : Finished edm surfaces: success
Fri Jan 31 21:26:12 2020	INFO : Checking topology...
Fri Jan 31 21:26:49 2020	INFO : Knot matrices done...
Fri Jan 31 21:26:49 2020	INFO : No knots found...
Fri Jan 31 21:26:49 2020	INFO : No lassos found...
Fri Jan 31 21:26:49 2020	INFO : Finishing...
Fri Jan 31 21:26:49 2020	INFO : Job done
Fri Jan 31 21:26:49 2020	STATUS CHANGED : P -> F
Fri Jan 31 21:26:49 2020	STATUS CHANGED : F -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling