Job name:

4BXW chain A

e7c6a9d4-9756-49a2-b6c2-5cca7503e632
Finished
Electron density map:

Differential EDM:
Models Number of gaps:2 Gap lengths: 33, 5
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Unknot -30009
Model 2 Unknot -30038
Model 3 Unknot -30068
Model 4 Unknot -29882
Model 5 Unknot -29410
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.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


4BXS

A

Unknot

97.98%

100.00%

100.00%

0.87

..Target: --CRVDNGNCWHFCKHVQNDIQCSCAEGYLLGEDGHSCVAGGNFSCGRNIKTRNKREANLPDFVQSQNATLLKKSDNPSPDIRIVNGMDCKLGECPWQAALVDEKEGVFCGGTILSPIYVLTAAHCINETETISVVVGEIDKSRIETGPLLSVDKIYVHKKFVPPQKAYKFDLAAYDYDIAIIQMKTPIQFSENVVPACLPTADFANQVLMKQDFGIVSGFGRIVEKGPKSKTLKVLKVPYVDRHTCMVSSETPITPNMFCAGYDTLPRDACQGDSGGPHTTVYRDTHFITGIVSSGEGCARNGKYGNYTKLSKFIPWIKRIMR--
Template: KSCRVDNGNCWHFCKHVQNDIQCSCAEGYLLGEDGHSCVAGGNFSCGRNIK------------------------------------MDCKLGECPWQAALVDEKEGVFCGGTILSPIYVLTAAHCINETETIS---GEIDK--------LSVDKIYVHKKFVPPQKAYKFDLAAYDYDIAIIQMKTPIQF----VPACLPTADFANQVLMKQDFGIVSGF--------KSKTLKVLKVPYVDRHTCMVSSETPITPNMFCA------------DSGGPHTTVYRDTHFITGIVSSGK-------YGNYTKLSKFIPWIKRIMRQK

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

NIKTRNKREANLPDFVQSQNATLLKKSDNPSPDIRIVNG

4BXS A Unknot 0.00% 0.00%

NIK------------------------------------

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

CKHVQNDIQCS

4BXS A Unknot 100.00% 100.00%

CKHVQNDIQCS


Fri Dec  1 09:51:26 2017	JOB CREATED : e7c6a9d4-9756-49a2-b6c2-5cca7503e632
Sat Dec  2 05:03:02 2017	STATUS CHANGED : N -> R
Sat Dec  2 05:03:02 2017	INFO : JOB STARTED AT: 2017-12-02 05:03:02.576666
Sat Dec  2 05:03:02 2017	INFO : METHOD: 1
Sat Dec  2 05:03:02 2017	INFO : Precalculated profile found...
Sat Dec  2 05:03:02 2017	INFO : Homologue pool found...
Sat Dec  2 05:03:02 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 06:23:57 2017	INFO : Starting homologue filtering...
Sat Dec  2 06:24:58 2017	INFO : Getting structures from PDB...
Sat Dec  2 06:25:03 2017	INFO : Creating modelling alignment...
Sat Dec  2 06:25:03 2017	INFO : Modelling...
Sat Dec  2 06:52:17 2017	INFO : Model 1 built
Sat Dec  2 06:52:17 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:52:17 2017	INFO : Model 1 distances correct: True
Sat Dec  2 06:52:17 2017	INFO : Modelling...
Sat Dec  2 07:10:21 2017	INFO : Model 2 built
Sat Dec  2 07:10:21 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:10:21 2017	INFO : Model 2 distances correct: True
Sat Dec  2 07:10:21 2017	INFO : Modelling...
Sat Dec  2 07:22:59 2017	INFO : Model 3 built
Sat Dec  2 07:22:59 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:23:00 2017	INFO : Model 3 distances correct: True
Sat Dec  2 07:23:00 2017	INFO : Modelling...
Sat Dec  2 07:33:22 2017	INFO : Model 4 built
Sat Dec  2 07:33:22 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:33:22 2017	INFO : Model 4 distances correct: True
Sat Dec  2 07:33:22 2017	INFO : Modelling...
Sat Dec  2 07:42:10 2017	INFO : Model 5 built
Sat Dec  2 07:42:10 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:42:10 2017	INFO : Model 5 distances correct: True
Sat Dec  2 07:42:36 2017	INFO : Finished modelling
Sat Dec  2 07:42:36 2017	STATUS CHANGED : R -> P
Sat Dec  2 07:42:36 2017	INFO : Checking topology...
Sat Dec  2 07:43:25 2017	INFO : Knot matrices done...
Sat Dec  2 07:43:25 2017	INFO : No knots found...
Sat Dec  2 07:43:29 2017	INFO : No lassos found...
Sat Dec  2 07:43:29 2017	INFO : Finishing...
Sat Dec  2 07:43:29 2017	STATUS CHANGED : P -> E
Sat Dec  2 07:43:29 2017	ERROR : Error while finishing
Sat Dec  2 07:43:29 2017	STATUS CHANGED : E -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling