Job name:

5TUO chain A

811d06af-40a2-43ad-ad00-cb3e373f79ac
Finished
Electron density map:

Differential EDM:
Models Number of gaps:1 Gap lengths: 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -24291
Model 2 Non-trivial -24237
Model 3 Non-trivial -24221
Model 4 Non-trivial -24154
Model 5 Non-trivial -24036
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
Provided protein had only one gap - thus there are no gap-filling combinations to be made.

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
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Knot K 31 31-221 -- -- --
Lasso SL 2++C -- -- 25-175
Model 2 Knot K 31 31-221 -- -- --
Lasso SL 2++C -- -- 25-175
Model 3 Knot K 31 31-221 -- -- --
Lasso SL 2++C -- -- 25-175
Model 4 Knot K 31 31-221 -- -- --
Lasso SL 2++C -- -- 25-175
Model 5 Knot K 31 32-221 -- -- --
Lasso SL 2++C -- -- 25-175
None
Topologies marked by an OK sign () are in accordance with the template topology.
Warning: Entanglement type is assigned automatically - for more complicated topologies there may be some disagreements with manually curated databases.
Model 1
Model 2
Model 3
Model 4
Model 5
Model 1
Model 2
Model 3
Model 4
Model 5
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


4YGF

A

Unknot

100.00%

100.00%

100.00%

0.62

..Target: TKWDYKNKENGPHRWDKLHKDFEVCKSGKSQSPINIEHYYHTQDKADLQFKYAASKPKAVFFTHHTLKASFEPTNHINYRGHDYVLDNVHFHAPMEFLINNKTRPLSAHFVHKDAKGRLLVLAIGFEEGKENPNLDPILEGIQKKQNFKEVALDAFLPKSINYYHFNGSLTAPPCTEGVAWFVIEEPLEVSAKQLAEIKKRMKNSPNQRPVQPDYNTVIIKSSAETR
Template: -KWDYKNKENGPHRWDKLHKDFEVCKSGKSQSPINIEHYYHTQDKADLQFKYAASKPKAVFFTHHTLKASFEPTNHINYRGHDYVLDNVHFHAPMEFLINNKTRPLSAHFVHKDAKGRLLVLAIGFEEGKENPNLDPILEGIQKKQNFKEVALDAFLPKSINYYHFNGSLTAPPCTEGVAWFVIEEPLEVSAKQLAEIKKRMKNSPNQRPVQPDYNTVIIKSSAETR

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

HTQDKADLQF

4YGF A Unknot 100.00% 100.00%

HTQDKADLQF


Fri Dec  1 09:34:21 2017	JOB CREATED : 811d06af-40a2-43ad-ad00-cb3e373f79ac
Fri Dec  1 09:35:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 09:35:02 2017	INFO : JOB STARTED AT: 2017-12-01 09:35:02.141508
Fri Dec  1 09:35:02 2017	INFO : METHOD: 1
Fri Dec  1 09:35:02 2017	INFO : Building Profile...
Fri Dec  1 09:35:02 2017	INFO : --E-value set to 0.001--
Fri Dec  1 09:50:20 2017	INFO : Homologue pool found...
Fri Dec  1 09:50:20 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 10:25:34 2017	INFO : Starting homologue filtering...
Fri Dec  1 10:26:20 2017	INFO : Getting structures from PDB...
Fri Dec  1 10:26:27 2017	INFO : Creating modelling alignment...
Fri Dec  1 10:26:27 2017	INFO : Modelling...
Fri Dec  1 10:28:41 2017	INFO : Model 1 built
Fri Dec  1 10:28:41 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:28:41 2017	INFO : Model 1 distances correct: True
Fri Dec  1 10:28:41 2017	INFO : Modelling...
Fri Dec  1 10:32:20 2017	INFO : Model 2 built
Fri Dec  1 10:32:20 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:32:20 2017	INFO : Model 2 distances correct: True
Fri Dec  1 10:32:20 2017	INFO : Modelling...
Fri Dec  1 10:37:59 2017	INFO : Model 3 built
Fri Dec  1 10:37:59 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:37:59 2017	INFO : Model 3 distances correct: True
Fri Dec  1 10:37:59 2017	INFO : Modelling...
Fri Dec  1 10:40:33 2017	INFO : Model 4 built
Fri Dec  1 10:40:33 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:40:33 2017	INFO : Model 4 distances correct: True
Fri Dec  1 10:40:33 2017	INFO : Modelling...
Fri Dec  1 10:42:45 2017	INFO : Model 5 built
Fri Dec  1 10:42:45 2017	INFO : Validating Calpha distances...
Fri Dec  1 10:42:45 2017	INFO : Model 5 distances correct: True
Fri Dec  1 10:43:23 2017	INFO : Finished modelling
Fri Dec  1 10:43:23 2017	STATUS CHANGED : R -> P
Fri Dec  1 10:43:23 2017	INFO : Checking topology...
Fri Dec  1 10:44:23 2017	INFO : Knot matrices done...
Fri Dec  1 10:45:35 2017	INFO : Some knots found!
Fri Dec  1 10:45:57 2017	INFO : Some lassos found!
Fri Dec  1 10:45:57 2017	INFO : Finishing...
Fri Dec  1 10:45:57 2017	STATUS CHANGED : P -> E
Fri Dec  1 10:45:57 2017	ERROR : Error while finishing
Fri Dec  1 10:45:57 2017	STATUS CHANGED : E -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling