Job name:

3TB3 chain A

48d597ec-c92e-4761-94bf-c5fa755f4b6d
Finished
Electron density map:

Differential EDM:
Models Number of gaps:1 Gap lengths: 17
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Non-trivial -26837
Model 2 Non-trivial -26763
Model 3 Non-trivial -26729
Model 4 Non-trivial -26638
Model 5 Non-trivial -26618
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 Slipknot S 31 3-190 190-217 -- --
Lasso SL 2--C -- -- 21-94
Model 2 Slipknot S 31 3-180 180-217 -- --
Lasso SL 2--C -- -- 21-94
Model 3 Slipknot S 31 3-180 180-217 -- --
Lasso SL 2--C -- -- 21-94
Model 4 Slipknot S 31 4-181 181-217 -- --
Lasso SL 2--C -- -- 21-94
Model 5 Slipknot S 31 3-180 180-217 -- --
Lasso SL 2--C -- -- 21-94
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.
Help
PDB
code		 Chain Entanglement
type		 Seq
identity		 Total gap
coverage		 Total gap
identity		 RMSD [Å] Pairwise alignment to the target: gap


3RIS
A
K -52,-31,-31
93.83%
64.71%
64.71%
0.79

..Target: EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNAAATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSD-------------
Template: EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTK------DAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQ

3RIS
B
K -52,-31,-31
93.83%
64.71%
64.71%
0.77

..Target: EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNAAATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSD-------------
Template: EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDT------EDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQ

3RII
B
K -52,-31,-31
97.66%
58.82%
58.82%
0.78

..Target: EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNAAATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSD-
Template: EWCLXESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNASATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAXKGLALSNSDVIRQVHNSFAR-------TKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLXAIVSDR
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

FARQQMFEFDTKTSAKEEDAFHF
3RIS A K -52,-31,-31 64.71% 64.71%

FARQQMFEFDTK------DAFHF
3RIS B K -52,-31,-31 64.71% 64.71%

FARQQMFEFDT------EDAFHF
3RII B K -52,-31,-31 58.82% 58.82%

FAR-------TKTSAKEEDAFHF

Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_1
Model_2
Model_3
Model_4
Model_5

Fri Dec  1 09:40:55 2017	JOB CREATED : 48d597ec-c92e-4761-94bf-c5fa755f4b6d
Fri Dec  1 16:52:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 16:52:02 2017	INFO : JOB STARTED AT: 2017-12-01 16:52:02.794728
Fri Dec  1 16:52:02 2017	INFO : METHOD: 1
Fri Dec  1 16:52:02 2017	INFO : Precalculated profile found...
Fri Dec  1 16:52:02 2017	INFO : Homologue pool found...
Fri Dec  1 16:52:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 16:53:24 2017	INFO : Starting homologue filtering...
Fri Dec  1 16:54:05 2017	INFO : Getting structures from PDB...
Fri Dec  1 16:54:17 2017	INFO : Creating modelling alignment...
Fri Dec  1 16:54:17 2017	INFO : Modelling...
Fri Dec  1 16:57:04 2017	INFO : Model 1 built
Fri Dec  1 16:57:04 2017	INFO : Validating Calpha distances...
Fri Dec  1 16:57:04 2017	INFO : Model 1 distances correct: True
Fri Dec  1 16:57:04 2017	INFO : Modelling...
Fri Dec  1 17:00:08 2017	INFO : Model 2 built
Fri Dec  1 17:00:08 2017	INFO : Validating Calpha distances...
Fri Dec  1 17:00:08 2017	INFO : Model 2 distances correct: True
Fri Dec  1 17:00:08 2017	INFO : Modelling...
Fri Dec  1 17:02:54 2017	INFO : Model 3 built
Fri Dec  1 17:02:54 2017	INFO : Validating Calpha distances...
Fri Dec  1 17:02:54 2017	INFO : Model 3 distances correct: True
Fri Dec  1 17:02:54 2017	INFO : Modelling...
Fri Dec  1 17:07:42 2017	INFO : Model 4 built
Fri Dec  1 17:07:42 2017	INFO : Validating Calpha distances...
Fri Dec  1 17:07:42 2017	INFO : Model 4 distances correct: True
Fri Dec  1 17:07:42 2017	INFO : Modelling...
Fri Dec  1 17:10:42 2017	INFO : Model 5 built
Fri Dec  1 17:10:42 2017	INFO : Validating Calpha distances...
Fri Dec  1 17:10:42 2017	INFO : Model 5 distances correct: True
Fri Dec  1 17:11:06 2017	INFO : Finished modelling
Fri Dec  1 17:11:06 2017	STATUS CHANGED : R -> P
Fri Dec  1 17:11:06 2017	INFO : Checking topology...
Fri Dec  1 17:11:45 2017	INFO : Knot matrices done...
Fri Dec  1 17:12:40 2017	INFO : Some knots found!
Fri Dec  1 17:12:45 2017	INFO : Some lassos found!
Fri Dec  1 17:12:45 2017	INFO : Finishing...
Fri Dec  1 17:12:45 2017	STATUS CHANGED : P -> E
Fri Dec  1 17:12:45 2017	ERROR : Error while finishing
Fri Dec  1 17:12:45 2017	STATUS CHANGED : E -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling