Job name:

4DJI chain A

04cfa95b-2f5f-485e-8de1-bed11dc40c8f
Finished
Electron density map:

Differential EDM:
Models Number of gaps:2 Gap lengths: 5, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Non-trivial -59541
Model 2 Non-trivial -59476
Model 3 Non-trivial -59329
Model 4 Non-trivial -59295
Model 5 Non-trivial -59174
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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
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Slipknot S 4131 31-304 304-487 -- --
Model 2 Slipknot S 4131 31-304 304-487 -- --
Model 3 Slipknot S 4131 31-304 304-487 -- --
Model 4 Slipknot S 4131 31-296 296-483 -- --
Model 5 Slipknot S 4131 31-298 298-487 -- --
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
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


4DJI
B
S +31,41,+31
100.00%
50.00%
50.00%
0.82

..Target: AKQLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSPHYIVMNDK
Template: --QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGA--AIEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHP----TFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVH-------TGVTLEPINSQNAPKGHFFLHPRARSPHYI-----

3NCY
B
S +31,41,+31
24.05%
200.00%
70.00%
1.72

..Target: AKQLTLLGFFAIT-----ASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFF----PDFSKVGTLVVFVAFIL-SYMGVEASATHVNEMSNPGRDYPLAML-LLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAV--HDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSPHYIVMNDK
Template: ------VGLIPVTLMVSGNIMGSGVFLLPANLAATGGIAIYGWLVTIIGALALSMVYAKMSSLDP-SPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF--PIL-KDPLVLTLTCVAVLWIFVLLNIVGPKMITRVQAV-----------------ATVLALVPIVGIAVFGWFWFKWNVSGMNTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCY-VLSTTAIMGMIPNAALRVSA---SPFGDAARMALGDTAGAI--VSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVNKAG---GLLIVGVLMT---IFQFSSMSPNAAKEFGLVSSVSVIFTLVPY--LYTCAALLLLGH---------------------------------------GHFGKARPLY---LLITF---VAFVYCIWAVIGSGAKEVMWSFVTLMVITALYA-----LNYNRIHKNPY--PLDA
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

VHDRKGKANTG
4DJI B S +31,41,+31 0.00% 0.00%

VH-------TG
3NCY B S +31,41,+31 20.00% 100.00%

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

SGAPVAIEMD
4DJI B S +31,41,+31 50.00% 50.00%

SGA--AIEMD
3NCY B S +31,41,+31 50.00% 100.00%

LVPIVGIAVF

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

Fri Dec  1 09:37:49 2017	JOB CREATED : 04cfa95b-2f5f-485e-8de1-bed11dc40c8f
Fri Dec  1 12:36:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 12:36:02 2017	INFO : JOB STARTED AT: 2017-12-01 12:36:02.345469
Fri Dec  1 12:36:02 2017	INFO : METHOD: 1
Fri Dec  1 12:36:02 2017	INFO : Precalculated profile found...
Fri Dec  1 12:36:02 2017	INFO : Homologue pool found...
Fri Dec  1 12:36:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 12:36:51 2017	INFO : Starting homologue filtering...
Fri Dec  1 12:37:33 2017	INFO : Getting structures from PDB...
Fri Dec  1 12:37:53 2017	INFO : Creating modelling alignment...
Fri Dec  1 12:37:53 2017	INFO : Modelling...
Fri Dec  1 12:44:21 2017	INFO : Model 1 built
Fri Dec  1 12:44:21 2017	INFO : Validating Calpha distances...
Fri Dec  1 12:44:21 2017	INFO : Model 1 distances correct: True
Fri Dec  1 12:44:21 2017	INFO : Modelling...
Fri Dec  1 12:50:56 2017	INFO : Model 2 built
Fri Dec  1 12:50:56 2017	INFO : Validating Calpha distances...
Fri Dec  1 12:50:56 2017	INFO : Model 2 distances correct: True
Fri Dec  1 12:50:56 2017	INFO : Modelling...
Fri Dec  1 12:57:28 2017	INFO : Model 3 built
Fri Dec  1 12:57:28 2017	INFO : Validating Calpha distances...
Fri Dec  1 12:57:28 2017	INFO : Model 3 distances correct: True
Fri Dec  1 12:57:28 2017	INFO : Modelling...
Fri Dec  1 13:03:30 2017	INFO : Model 4 built
Fri Dec  1 13:03:30 2017	INFO : Validating Calpha distances...
Fri Dec  1 13:03:30 2017	INFO : Model 4 distances correct: True
Fri Dec  1 13:03:30 2017	INFO : Modelling...
Fri Dec  1 13:09:51 2017	INFO : Model 5 built
Fri Dec  1 13:09:51 2017	INFO : Validating Calpha distances...
Fri Dec  1 13:09:51 2017	INFO : Model 5 distances correct: True
Fri Dec  1 13:11:01 2017	INFO : Finished modelling
Fri Dec  1 13:11:01 2017	STATUS CHANGED : R -> P
Fri Dec  1 13:11:01 2017	INFO : Checking topology...
Fri Dec  1 13:55:01 2017	INFO : Knot matrices done...
Fri Dec  1 13:58:05 2017	INFO : Some knots found!
Fri Dec  1 13:58:05 2017	INFO : No lassos found...
Fri Dec  1 13:58:05 2017	INFO : Finishing...
Fri Dec  1 13:58:05 2017	STATUS CHANGED : P -> E
Fri Dec  1 13:58:05 2017	ERROR : Error while finishing
Fri Dec  1 13:58:05 2017	STATUS CHANGED : E -> F
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