Job name:

4O6D chain B

6494a906-e54e-47e3-9d87-ee87b6344a9b
Finished
Electron density map:

Differential EDM:
Models Number of gaps:2 Gap lengths: 23, 15
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Non-trivial -35394
Model 2 Non-trivial -35274
Model 3 Non-trivial -35268
Model 4 Non-trivial -35311
Model 5 Non-trivial -33204
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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.
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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 83-175 175-376 -- --
Lasso L -1C -- -- 305-354
Model 2 Slipknot S 31 82-192 192-376 -- --
Lasso L -1C -- -- 305-354
Model 3 Slipknot S 31 81-197 197-376 -- --
Lasso L -1C -- -- 305-354
Model 4 Slipknot S 31 82-175 175-376 -- --
Lasso L -1C -- -- 305-354
Model 5 Slipknot S 31 112-176 176-376 -- --
Lasso L -1C -- -- 305-354
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


4TPL

B

Unknot

99.43%

108.70%

108.70%

0.52

..Target: XXXXXXHHSSGVDLGTENLYFQSNADTGCAIDISRQELRCGSGVFIHNDVEAWMDRYKYYPETPQGLAKIIQKAHKEGVCGLRSVSRLEHQMWEAVKDELNTLLKENGVDLSVVVEKQEGMYKSAPKRLTATTEKLEIGWKAWGKSILFAPELANNTFVVDGPETKECPTQNRAWNSLEVEDFGFGLTSTRMFLKVRESNTTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA
Template: ----HHHHSSGVDLGTENLYFQSNADTGCAIDISRQELRCGSGVFIHNDVEAWMDRYKYYPETPQGLAKIIQKAHKEGVCGLRSVSRLEHQMWEAVKDELNTLLKENGVDLSVVVEKQEGMYKSAPKRLTATT---------------------NNTFVVDGPETKECPTQNRAWNSLEVEDFGFGLTSTRMFLKVRESNTTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA


5GS6

B

Unknot

54.73%

126.67%

56.81%

0.87

..Target: XXXXXXHHSSGVDLGTENLYFQSNADTGCAIDISRQELRCGSGVFIHNDVEAWMDRYKYYPETPQGLAKIIQKAHKEGVCGLRSVSRLEHQMWEAVKDELNTLLKENGVDLSVVVEKQEGMYKSAPKRLTATTEKLEIGWKAWGKSILFAPELANNTFVVDGPETKECPTQNRAWNSLEVEDFGFGLTSTRMFLKVRESNTTECDSKIIGTAVKNNLAIHSDLSYWIESRLNDTWKLERAVLGEVKSCTWPETHTLWGDGILESDLIIPVTLAGPRSNHNRRPGYKTQNQGPWDEGRVEIDFDYCPGTTVTLSESCGHRGPATRTTTESGKLITDWCCRSCTLPPLRYQTDSGCWYGMEIRPQRHDEKTLVQSQVNA
Template: ------HHHH--------------HHVGCSVDFSKKETRCGTGVFVYNDV--------YHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIEESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTA

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

TATTEKLEIGWKAWGKSILFAPELANNTF

4TPL B Unknot 8.70% 8.70%

TATT---------------------NNTF

5GS6 B Unknot 43.48% 100.00%

PVPVNELPHGWKAWGKSYFVRAAKTNNSF

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

XXXHHSSGVDLGTENLYFQSN

4TPL B Unknot 100.00% 100.00%

-HHHHSSGVDLGTENLYFQSN

5GS6 B Unknot 13.33% 26.67%

---HHHH--------------


Fri Dec  1 09:52:56 2017	JOB CREATED : 6494a906-e54e-47e3-9d87-ee87b6344a9b
Sat Dec  2 06:37:02 2017	STATUS CHANGED : N -> R
Sat Dec  2 06:37:02 2017	INFO : JOB STARTED AT: 2017-12-02 06:37:02.436728
Sat Dec  2 06:37:02 2017	INFO : METHOD: 1
Sat Dec  2 06:37:02 2017	INFO : Building Profile...
Sat Dec  2 06:37:02 2017	INFO : --E-value set to 0.001--
Sat Dec  2 06:54:00 2017	INFO : Homologue pool found...
Sat Dec  2 06:54:00 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 06:55:17 2017	INFO : Starting homologue filtering...
Sat Dec  2 06:56:02 2017	INFO : Getting structures from PDB...
Sat Dec  2 06:56:12 2017	INFO : Creating modelling alignment...
Sat Dec  2 06:56:13 2017	INFO : Modelling...
Sat Dec  2 07:15:30 2017	INFO : Model 1 built
Sat Dec  2 07:15:30 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:15:30 2017	INFO : Model 1 distances correct: True
Sat Dec  2 07:15:30 2017	INFO : Modelling...
Sat Dec  2 07:33:11 2017	INFO : Model 2 built
Sat Dec  2 07:33:11 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:33:11 2017	INFO : Model 2 distances correct: True
Sat Dec  2 07:33:11 2017	INFO : Modelling...
Sat Dec  2 07:48:29 2017	INFO : Model 3 built
Sat Dec  2 07:48:29 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:48:29 2017	INFO : Model 3 distances correct: True
Sat Dec  2 07:48:29 2017	INFO : Modelling...
Sat Dec  2 07:57:54 2017	INFO : Model 4 built
Sat Dec  2 07:57:54 2017	INFO : Validating Calpha distances...
Sat Dec  2 07:57:54 2017	INFO : Model 4 distances correct: True
Sat Dec  2 07:57:54 2017	INFO : Modelling...
Sat Dec  2 08:10:14 2017	INFO : Model 5 built
Sat Dec  2 08:10:14 2017	INFO : Validating Calpha distances...
Sat Dec  2 08:10:14 2017	INFO : Model 5 distances correct: True
Sat Dec  2 08:10:42 2017	INFO : Finished modelling
Sat Dec  2 08:10:42 2017	STATUS CHANGED : R -> P
Sat Dec  2 08:10:42 2017	INFO : Checking topology...
Sat Dec  2 08:12:11 2017	INFO : Knot matrices done...
Sat Dec  2 08:13:11 2017	INFO : Some knots found!
Sat Dec  2 08:13:14 2017	INFO : Some lassos found!
Sat Dec  2 08:13:14 2017	INFO : Finishing...
Sat Dec  2 08:13:14 2017	STATUS CHANGED : P -> E
Sat Dec  2 08:13:14 2017	ERROR : Error while finishing
Sat Dec  2 08:13:14 2017	STATUS CHANGED : E -> F

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