Job name:

5L25 chain A

128d9d79-cfd4-416e-995d-ae01612e0036
Finished
Models Number of gaps:6 Gap lengths: 95, 37, 11, 8, 4, 4
Model Entanglement Average DOPE-HR (by gap length) Smaller
DOPE-HR 1st gap2nd gap3rd gapgaps
Model 1 Non-trivial -48072

Model 2 Non-trivial -51202

Model 3 Non-trivial -48251

Model 4 Non-trivial -48561

None
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.
Warning: JSmol may at times display gaps where there are none - due to some overlaps in models. This does not indicate presence of gaps in downloaded structure!
EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Slipknot S +31 90-279 279-553 -- --
Lasso L -4N -- -- 97-314 -23,+33,-64,+89
Model 2 Slipknot S 31 96-277 277-553 -- --
Lasso L -4N -- -- 97-314 -21,+36,-64,+90
Model 3 Slipknot S 31 93-278 278-553 -- --
Lasso L -4N -- -- 97-314 -20,+34,-64,+92
Model 4 Slipknot S 31 92-280 280-553 -- --
Lasso L -4N -- -- 97-314 -20,+35,-64,+90
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 1
Model 2
Model 3
Model 4
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.
Warning: No templates were used. Models were generated using de novo prediction. Possible reasons include: no homologues similar enough; homologues do not cover the gaps in the target; all gaps at most 2 amino acids long.

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

Sun Jul 23 14:55:50 2017	JOB CREATED : 128d9d79-cfd4-416e-995d-ae01612e0036
Sun Jul 23 16:53:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 16:53:02 2017	INFO : JOB STARTED AT: 2017-07-23 16:53:02.203871
Sun Jul 23 16:53:02 2017	INFO : METHOD: 1
Sun Jul 23 16:53:02 2017	INFO : Precalculated profile found...
Sun Jul 23 16:53:02 2017	INFO : Homologue pool found...
Sun Jul 23 16:53:02 2017	ERROR : No homologues found using selected method. Maybe try specifying your own?
Sun Jul 23 16:53:02 2017	INFO : Proceeding using de novo modelling
Sun Jul 23 16:53:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 16:53:02 2017	INFO : Getting structures from PDB...
Sun Jul 23 16:53:02 2017	INFO : Creating modelling alignment...
Sun Jul 23 16:53:02 2017	INFO : Modelling...
Sun Jul 23 17:58:32 2017	INFO : Model 1 built
Sun Jul 23 17:58:32 2017	INFO : Validating Calpha distances...
Sun Jul 23 17:58:32 2017	INFO : Model 1 distances correct: True
Sun Jul 23 17:58:32 2017	INFO : Modelling...
Sun Jul 23 19:37:56 2017	INFO : Model 2 built
Sun Jul 23 19:37:56 2017	INFO : Validating Calpha distances...
Sun Jul 23 19:37:56 2017	INFO : Model 2 distances correct: True
Sun Jul 23 19:37:56 2017	INFO : Modelling...
Sun Jul 23 21:49:50 2017	INFO : Model 3 built
Sun Jul 23 21:49:50 2017	INFO : Validating Calpha distances...
Sun Jul 23 21:49:50 2017	INFO : Model 3 distances correct: True
Sun Jul 23 21:49:50 2017	INFO : Modelling...
Sun Jul 23 23:53:26 2017	INFO : Model 4 built
Sun Jul 23 23:53:26 2017	INFO : Validating Calpha distances...
Sun Jul 23 23:53:26 2017	INFO : Model 4 distances correct: True
Sun Jul 23 23:53:26 2017	INFO : Modelling...
Sun Jul 23 23:53:43 2017	INFO : Model 5 creation failed - VTFM optimization failed. Possibly really bad templates were used?
Sun Jul 23 23:54:14 2017	INFO : Finished modelling
Sun Jul 23 23:54:14 2017	STATUS CHANGED : R -> P
Sun Jul 23 23:54:14 2017	INFO : Checking topology...
Mon Jul 24 00:51:22 2017	INFO : Knot matrices done...
Mon Jul 24 00:55:46 2017	INFO : Some knots found!
Mon Jul 24 00:57:13 2017	INFO : Some lassos found!
Mon Jul 24 00:57:13 2017	INFO : Finishing...
Mon Jul 24 00:57:14 2017	INFO : Job done
Mon Jul 24 00:57:14 2017	STATUS CHANGED : P -> F
Mon Jul 24 00:57:14 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling