Job name:

4MM7 chain A

4aaf5c36-a7bb-4b87-b116-ea86ec71d40f
Finished
Models Number of gaps:2 Gap lengths: 6, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Non-trivial -84431
Model 2 Non-trivial -84547
Model 3 Non-trivial -84466
Model 4 Non-trivial -84266
Model 5 Non-trivial -84424
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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 624131 36-349 349-506 -- --
Model 2 Slipknot S 624131 36-350 350-506 -- --
Model 3 Slipknot S 624131 36-349 349-506 -- --
Model 4 Slipknot S 624131 36-349 349-506 -- --
Model 5 Slipknot S 624131 36-348 348-506 -- --
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.
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PDB
code		 Chain Entanglement
type		 Seq
identity		 Total gap
coverage		 Total gap
identity		 RMSD [Å] Pairwise alignment to the target: gap


4HOD
A
S +31,41,+31
96.86%
150.00%
150.00%
0.87

..Target: REHWATRLGLILAMAGYAVDLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVASYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFSLGLGFGVLITFASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAGMQGMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWATGIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHE----
Template: REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPP--TDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHESAGT

3GJC
A
S +31,41,+31
96.79%
133.33%
133.33%
0.90

..Target: --REHWATRLGLILAMAGYAVDLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVASYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFSLGLGFGVLITFASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAGMQGMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWATGIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHE
Template: VKREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREE------ETHWTVWITRFYIIGLFLFLTFLVFLAE-----R
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YIPKIMEETHWT
4HOD A S +31,41,+31 100.00% 100.00%

YIPKIMEETHWT
3GJC A S +31,41,+31 33.33% 33.33%

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

EPPPNATDPD
4HOD A S +31,41,+31 50.00% 50.00%

EPPP--TDPD
3GJC A S +31,41,+31 100.00% 100.00%

EPPPNATDPD

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

Fri Dec  1 09:52:29 2017	JOB CREATED : 4aaf5c36-a7bb-4b87-b116-ea86ec71d40f
Sat Dec  2 06:17:01 2017	STATUS CHANGED : N -> R
Sat Dec  2 06:17:01 2017	INFO : JOB STARTED AT: 2017-12-02 06:17:01.918666
Sat Dec  2 06:17:01 2017	INFO : METHOD: 1
Sat Dec  2 06:17:02 2017	INFO : Precalculated profile found...
Sat Dec  2 06:17:02 2017	INFO : Homologue pool found...
Sat Dec  2 06:17:02 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 06:19:16 2017	INFO : Starting homologue filtering...
Sat Dec  2 06:20:25 2017	INFO : Getting structures from PDB...
Sat Dec  2 06:20:40 2017	INFO : Creating modelling alignment...
Sat Dec  2 06:20:40 2017	INFO : Modelling...
Sat Dec  2 06:27:57 2017	INFO : Model 1 built
Sat Dec  2 06:27:57 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:27:58 2017	INFO : Model 1 distances correct: True
Sat Dec  2 06:27:58 2017	INFO : Modelling...
Sat Dec  2 06:35:03 2017	INFO : Model 2 built
Sat Dec  2 06:35:03 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:35:03 2017	INFO : Model 2 distances correct: True
Sat Dec  2 06:35:03 2017	INFO : Modelling...
Sat Dec  2 06:42:44 2017	INFO : Model 3 built
Sat Dec  2 06:42:44 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:42:44 2017	INFO : Model 3 distances correct: True
Sat Dec  2 06:42:44 2017	INFO : Modelling...
Sat Dec  2 06:50:32 2017	INFO : Model 4 built
Sat Dec  2 06:50:32 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:50:32 2017	INFO : Model 4 distances correct: True
Sat Dec  2 06:50:32 2017	INFO : Modelling...
Sat Dec  2 06:58:01 2017	INFO : Model 5 built
Sat Dec  2 06:58:01 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:58:01 2017	INFO : Model 5 distances correct: True
Sat Dec  2 06:59:11 2017	INFO : Finished modelling
Sat Dec  2 06:59:11 2017	STATUS CHANGED : R -> P
Sat Dec  2 06:59:11 2017	INFO : Checking topology...
Sat Dec  2 07:34:27 2017	INFO : Knot matrices done...
Sat Dec  2 07:36:34 2017	INFO : Some knots found!
Sat Dec  2 07:36:34 2017	INFO : No lassos found...
Sat Dec  2 07:36:34 2017	INFO : Finishing...
Sat Dec  2 07:36:34 2017	STATUS CHANGED : P -> E
Sat Dec  2 07:36:34 2017	ERROR : Error while finishing
Sat Dec  2 07:36:34 2017	STATUS CHANGED : E -> F
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