Job name:

3MPQ chain A

e8c59cd0-a2da-4c32-94cf-ab4a2c73cea7
Finished
Models Number of gaps:2 Gap lengths: 13, 6
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Non-trivial -85653
Model 2 Non-trivial -85392
Model 3 Non-trivial -84881
Model 4 Non-trivial -85600
Model 5 Non-trivial -85578
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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 4131 40-360 360-506 -- --
Model 2 Slipknot S 4131 39-360 360-506 -- --
Model 3 Slipknot S 4131 39-360 360-506 -- --
Model 4 Slipknot S 4131 39-360 360-506 -- --
Model 5 Slipknot S 4131 39-360 360-506 -- --
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


2A65
A
S +31,41,+31
98.82%
166.67%
166.67%
0.28

..Target: KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFCLAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNH-----
Template: -REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPP--TDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNHESAGT

3GJC
A
S +31,41,+31
99.20%
153.85%
153.85%
0.52

..Target: -KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFCLAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWAREYIPKIMEETHWTVWITRFYIIGLFLFLTFLVFLAERRRNH
Template: VKREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKASVILGGSISIPAAVAFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLVVWARE------EETHWTVWITRFYIIGLFLFLTFLVFLAE----R
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

LVVWAREYIPKIMEETHWT
2A65 A S +31,41,+31 100.00% 100.00%

LVVWAREYIPKIMEETHWT
3GJC A S +31,41,+31 53.85% 53.85%

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

PEPPPNATDPDS
2A65 A S +31,41,+31 66.67% 66.67%

PEPPP--TDPDS
3GJC A S +31,41,+31 100.00% 100.00%

PEPPPNATDPDS

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

Fri Dec  1 09:49:29 2017	JOB CREATED : e8c59cd0-a2da-4c32-94cf-ab4a2c73cea7
Sat Dec  2 03:06:02 2017	STATUS CHANGED : N -> R
Sat Dec  2 03:06:02 2017	INFO : JOB STARTED AT: 2017-12-02 03:06:02.460725
Sat Dec  2 03:06:02 2017	INFO : METHOD: 1
Sat Dec  2 03:06:02 2017	INFO : Precalculated profile found...
Sat Dec  2 03:06:02 2017	INFO : Homologue pool found...
Sat Dec  2 03:06:02 2017	INFO : Verifying structure sequences of homologues...
Sat Dec  2 03:08:56 2017	INFO : Starting homologue filtering...
Sat Dec  2 03:10:12 2017	INFO : Getting structures from PDB...
Sat Dec  2 03:10:29 2017	INFO : Creating modelling alignment...
Sat Dec  2 03:10:29 2017	INFO : Modelling...
Sat Dec  2 03:19:00 2017	INFO : Model 1 built
Sat Dec  2 03:19:00 2017	INFO : Validating Calpha distances...
Sat Dec  2 03:19:00 2017	INFO : Model 1 distances correct: True
Sat Dec  2 03:19:00 2017	INFO : Modelling...
Sat Dec  2 03:27:36 2017	INFO : Model 2 built
Sat Dec  2 03:27:36 2017	INFO : Validating Calpha distances...
Sat Dec  2 03:27:36 2017	INFO : Model 2 distances correct: True
Sat Dec  2 03:27:36 2017	INFO : Modelling...
Sat Dec  2 03:48:12 2017	INFO : Model 3 built
Sat Dec  2 03:48:12 2017	INFO : Validating Calpha distances...
Sat Dec  2 03:48:12 2017	INFO : Model 3 distances correct: True
Sat Dec  2 03:48:12 2017	INFO : Modelling...
Sat Dec  2 03:56:56 2017	INFO : Model 4 built
Sat Dec  2 03:56:56 2017	INFO : Validating Calpha distances...
Sat Dec  2 03:56:56 2017	INFO : Model 4 distances correct: True
Sat Dec  2 03:56:56 2017	INFO : Modelling...
Sat Dec  2 04:05:25 2017	INFO : Model 5 built
Sat Dec  2 04:05:25 2017	INFO : Validating Calpha distances...
Sat Dec  2 04:05:25 2017	INFO : Model 5 distances correct: True
Sat Dec  2 04:06:39 2017	INFO : Finished modelling
Sat Dec  2 04:06:39 2017	STATUS CHANGED : R -> P
Sat Dec  2 04:06:39 2017	INFO : Checking topology...
Sat Dec  2 04:57:03 2017	INFO : Knot matrices done...
Sat Dec  2 04:59:49 2017	INFO : Some knots found!
Sat Dec  2 04:59:49 2017	INFO : No lassos found...
Sat Dec  2 04:59:49 2017	INFO : Finishing...
Sat Dec  2 04:59:49 2017	STATUS CHANGED : P -> E
Sat Dec  2 04:59:49 2017	ERROR : Error while finishing
Sat Dec  2 04:59:49 2017	STATUS CHANGED : E -> F
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