Job name:

4DJK chain A

1a219783-c11b-4ddc-b9ca-4559622bfee1
Finished
Electron density map:

Differential EDM:
Models Number of gaps:3 Gap lengths: 25, 13, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Non-trivial -52842
Model 2 Non-trivial -53083
Model 3 Non-trivial -51397
Model 4 Non-trivial -50369
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Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
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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 32-300 300-489 -- --
Model 2 Knot S 4131 30-209 -- -- --
Model 3 Slipknot S 4131 207-475 475-489 -- --
Model 4 Slipknot S 824131 208-474 474-489 -- --
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
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
A
S +31,41,+31
97.97%
260.92%
260.92%
0.86

..Target: --QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSP--------
Template: AKQLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGA---IEMDSKTFFPDFSKVGTLVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHD----ANTGVTLEPINSQNAPKGHFFLHPRARSPHYIVMNDK

4DJI
B
S +31,41,+31
99.38%
256.62%
256.62%
0.88

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

3LRB
A
S +31,41,+31
25.12%
226.77%
89.38%
1.61

..Target: QLTLLGFFAIT-----ASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFFPDF--SKVGT----LVVFVAFILSYMGVEASATHVNEMSNPGRDYPLAMLLLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGK--ANTGVTLEPINSQNAPKGHFFLHPRARSP
Template: DAHKVGLIPVTLMVSGNIMGSGVFLLPANLASTGGIAIYGWLVTIIGALGLSMVYAKMSFLDP-SPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF--PIL-KDPLVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLA-LIP-IVGIAVFGWFWFRG---------ETYMAAWNVSGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVP------------IATIGGVLIAAVC---------YVLST-TAIMGMIPN---TAGAIVSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFARVNKAGTP----VAGLIIVGILMTIFQLSSISPNATKEFGLVSSVSVIFTLVPYLYTCAALLLLGH---------------------------------------GHFGKARPAYLAVTTIAF------LYCIWAVVGSGAKEVMWSFVTLMVITAMYA-LNYNRLH---KNP

3NCY
C
S +31,41,+31
23.10%
228.00%
73.38%
1.62

..Target: QLTLLGFFAITASMVMAVYEYPTFATSGFSLVFFLLLGGILWFIPVGLCAAEMATVDGWEEGGVFAWVSNTLGPRWGFAAISFGYLQIAIGFIPMLYFVLGALSYILKWPALNEDPITKTIAALIILWALALTQFGGTKYTARIAKVGFFAGILLPAFILIALAAIYLHSGAPVAIEMDSKTFF----PDFSKVGTLVVFVAFIL-SYMGVEASATHVNEMSNPGRDYPLAML-LLMVAAICLSSVGGLSIAMVIPGNEINLSAGVMQTFTVLMSHVAPEIEWTVRVISALLLLGVLAEIASWIVGPSRGMYVTAQKNLLPAAFAKMNKNGVPVTLVISQLVITSIALIILTNTGGGNNMSFLIALALTVVIYLCAYFMLFIGYIVLVLKHPDLKRTFNIPGGKGVKLVVAIVGLLTSIMAFIVSFLPPDNIQGDSTDMYVELLVVSFLVVLALPFILYAVHDRKGKANTGVTLEPINSQNAPKGHFFLHPRARSP
Template: GLIPVTLMVSGNIMGSGVFLLPANLAATGGIAIYGWLVTIIGALALSMVYAKMSSLDP-SPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFF--PIL-KDPLVLTLTCVAVLWIFVLLNIVGPKMITRVQAV-----------------ATVLALVPIVGIAVFGWFWFKWNVSGMNTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCY-VLSTTAIMGMIPNAALRVSA---SPFGDAARMALGDTAGAI--VSFCAAAGCLGSLGGWTLLAGQTAKAAADDGLFPPIFAR----GTP----VAGLLIVGVLMTIFQFSSMSPNAAKEFGLVSSVSVIFTLVPYLYTCAALLLLGH------GHFGKARPLYLLITFVAFVYCIWAVIGSG--------------AKEVMWSFVTLMVIT-ALYA-------------------LNYNRIHKNPYP-LDAP
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

YAVHDRKGKANTGVTLEPINSQNAPKGHFFL
4DJI A S +31,41,+31 84.00% 84.00%

YAVHD----ANTGVTLEPINSQNAPKGHFFL
4DJI B S +31,41,+31 72.00% 72.00%

YAVH-------TGVTLEPINSQNAPKGHFFL
3LRB A S +31,41,+31 24.00% 96.00%

WAVVGSGAKEVMWSFVTLMVITAMYA-LNYNRL
3NCY C S +31,41,+31 8.00% 28.00%

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

YLHSGAPVAIEMDSKTFFP
4DJI A S +31,41,+31 76.92% 76.92%

YLHSGA---IEMDSKTFFP
4DJI B S +31,41,+31 84.62% 84.62%

YLHSGA--AIEMDSKTFFP
3LRB A S +31,41,+31 15.38% 30.77%

FWFRG---------ETYMA
3NCY C S +31,41,+31 15.38% 100.00%

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

DGWEEGGVFA
4DJI A S +31,41,+31 100.00% 100.00%

DGWEEGGVFA
4DJI B S +31,41,+31 100.00% 100.00%

DGWEEGGVFA
3LRB A S +31,41,+31 50.00% 100.00%

DP-SPGGSYA
3NCY C S +31,41,+31 50.00% 100.00%

DP-SPGGSYA

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

Fri Dec  1 09:37:53 2017	JOB CREATED : 1a219783-c11b-4ddc-b9ca-4559622bfee1
Fri Dec  1 12:37:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 12:37:02 2017	INFO : JOB STARTED AT: 2017-12-01 12:37:02.855429
Fri Dec  1 12:37:02 2017	INFO : METHOD: 1
Fri Dec  1 12:37:02 2017	INFO : Precalculated profile found...
Fri Dec  1 12:37:02 2017	INFO : Homologue pool found...
Fri Dec  1 12:37:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 12:37:48 2017	INFO : Starting homologue filtering...
Fri Dec  1 12:38:31 2017	INFO : Getting structures from PDB...
Fri Dec  1 12:39:08 2017	INFO : Creating modelling alignment...
Fri Dec  1 12:39:08 2017	INFO : Modelling...
Fri Dec  1 13:32:31 2017	INFO : Model 1 built
Fri Dec  1 13:32:31 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 13:49:40 2017	INFO : Validating Calpha distances...
Fri Dec  1 13:49:40 2017	INFO : Model 1 distances correct: True
Fri Dec  1 13:49:40 2017	INFO : Modelling...
Fri Dec  1 14:24:21 2017	INFO : Model 2 built
Fri Dec  1 14:24:21 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 14:40:30 2017	INFO : Validating Calpha distances...
Fri Dec  1 14:40:30 2017	INFO : Model 2 distances correct: True
Fri Dec  1 14:40:30 2017	INFO : Modelling...
Fri Dec  1 15:26:04 2017	INFO : Model 3 built
Fri Dec  1 15:26:04 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 15:42:28 2017	INFO : Validating Calpha distances...
Fri Dec  1 15:42:28 2017	INFO : Model 3 distances correct: True
Fri Dec  1 15:42:28 2017	INFO : Modelling...
Fri Dec  1 16:27:58 2017	INFO : Model 4 built
Fri Dec  1 16:27:58 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 16:48:50 2017	INFO : Validating Calpha distances...
Fri Dec  1 16:48:50 2017	INFO : Model 4 distances correct: False
Fri Dec  1 16:48:50 2017	INFO : Modelling...
Fri Dec  1 17:34:45 2017	INFO : Model 5 built
Fri Dec  1 17:34:45 2017	INFO : 1/3 gaps will be remodelled
Fri Dec  1 17:55:42 2017	INFO : Validating Calpha distances...
Fri Dec  1 17:55:42 2017	INFO : Model 5 distances correct: True
Fri Dec  1 17:56:38 2017	INFO : Finished modelling
Fri Dec  1 17:56:38 2017	STATUS CHANGED : R -> P
Fri Dec  1 17:56:38 2017	INFO : Checking topology...
Fri Dec  1 19:02:18 2017	INFO : Knot matrices done...
Fri Dec  1 19:04:38 2017	INFO : Some knots found!
Fri Dec  1 19:04:38 2017	INFO : No lassos found...
Fri Dec  1 19:04:38 2017	INFO : Finishing...
Fri Dec  1 19:04:38 2017	STATUS CHANGED : P -> E
Fri Dec  1 19:04:38 2017	ERROR : Error while finishing
Fri Dec  1 19:04:38 2017	STATUS CHANGED : E -> F
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