Job name:

1F48 chain A

b31d26e2-655c-4e0c-8ba3-1cb16bfad4df
Finished
Models Number of gaps:3 Gap lengths: 19, 13, 9
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Non-trivial -48548
Model 2 Non-trivial -52509
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Warning: All models are renumbered - the first residue in the structure has index 1.
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EntanglementHelpKnotProtLassoProtLinkProt
Model Type Knot core Slipknot Lasso Piercing Show
range loop range loop position in JSmol
Model 1 Lasso L +3C -- -- 113-422
Model 2 Knot K 31 308-564 -- -- --
Lasso SL 2++C -- -- 113-422
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 2
Model 1
Model 2
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


3SJC
F
Unknot
28.99%
150.61%
51.82%
1.30

..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE-KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSL---SIADTRSPLLRMRAQQE-LPQIESVKRQHASRVALVPVLASEPTGIDKL-----------------KQLAGHHH
Template: VEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTDPAHNLSDAFGEKFGKDARKVTGMNNLSCMEID----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PSAAL------------------------------------GSIPGIDEAL-------SFMEVMKHIKRQE-------------------------------------------------------------------------QGEGETFD-----------------------------------TVIFDTAPTGHTLRFLQLPNT-----SGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAE----CKRCQARWKMQKKYLDQIDEL--YEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELED

3IDQ
A
Unknot
34.19%
88.89%
55.56%
1.44

..Target: ---MQFLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDS-NPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTL--NGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKLKQLAGHHH
Template: NLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTDPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDDEALS---------------FMEVMKHIKRQEQG--------------------EGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFNELKAN-------VETIRQQ-------FTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLL----FANCKRCQARWKMQKKYL----------------------------------------------------------------------------------------DQIDELYEDFHV--------VKMPLEIRG-LNNL--------------------------------------------------------------------------------------------------------------TKFSQFLNKEYNPI------------------------------TDGKVI--------------------------YELEDKEGL------HHHHH

3IO3
A
Unknot
30.87%
92.31%
7.69%
1.23

..Target: --------MQFLQNIP-PYLFFTGKGGVGKTSISCATAIR--LAEQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADTRSPLLRMRAQQELPQIESVKRQHASRVALVPVLASEPTGIDKLKQLAGHHH
Template: DLELEPTLESIVQHDSLKWIFVGGKGGVGKTTTSSSVAVQLALAQPNEQFLLISTDPAHNLSDAFCQKFGKDARKVEGLPNLSCMEIDP---------------------------------------------------------YKTIIFDTAPTGHTLRFLQ--------------------------------SEVNEQFTNPELTTFICVCISEFLSLYETERMIQELMSYNMDVNSIVVN------------------------------------------------------QLLFAE--CKRCESRWKMQKKYLDQMGELYED--------------------------------------------------------------------------YHLVK----------MPLLGCEIRG-----VENLKKFS--------KFLLKPYDPKADSDIVFD-----------------------------------------------------------------------------------------------------------------------------LE

3ZS9
A
Unknot
31.40%
68.42%
26.32%
1.04

..Target: MQ------FLQNIPPYLFFTGKGGVGKTSISCATAIRLA--EQGKRVLLVSTDPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYR--ARIVDPIKGVLPDDVVSSINEQLSGACTTEIAAFDEFTGLLTDASLLTRFDHIIFDTAPTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEALSDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPTDTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPAAHLSMTLNGSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTEEIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE-KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGWIINNSLSIADT-RSPLLRMRAQQE-LPQIESVKRQHASRVALVPVLASEPTGIDKL-----------------KQLAGHHH
Template: VEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTDPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMNDMADLTGSIPGI---DEALSFMEVMK-----HIKRQEQGEG--------ETFDTVIFDTAPTGHTLR----------------------------------------------------------------------------------------------------------------------------FLQLPN-----TLSKLL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDV-NSIIVNQLLFAENCKRCQARWKMQKKYLDQIDEL--YEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELED
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

DATGAYHREIAKKMGE-KGHFTTPMM
3SJC F Unknot 21.05% 73.68%

QLPNT-----SGKLNELKANVETIRQ
3IDQ A Unknot 0.00% 0.00%

-------------------------
3IO3 A Unknot 0.00% 0.00%

D------------------------
3ZS9 A Unknot 26.32% 68.42%

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

TQPVASPSSDEYLQQRPDI
3SJC F Unknot 30.77% 76.92%

---GSIPGIDEAL------
3IDQ A Unknot 0.00% 0.00%

-------------------
3IO3 A Unknot 7.69% 92.31%

AE--CKRCESRWKMQKKYL
3ZS9 A Unknot 0.00% 0.00%

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

AHLSMTLNGSLNNLQ
3SJC F Unknot 0.00% 0.00%

---------------
3IDQ A Unknot 55.56% 88.89%

--VKMPLEIRG-LNNL-
3IO3 A Unknot 0.00% 0.00%

---------------
3ZS9 A Unknot 0.00% 0.00%

---------------

Models
Similarity profile
Modelling alignment
Raw knot fingerprint matrices:
Model_2

Fri Dec  1 09:43:46 2017	JOB CREATED : b31d26e2-655c-4e0c-8ba3-1cb16bfad4df
Fri Dec  1 20:23:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 20:23:02 2017	INFO : JOB STARTED AT: 2017-12-01 20:23:02.169131
Fri Dec  1 20:23:02 2017	INFO : METHOD: 1
Fri Dec  1 20:23:02 2017	INFO : Precalculated profile found...
Fri Dec  1 20:23:02 2017	INFO : Homologue pool found...
Fri Dec  1 20:23:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 20:26:27 2017	INFO : Starting homologue filtering...
Fri Dec  1 20:27:40 2017	INFO : Getting structures from PDB...
Fri Dec  1 20:27:52 2017	INFO : Creating modelling alignment...
Fri Dec  1 20:27:52 2017	INFO : Modelling...
Fri Dec  1 21:24:41 2017	INFO : Model 1 built
Fri Dec  1 21:24:41 2017	INFO : 3/3 gaps will be remodelled
Fri Dec  1 23:05:12 2017	INFO : Validating Calpha distances...
Fri Dec  1 23:05:12 2017	INFO : Model 1 distances correct: False
Fri Dec  1 23:05:12 2017	INFO : Modelling...
Sat Dec  2 00:01:00 2017	INFO : Model 2 built
Sat Dec  2 00:01:00 2017	INFO : 2/3 gaps will be remodelled
Sat Dec  2 01:20:00 2017	INFO : Validating Calpha distances...
Sat Dec  2 01:20:00 2017	INFO : Model 2 distances correct: False
Sat Dec  2 01:20:00 2017	INFO : Modelling...
Sat Dec  2 02:18:54 2017	INFO : Model 3 built
Sat Dec  2 02:18:54 2017	INFO : 2/3 gaps will be remodelled
Sat Dec  2 03:20:20 2017	INFO : Validating Calpha distances...
Sat Dec  2 03:20:20 2017	INFO : Model 3 distances correct: False
Sat Dec  2 03:20:20 2017	INFO : Modelling...
Sat Dec  2 04:22:29 2017	INFO : Model 4 built
Sat Dec  2 04:22:29 2017	INFO : 1/3 gaps will be remodelled
Sat Dec  2 04:58:11 2017	INFO : Validating Calpha distances...
Sat Dec  2 04:58:11 2017	INFO : Model 4 distances correct: True
Sat Dec  2 04:58:11 2017	INFO : Modelling...
Sat Dec  2 05:52:24 2017	INFO : Model 5 built
Sat Dec  2 05:52:24 2017	INFO : 1/3 gaps will be remodelled
Sat Dec  2 06:27:42 2017	INFO : Validating Calpha distances...
Sat Dec  2 06:27:42 2017	INFO : Model 5 distances correct: True
Sat Dec  2 06:28:10 2017	INFO : Finished modelling
Sat Dec  2 06:28:10 2017	STATUS CHANGED : R -> P
Sat Dec  2 06:28:10 2017	INFO : Checking topology...
Sat Dec  2 06:50:30 2017	INFO : Knot matrices done...
Sat Dec  2 06:51:19 2017	INFO : Some knots found!
Sat Dec  2 06:52:05 2017	INFO : Some lassos found!
Sat Dec  2 06:52:05 2017	INFO : Finishing...
Sat Dec  2 06:52:05 2017	STATUS CHANGED : P -> E
Sat Dec  2 06:52:05 2017	ERROR : Error while finishing
Sat Dec  2 06:52:05 2017	STATUS CHANGED : E -> F
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