Job name:

noname(2BM0 chain A)

6fc25efd-8067-4157-9961-3b2227747cdd
Finished
Models Number of gaps:1 Gap lengths: 21
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap
Model 1 Unknot -68260
Model 2 Unknot -67272
Reload
Warning: All models are renumbered - the first residue in the structure has index 1.
Mix & match
Provided protein had only one gap - thus there are no gap-filling combinations to be made.

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!
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.
PDB
code
Chain Entanglement
type
Seq
identity
Total gap
coverage
Total gap
identity
RMSD [Å] Pairwise alignment to the target: gap


2DY1

A

Unknot

38.33%

100.00%

28.57%

1.57

..Target: KVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIAEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDAPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVV-MQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAA----IRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVP-----EPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRQTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQ-----VQEKLIK-
Template: -----GAMIRTVALVGHAGSGKTTLTEALLYKTGAKERRGRVEEGTTTTDYTPEAKLHRTTVRTGVAPLLFRGHRVFLLDAPGYGDFVGEIRGALEAADAALVAVSAEAGVQVGTERAWTVAERLGLPRMVVVTKLDK-GGDYYALLEDLRSTLG--PILPIDLPLYEGGKWVGLIDVFHGKAYRYEN--GEE-REAEVPPEERERVQRFRQEVLEAIVETDEGLLEKYLEGEEVTGEALEKAFHEAVRRG----LLYPVALASGEREIGVLPLLELILEALPSPTE-----------------RFGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDSL--QSEAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEGLHRGMVLWQGEKP----ESEEVPFARLPDPNVPVALHPKGRTDEARLGEALRKLLEEDPSLKLERQEETGELLLWGHGELHLATAKERL-QDYGVEVEFSVPKVPYRETIKKVAEGQGKYKKQTGGHGQYGDVWLRLEPASE-YGFEW--RITGGVIPSKYQEAIEEGIKEAAKKGVLAGFPVMGFKAIVYNGSYHEVDSSDLAFQIAASLAFKKVMAEAHPVLLEPIYRLKVLAPQERVGDVLSDLQARRGRILGMEQEGALSVVHAEVPLAEVLEYYKALPGLTGGAGAYTLEFSHYAEVPPHLAQRIVQERAQEG

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

KIAEVHEGAATMDFMEQERERGITITA

2DY1 A Unknot 28.57% 100.00%

RRGRVEEGTTTTDYTPEAKLHRTTVRT


Sun Jul 23 14:58:56 2017	JOB CREATED : 6fc25efd-8067-4157-9961-3b2227747cdd
Sun Jul 23 22:03:02 2017	STATUS CHANGED : N -> R
Sun Jul 23 22:03:02 2017	INFO : JOB STARTED AT: 2017-07-23 22:03:02.133496
Sun Jul 23 22:03:02 2017	INFO : METHOD: 1
Sun Jul 23 22:03:02 2017	INFO : Precalculated profile found...
Sun Jul 23 22:03:02 2017	INFO : Homologue pool found...
Sun Jul 23 22:03:02 2017	INFO : Verifying structure sequences of homologues...
Sun Jul 23 22:14:07 2017	INFO : Starting homologue filtering...
Sun Jul 23 22:15:38 2017	INFO : Getting structures from PDB...
Sun Jul 23 22:15:47 2017	INFO : Creating modelling alignment...
Sun Jul 23 22:15:47 2017	INFO : Modelling...
Sun Jul 23 22:47:05 2017	INFO : Model 1 built
Sun Jul 23 22:47:05 2017	INFO : 1 gaps will be remodelled
Sun Jul 23 23:06:33 2017	INFO : Validating Calpha distances...
Sun Jul 23 23:06:33 2017	INFO : Model 1 distances correct: False
Sun Jul 23 23:06:33 2017	INFO : Modelling...
Sun Jul 23 23:37:05 2017	INFO : Model 2 built
Sun Jul 23 23:37:05 2017	INFO : 1 gaps will be remodelled
Sun Jul 23 23:56:34 2017	INFO : Validating Calpha distances...
Sun Jul 23 23:56:34 2017	INFO : Model 2 distances correct: False
Sun Jul 23 23:56:34 2017	INFO : Modelling...
Mon Jul 24 00:24:29 2017	INFO : Model 3 built
Mon Jul 24 00:24:29 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 00:41:23 2017	INFO : Validating Calpha distances...
Mon Jul 24 00:41:23 2017	INFO : Model 3 distances correct: True
Mon Jul 24 00:41:23 2017	INFO : Modelling...
Mon Jul 24 01:08:37 2017	INFO : Model 4 built
Mon Jul 24 01:08:37 2017	INFO : Validating Calpha distances...
Mon Jul 24 01:08:37 2017	INFO : Model 4 distances correct: True
Mon Jul 24 01:08:37 2017	INFO : Modelling...
Mon Jul 24 01:32:54 2017	INFO : Model 5 built
Mon Jul 24 01:32:54 2017	INFO : 1 gaps will be remodelled
Mon Jul 24 01:50:03 2017	INFO : Validating Calpha distances...
Mon Jul 24 01:50:03 2017	INFO : Model 5 distances correct: False
Mon Jul 24 01:50:24 2017	INFO : Finished modelling
Mon Jul 24 01:50:24 2017	STATUS CHANGED : R -> P
Mon Jul 24 01:50:24 2017	INFO : Checking topology...
Mon Jul 24 02:38:05 2017	INFO : Knot matrices done...
Mon Jul 24 02:38:05 2017	INFO : No knots found...
Mon Jul 24 02:38:05 2017	INFO : No lassos found...
Mon Jul 24 02:38:05 2017	INFO : Finishing...
Mon Jul 24 02:38:06 2017	INFO : Job done
Mon Jul 24 02:38:06 2017	STATUS CHANGED : P -> F
Mon Jul 24 02:38:06 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling