Job name:

noname(4NM3 chain A)

5c7147f4-51a2-45aa-b90b-8a3141046e32
Finished
Models Number of gaps:2 Gap lengths: 16, 5
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Unknot -46393
Model 2 Unknot -46312
Model 3 Unknot -46300
Model 4 Unknot -46207
Model 5 Unknot -45659
Reload
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.
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


1J1B

B

Unknot

99.18%

125.00%

125.00%

0.76

..Target: RTTXFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHAR--H
Template: -----------------FGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQA

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

TXFAESCKPVQQPSAFGSMKVS

1J1B B Unknot 25.00% 25.00%

---------------FGSMKVS

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

VSRDKDGSKVT

1J1B B Unknot 100.00% 100.00%

VSRDKDGSKVT


Sun Jul 23 14:59:42 2017	JOB CREATED : 5c7147f4-51a2-45aa-b90b-8a3141046e32
Mon Jul 24 01:21:02 2017	STATUS CHANGED : N -> R
Mon Jul 24 01:21:02 2017	INFO : JOB STARTED AT: 2017-07-24 01:21:02.562935
Mon Jul 24 01:21:02 2017	INFO : METHOD: 1
Mon Jul 24 01:21:02 2017	INFO : Precalculated profile found...
Mon Jul 24 01:21:02 2017	INFO : Homologue pool found...
Mon Jul 24 01:21:02 2017	INFO : Verifying structure sequences of homologues...
Mon Jul 24 03:25:41 2017	INFO : Starting homologue filtering...
Mon Jul 24 03:26:32 2017	INFO : Getting structures from PDB...
Mon Jul 24 03:26:38 2017	INFO : Creating modelling alignment...
Mon Jul 24 03:26:38 2017	INFO : Modelling...
Mon Jul 24 03:33:53 2017	INFO : Model 1 built
Mon Jul 24 03:33:53 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:33:53 2017	INFO : Model 1 distances correct: True
Mon Jul 24 03:33:53 2017	INFO : Modelling...
Mon Jul 24 03:41:21 2017	INFO : Model 2 built
Mon Jul 24 03:41:21 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:41:21 2017	INFO : Model 2 distances correct: True
Mon Jul 24 03:41:21 2017	INFO : Modelling...
Mon Jul 24 03:48:15 2017	INFO : Model 3 built
Mon Jul 24 03:48:15 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:48:15 2017	INFO : Model 3 distances correct: True
Mon Jul 24 03:48:15 2017	INFO : Modelling...
Mon Jul 24 03:56:08 2017	INFO : Model 4 built
Mon Jul 24 03:56:08 2017	INFO : Validating Calpha distances...
Mon Jul 24 03:56:08 2017	INFO : Model 4 distances correct: True
Mon Jul 24 03:56:08 2017	INFO : Modelling...
Mon Jul 24 04:08:29 2017	INFO : Model 5 built
Mon Jul 24 04:08:29 2017	INFO : Validating Calpha distances...
Mon Jul 24 04:08:29 2017	INFO : Model 5 distances correct: True
Mon Jul 24 04:09:00 2017	INFO : Finished modelling
Mon Jul 24 04:09:00 2017	STATUS CHANGED : R -> P
Mon Jul 24 04:09:00 2017	INFO : Checking topology...
Mon Jul 24 04:15:54 2017	INFO : Knot matrices done...
Mon Jul 24 04:15:54 2017	INFO : No knots found...
Mon Jul 24 04:15:55 2017	INFO : No lassos found...
Mon Jul 24 04:15:55 2017	INFO : Finishing...
Mon Jul 24 04:15:55 2017	INFO : Job done
Mon Jul 24 04:15:55 2017	STATUS CHANGED : P -> F
Mon Jul 24 04:15:55 2017	STATUS CHANGED : F -> F

GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling