Job name:

1BY7 chain A

934f951b-6578-42df-b76b-3dc0b9f3130b
Finished
Models Number of gaps:3 Gap lengths: 18, 7, 4
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Unknot -47123
Model 2 Unknot -46958
Model 3 Unknot -46664
Model 4 Unknot -47052
Model 5 Unknot -47276
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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.
Pro Tip: Since you provided a structure that contains some crystallographic information you can verify our models using the wwPDB service.
Validity report for the RCSB PDB structure you were repairing can be accessed here
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


2ARQ
A
Unknot
99.44%
194.44%
194.44%
0.98

..Target: EDLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVGAAADKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP
Template: -DLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMASVLQFNE-----DKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKL--LFPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPD--ADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEG-----------TGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP

2DUT
A
Unknot
43.17%
294.44%
61.90%
1.14

..Target: -EDLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVGAAADKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYA-GDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTG-HGGPQFVADHPFLFLIMHKITNCILFFGRFSSP--
Template: MEQVSASIGNFTVDLFNKLNETNRDKNIFFSPWSISSALALTYLAAKGSTAREMAEVLHF---------IHSGFKELLTAFNKPRNNYSLRSANRIYVEKTYALLPTYLQLSKKYYKAEPQKVNFKTAPEQSRKEINTWVEKQTESKIKNLLSSDDVKATTRLILVNAIYFKAEWEVKFQAEKTSIQPFRL-KNKSKPVKMMYMRDTFPVLIMEKMNFKMIELPYVKRELSMFILLPDD-----TGLEQLERELTYERLSEWADSKMMTETLVDLHLPKFSLEDRIDLRDTLRNMGMTTAFTT-NADFRGMTD---LAISKVIHQSFVAVDEKGTEAAAATAVIISFTTSV-HVLKFKVDHPFHFFIRHNKSKTILFFGRFCCPVE
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

EGTEAAAGTGGVMTGRTGHGGPQF
2ARQ A Unknot 44.44% 44.44%

EG-----------TGRTGHGGPQF
2DUT A Unknot 33.33% 94.44%

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

AINASTGNYLLES
2ARQ A Unknot 100.00% 100.00%

AINASTGNYLLES
2DUT A Unknot 28.57% 100.00%

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

EKKLNGLYPF
2ARQ A Unknot 50.00% 50.00%

EKKL--LFPF
2DUT A Unknot 0.00% 100.00%

QAEKTSIQPF

Models
Similarity profile
Modelling alignment

Fri Dec  1 09:43:06 2017	JOB CREATED : 934f951b-6578-42df-b76b-3dc0b9f3130b
Fri Dec  1 19:05:02 2017	STATUS CHANGED : N -> R
Fri Dec  1 19:05:02 2017	INFO : JOB STARTED AT: 2017-12-01 19:05:02.352540
Fri Dec  1 19:05:02 2017	INFO : METHOD: 1
Fri Dec  1 19:05:02 2017	INFO : Precalculated profile found...
Fri Dec  1 19:05:02 2017	INFO : Homologue pool found...
Fri Dec  1 19:05:02 2017	INFO : Verifying structure sequences of homologues...
Fri Dec  1 19:14:22 2017	INFO : Starting homologue filtering...
Fri Dec  1 19:15:23 2017	INFO : Getting structures from PDB...
Fri Dec  1 19:15:37 2017	INFO : Creating modelling alignment...
Fri Dec  1 19:15:37 2017	INFO : Modelling...
Fri Dec  1 19:25:15 2017	INFO : Model 1 built
Fri Dec  1 19:25:15 2017	INFO : Validating Calpha distances...
Fri Dec  1 19:25:15 2017	INFO : Model 1 distances correct: True
Fri Dec  1 19:25:15 2017	INFO : Modelling...
Fri Dec  1 19:49:42 2017	INFO : Model 2 built
Fri Dec  1 19:49:42 2017	INFO : Validating Calpha distances...
Fri Dec  1 19:49:42 2017	INFO : Model 2 distances correct: True
Fri Dec  1 19:49:42 2017	INFO : Modelling...
Fri Dec  1 19:59:10 2017	INFO : Model 3 built
Fri Dec  1 19:59:10 2017	INFO : Validating Calpha distances...
Fri Dec  1 19:59:10 2017	INFO : Model 3 distances correct: True
Fri Dec  1 19:59:10 2017	INFO : Modelling...
Fri Dec  1 20:08:17 2017	INFO : Model 4 built
Fri Dec  1 20:08:17 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:08:17 2017	INFO : Model 4 distances correct: True
Fri Dec  1 20:08:17 2017	INFO : Modelling...
Fri Dec  1 20:17:57 2017	INFO : Model 5 built
Fri Dec  1 20:17:57 2017	INFO : Validating Calpha distances...
Fri Dec  1 20:17:57 2017	INFO : Model 5 distances correct: True
Fri Dec  1 20:18:48 2017	INFO : Finished modelling
Fri Dec  1 20:18:48 2017	STATUS CHANGED : R -> P
Fri Dec  1 20:18:48 2017	INFO : Checking topology...
Fri Dec  1 20:20:36 2017	INFO : Knot matrices done...
Fri Dec  1 20:21:01 2017	INFO : No knots found...
Fri Dec  1 20:22:03 2017	INFO : No lassos found...
Fri Dec  1 20:22:03 2017	INFO : Finishing...
Fri Dec  1 20:22:03 2017	STATUS CHANGED : P -> E
Fri Dec  1 20:22:03 2017	ERROR : Error while finishing
Fri Dec  1 20:22:03 2017	STATUS CHANGED : E -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling