Job name:

6K72 chain K

820e28d2-d124-47db-bbe6-611d039a73f6
Finished
Models Number of gaps:3 Gap lengths: 12, 11, 6
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap3rd gap
Model 1 Unknot -22527
Model 2 Unknot -22633
Model 3 Unknot -22125
Model 4 Unknot -22003
Model 5 Unknot -22136
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.
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.
Help
PDB
code		 Chain Entanglement
type		 Seq
identity		 Total gap
coverage		 Total gap
identity		 RMSD [Å] Pairwise alignment to the target: gap


1Q8K
A
Unknot
86.67%
300.00%
290.91%
1.61

..Target: ---RFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVF--------------------------------NV
Template: MSCRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEVDGD
Help
PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

EVLINNINRRLTPQAVKI
1Q8K A Unknot 100.00% 100.00%

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

GMILLSELSRRRIRSIN
1Q8K A Unknot 90.91% 100.00%

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

AEVLEYTKDEQL
1Q8K A Unknot 100.00% 100.00%

AEVLEYTKDEQL

Models
Similarity profile
Modelling alignment

Thu Dec 26 14:30:33 2019	JOB CREATED : 820e28d2-d124-47db-bbe6-611d039a73f6
Thu Dec 26 14:31:01 2019	STATUS CHANGED : N -> R
Thu Dec 26 14:31:01 2019	INFO : JOB STARTED AT: 2019-12-26 14:31:01.615890
Thu Dec 26 14:31:01 2019	INFO : METHOD: 1
Thu Dec 26 14:31:01 2019	INFO : Building Profile...
Thu Dec 26 14:31:01 2019	INFO : --E-value set to 0.001--
Thu Dec 26 14:47:20 2019	INFO : Homologue pool found...
Thu Dec 26 14:47:20 2019	INFO : Verifying structure sequences of homologues...
Thu Dec 26 14:48:08 2019	INFO : Starting homologue filtering...
Thu Dec 26 14:48:28 2019	INFO : Getting structures from PDB...
Thu Dec 26 14:48:34 2019	INFO : Creating modelling alignment...
Thu Dec 26 14:48:34 2019	INFO : Modelling...
Thu Dec 26 14:52:41 2019	INFO : Model 1 built
Thu Dec 26 14:52:41 2019	INFO : Validating Calpha distances...
Thu Dec 26 14:52:41 2019	INFO : Model 1 distances correct: True
Thu Dec 26 14:52:41 2019	INFO : Modelling...
Thu Dec 26 15:02:15 2019	INFO : Model 2 built
Thu Dec 26 15:02:15 2019	INFO : Validating Calpha distances...
Thu Dec 26 15:02:15 2019	INFO : Model 2 distances correct: True
Thu Dec 26 15:02:15 2019	INFO : Modelling...
Thu Dec 26 15:08:51 2019	INFO : Model 3 built
Thu Dec 26 15:08:51 2019	INFO : Validating Calpha distances...
Thu Dec 26 15:08:51 2019	INFO : Model 3 distances correct: True
Thu Dec 26 15:08:51 2019	INFO : Modelling...
Thu Dec 26 15:12:56 2019	INFO : Model 4 built
Thu Dec 26 15:12:56 2019	INFO : Validating Calpha distances...
Thu Dec 26 15:12:56 2019	INFO : Model 4 distances correct: True
Thu Dec 26 15:12:56 2019	INFO : Modelling...
Thu Dec 26 15:19:36 2019	INFO : Model 5 built
Thu Dec 26 15:19:36 2019	INFO : Validating Calpha distances...
Thu Dec 26 15:19:36 2019	INFO : Model 5 distances correct: True
Thu Dec 26 15:19:52 2019	INFO : Finished modelling
Thu Dec 26 15:19:52 2019	STATUS CHANGED : R -> P
Thu Dec 26 15:19:54 2019	INFO : Finished edm surfaces: no map
Thu Dec 26 15:19:54 2019	INFO : Checking topology...
Thu Dec 26 15:20:26 2019	INFO : Knot matrices done...
Thu Dec 26 15:20:26 2019	INFO : No knots found...
Thu Dec 26 15:20:26 2019	INFO : No lassos found...
Thu Dec 26 15:20:26 2019	INFO : Finishing...
Thu Dec 26 15:20:27 2019	INFO : Job done
Thu Dec 26 15:20:27 2019	STATUS CHANGED : P -> F
Thu Dec 26 15:20:27 2019	STATUS CHANGED : F -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling