Job name:

5NPS chain A

9e72e51c-3fd8-4ea8-910a-2efd6f0fee6d
Finished
Models Number of gaps:2 Gap lengths: 16, 6
Model Entanglement Average DOPE-HR (by gap length)
DOPE-HR 1st gap2nd gap
Model 1 Unknot -94207
Model 2 Unknot -94147
Model 3 Unknot -94259
Model 4 Unknot -94013
Model 5 Unknot -93977
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Warning: All models are renumbered - the first residue in the structure has index 1.
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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


5C1D
A
Unknot
100.00%
56.25%
56.25%
0.35

..Target: PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI
Template: -THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKS---IYDNRIVLNGIDLKAFLDSLPDVKIVKM---------------LNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI

4GYW
C
Unknot
99.85%
50.00%
50.00%
0.74

..Target: PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMI-
Template: ----------------------AVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFK---HIYDNRIVLNGIDLKAFLDSLPDVKIVKM----------------NMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK
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PDB
code		 Chain Knot
type		 Gap
coverage		 Gap
identity		 >Target_Sequence: gap

VKMKCPDGGDNADSSNTALNMP
5C1D A Unknot 6.25% 6.25%

VKM---------------LNMP
4GYW C Unknot 0.00% 0.00%

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

IDFKSNGHIYDN
5C1D A Unknot 50.00% 50.00%

IDFKS---IYDN
4GYW C Unknot 50.00% 50.00%

IDFK---HIYDN

Models
Similarity profile
Modelling alignment

Wed Dec  4 13:31:36 2019	JOB CREATED : 9e72e51c-3fd8-4ea8-910a-2efd6f0fee6d
Wed Dec  4 13:32:02 2019	STATUS CHANGED : N -> R
Wed Dec  4 13:32:02 2019	INFO : JOB STARTED AT: 2019-12-04 13:32:02.128642
Wed Dec  4 13:32:02 2019	INFO : METHOD: 1
Wed Dec  4 13:32:02 2019	INFO : Building Profile...
Wed Dec  4 13:32:02 2019	INFO : --E-value set to 0.001--
Wed Dec  4 14:09:32 2019	INFO : Homologue pool found...
Wed Dec  4 14:09:32 2019	INFO : Verifying structure sequences of homologues...
Wed Dec  4 14:23:05 2019	INFO : Starting homologue filtering...
Wed Dec  4 14:23:53 2019	INFO : Getting structures from PDB...
Wed Dec  4 14:24:20 2019	INFO : Creating modelling alignment...
Wed Dec  4 14:24:20 2019	INFO : Modelling...
Wed Dec  4 14:30:46 2019	INFO : Model 1 built
Wed Dec  4 14:30:46 2019	INFO : Validating Calpha distances...
Wed Dec  4 14:30:46 2019	INFO : Model 1 distances correct: True
Wed Dec  4 14:30:46 2019	INFO : Modelling...
Wed Dec  4 14:36:51 2019	INFO : Model 2 built
Wed Dec  4 14:36:51 2019	INFO : Validating Calpha distances...
Wed Dec  4 14:36:51 2019	INFO : Model 2 distances correct: True
Wed Dec  4 14:36:51 2019	INFO : Modelling...
Wed Dec  4 14:43:10 2019	INFO : Model 3 built
Wed Dec  4 14:43:10 2019	INFO : Validating Calpha distances...
Wed Dec  4 14:43:10 2019	INFO : Model 3 distances correct: True
Wed Dec  4 14:43:10 2019	INFO : Modelling...
Wed Dec  4 14:49:17 2019	INFO : Model 4 built
Wed Dec  4 14:49:17 2019	INFO : Validating Calpha distances...
Wed Dec  4 14:49:17 2019	INFO : Model 4 distances correct: True
Wed Dec  4 14:49:17 2019	INFO : Modelling...
Wed Dec  4 14:55:22 2019	INFO : Model 5 built
Wed Dec  4 14:55:22 2019	INFO : Validating Calpha distances...
Wed Dec  4 14:55:22 2019	INFO : Model 5 distances correct: True
Wed Dec  4 14:56:14 2019	INFO : Finished modelling
Wed Dec  4 14:56:14 2019	STATUS CHANGED : R -> P
Wed Dec  4 14:57:29 2019	INFO : Finished edm surfaces: success
Wed Dec  4 14:57:29 2019	INFO : Checking topology...
Wed Dec  4 15:00:44 2019	INFO : Knot matrices done...
Wed Dec  4 15:00:48 2019	INFO : No knots found...
Wed Dec  4 15:00:49 2019	INFO : No lassos found...
Wed Dec  4 15:00:49 2019	INFO : Finishing...
Wed Dec  4 15:00:49 2019	INFO : Job done
Wed Dec  4 15:00:49 2019	STATUS CHANGED : P -> F
Wed Dec  4 15:00:49 2019	STATUS CHANGED : F -> F
GapRepairer | Interdisciplinary Laboratory of Biological Systems Modelling