[phenixbb] Ensemble refinement

Tristan Croll tristan.croll at qut.edu.au
Fri Apr 3 18:30:41 PDT 2015

If I understand correctly, since ensemble refinement is a dynamics-based method your starting structure needs to be effectively "perfect" (i.e. a true representation of one of the conformations that makes up the real-world ensemble). Any error in your assignment that's separated from the true structure by a large enough energy barrier will throw it right out.

With that in mind, I wouldn't throw out the ensemble refinement results immediately. Why not have a closer look and see what's moved substantially? There may be some clues in there for you.



Tristan Croll
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
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Kelvin Grove QLD 4059 Australia
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> On 2 Apr 2015, at 8:28 pm, mohamed noor <mohamed.noor34 at gmail.com> wrote:
> Using the FEM map, I managed to remove more bad waters and add instead ions from the crystallization mix.
> I tried phenix.ensemble_refinement but the Rfactor increased by 2 % (originally 19/22 % from phenix.refine).
> Before it crashes at the validation point all the time, it prints out the validation summary with 0.53-3.48 % and 1.87-7.22 % Ramachandran outlier (from 0.3 %, supported by density) and a Molprobity score of 1.57-1.92 and 1.82-2.14 depending on pTLS used (original single model score was 2.08). The clashscore in both settings (pTLS=0.6 and 1) are 0.
> Do I still go by the Rfactor and decide to not use ensemble refinement at all?
> Thanks.
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