[phenixbb] Low resolution refinement - rotamers and Ramachandran

Tristan Croll tristan.croll at qut.edu.au
Thu May 21 15:32:33 PDT 2015

> So, it seems weight optimization is trying to lower the clashes and outliers at the expense of R factor.

That's certainly not a bad thing. Remember, the object of refinement is to get the best possible model, not the best possible R-factor. I suspect that what these results are trying to tell you is that there's something fundamentally wrong somewhere in your model - something out of register, perhaps? Some close inspection of regions where lots of outliers appear may be in order.

Tristan Croll
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
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On 22 May 2015, at 8:27 am, mohamed noor <mohamed.noor34 at gmail.com<mailto:mohamed.noor34 at gmail.com>> wrote:

Hi Pavel

Just to let you know, I ran phenix.refine with and without weight optimization and I summarize the results below (R, clashscore, Ramachandran and rotamer outliers)

without - 27.9/32.1, 21.9, 4.71, 11.08
with - 32.8/35.1, 8.6, 3.89, 6.44
without (torsion-angle NCS) - 27.9/31.0, 26.5, 4.1, 10.82

So, it seems weight optimization is trying to lower the clashes and outliers at the expense of R factor.

On Wed, May 20, 2015 at 11:39 AM, Pavel Afonine <pafonine at lbl.gov<mailto:pafonine at lbl.gov>> wrote:
Hi Mohamed,

I am refining a low resolution structure (3.8 A). After I fix most of the outliers (red bars) in Coot, phenix.refine is causing my structure to be worse than the start with 13 % Ramachandran outlier and 13 % rotamer outlier.

could you please send me data and model (before refinement) files then I will have a look. Refinement at low resolution is generally tricky and often requires using beyond the default settings such as secondary structure, rotamer and Ramachandran plot restraints, NCS (at 3.8A Cartesian NCS or even NCS constraints might be a better option).

If you send me files I will try plausible options to see what can be done.


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