[phenixbb] Low resolution refinement - rotamers and Ramachandran

[mohamed noor]

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> 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.
>
> Pavel
>
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