[phenixbb] Low resolution refinement - rotamers and Ramachandran

mohamed noor mohamed.noor34 at gmail.com
Fri May 29 02:51:35 PDT 2015

Hi Pavel

I have two more questions:

1. If I see a small drop in R/Rfree when I request solvent update (I
over-rode the default cut-off of 2.8 A), should I keep those waters?

2. Where can I find the values for favored phi/psi values for Ramachandran?
Using the FEM map, I can see some residues flagged as outliers but when
they are fixed in Coot (real space refine tool) to a favored region, they
actually come out of the density. This makes me suspect that those outliers
are real. When I use Ramachandran restraints, obviously the outliers are
'fixed' but clashscore increases. In other cases, the tweak needed to fix
them are quite small.

3. For publication, do I need to make an image of each outlier that was not


On Thu, May 21, 2015 at 11:32 PM, Tristan Croll <tristan.croll at qut.edu.au>

>  > 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
> Lecturer
> 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> 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> 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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