[phenixbb] RMS angles and comprehensive validation in phenix

Katherine Sippel katherine.sippel at gmail.com
Fri Sep 19 09:50:11 PDT 2014

This is from Phenix's FAQ page...

*"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*

This is somewhat controversial, but absolute upper limits for a
well-refined protein structure at high resolution are typically 0.02 for
RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly
lower. As resolution decreases the acceptable deviation from geometry
restraints also decreases, so at 3.5 Angstrom, more appropriate values
would be 0.01 and 1.0."

If the histogram shows that the RMS(angles) average higher than 2 then I
think that would be a result of poorly refined structures skewing the graph
rather than a reflection of what the RMS should be.

On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hi,
> if you make sure these values are not caused by a handful of atoms that
> flew a distance apart for whatever reason then values like ok to me. This
> is why looking at a histogram of deviations (bond, angles etc) is way more
> useful than looking at just one number!
> Pavel
> On 9/18/14 1:32 PM, C wrote:
> Hi,
>  Refining using phenix I find the RMS angle drifting towards 2.3-2.7
> range when validating the resulting structure.
>  These are high resolution structures and I was wondering if someone
> could comment on whether 2.3-2.7 values are worrisome?
> Thank you
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"Nil illegitimo carborundum"* - *Didactylos
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