[phenixbb] Clashscore and average B

Sam Tang samtys0910 at gmail.com
Mon Apr 8 11:30:55 PDT 2019

Hello Pavel and Robert

Thanks for your replies. After re-investigating the model we didn't find
any major issues and the electron densities are fitted pretty well. Even
the ligand shows strong density on a SA-omit map. So I think we will stop
at this stage and take this model for further analysis.

Thanks again!


On Sat, 6 Apr 2019 at 03:30, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Sam,
> > I am refining a structure with Phenix.refine and encounter an issue
> > which I appreciate your comments. The structure is in P1 and refined
> > to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544,
> > Ramachandran favoured 97.5%. The statistics is acceptable to me
> This look fine to me too!
> > but two numbers raised my concern. First is the clashscore of 7.7,
> > which is below minimum of other structures shown by Polygon.
> The lower, the better. So this is good! If it's lower than the others
> (as shown by Polygon) then you are doing better on this one!
> > Second is an average B of 37, with a minimum of 9.2. When I checked
> > again in Coot (Average Temp fact. analysis), none of the residues or
> > water look abnormal. I refined both individual and group B-factors and
> > applied 'Optimize X-ray/adp weight'.
> This looks fine too.
> > So my questions are:
> > (1) if a clashscore too high means a lot of bad contacts, how do you
> > comprehend a clashscore too low? How can I modify my strategy to get
> > around?
> It can't be "too low". Zero means you don't have any single steric
> clash, which is good.
> > (2) is there an acceptable low value of B? (I sort of went through a
> > similar thread in phenixbb appeared 9 years ago but seems the
> > discussion did not come to a conclusion). Any advice I should reliax
> > or tighten the adp restraints?
> Check out recent thread on ccp4bb: "acceptable difference between
> Average B-factor and Wilson B".
> Bottom line, I think what you have is just fine, unless you meaningfully
> and clearly define "low".
> Pavel
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