[phenixbb] How to reduce clashscore value

Tim Fenn tim.fenn at gmail.com
Fri Nov 18 12:24:05 PST 2011

2011/11/17 CelinaSocek <oceanlinerth at hotmail.com>

>  Hi all,
> I'm now using phenix to refine a small protein about 300 residues long.
> The resolution of my data is about 2.9 angstrom. Currently I got a refined
> model with good R-factors about 23/26, RMSD very reasonable and no
> Ramanchandran outliers. However,  I found that the clashscore is extremely
> high: 63!! And rotamer outliers are also a lot: 8.5%. I wonder, what kind
> of stretagy I can use to reduce this? Thank you very much!

There are most likely two reasons for the poor clash score:

1) the weighting between the chemical and X-ray potentials is putting too
much emphasis on the data (see http://dx.doi.org/10.1107/S0907444911039060)

2) I'm not sure what kind of vdW function phenix uses by default (repulsive
only?), but its very difficult, if not impossible, to get accurate
interatomic separation distances without summing a Lennard-Jones style vdW
potential and (at least) fixed atomic charge electrostatics.

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