2011/11/17 CelinaSocek <oceanlinerth@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.

Regards,

Tim