Hi,

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)

most of the time the default weight used in Phenix is good enough. Once it's not the case, then you can always use "optimize_xyz_weight=true" to get the optimal value. This is described in details here:

http://www.phenix-online.org/newsletter/

see article "Improved target weight optimization in phenix.refine".

Adding H may help further.

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.

phenix.refine uses repulsion term only. Although one can imagine reasons why attraction terms may be helpful, in reality they may be counterproductive if the model geometry quality is not great since attractive terms may lock wrong conformations and not let them move towards correct positions dictated by the electron density.

Pavel