Hi Bill and all interested in this,
Why is the weight multiplied by 0.5 by default? Since changing that to 1.0 slightly increases freeR, I assume it is the default for some reason.
the total target for refinement of coordinates in phenix.refine is defined as: Etotal = wc_scale * wxc * Exray + wc * Egeom Similar for refinement of isotropic or anisotropic ADP. Here: - Exray is least-squares (LS), maximum-likelihood (ML) or any other kind of x-ray target; - Egeom is geometry restrains target (Ebonds + Eangles + Eplanarities + Enonboned +...); - wc = 1.0 and used to exclude geometry restraints by setting wc = 0.0; - wxc ~ ratio of gradient's norms for geometry and x-ray targets as defined in (Adams et al, 1997, PNAS, Vol. 94, p. 5018); - wc_scale is 'ad hoc' scale found empirically to be ok for most of the cases at medium resolution. It should be optimized at higher and lower resolutions. The default values are most likely NOT optimal at resolutions higher then 1.5A. Currently we are working on making it resolution dependent rather than one single value for all resolutions. It is advised to play with wc_scale manually if: - Rfree or Rfree - Rwork look not realistic; - geometry deviations look not good (too tight or too loose at given resolution). However, once again, the default values for most of cases at "normal" resolution are OK. In future we are planning to work out more robust and sophisticated methodology for automatic weights determination. Pavel.