Hi John,
1. Can Phenix do B-factor sharpening for improved maps?
This is not implemented in phenix.refine. CNS can do this.
2. How can one optimize Ksol and Rprobe (bulk solvent model) in Phenix?
This is highly optimized in phenix.refine. I believe we have the most sophisticated protocol for doing this (Acta Cryst. (2005). D61, 850-855, "A robust bulk-solvent correction and anisotropic scaling procedure" P. V. Afonine, R. W. Grosse-Kunstleve and P. D. Adams). What you can try to do is to optimize the mask calculation parameters: solvent_radius and shrink_truncation_radius (the default values are 1.11 and 0.9). To do specify in the command line (or in the parameter file, whatever you use) one extra parameter: optimize_mask=True; for example: % phenix.refine model.pdb data.mtz optimize_mask=True This will tun much longer but may result in slightly improved statistics.
3. Are there any other suggestions for dealing with low resolution structures in Phenix?
How you refine the ADPs? TLS might be an option to try out. Pavel.