Hi Hailiang,
I ccp4-refmac, there is a "BREF OVER" mechanism to refine the overall B-factor (Boverall, obtained from scaling is added to the atomic B values, or, http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#refi_bref). I am just wondering in phenix.refine, whether we could do this after positional and tls refinement. It seems to me the Boverall corresponds to the overall anisotropic scaling factor and will be refined prior to any positional/B-factor refinement in phenix.refine by default. I may be wrong, but if not, my question was whether we could do it afterward.
this is described in great details here: http://www.phenix-online.org/newsletter/CCN_2010_07.pdf see article "On atomic displacement parameters ...". In this article it's called Ucryst. I guess this is more or less what is called Boverall in Refmac. Pavel.