I think you are just confused. The solvent flattening is just a step to make your map clearer. You do not carry the modified phases from solvent flattening to refinement (and I sincerely hope you don't refine against the solvent flattened amplitudes but against the original data!)
Herman's observation is right, i think. One of the reasons that high solvent content will give better Rfree is also that this wY you have more reflections than usual per atom: considering two asymmetric units with the same volume, they have the same number of reflections at a given resolution, but if one has higher solvent it has less atoms so you refine better. A. Sent from my iPhone On 24 May 2011, at 11:18, Clement Angkawidjaja <clem...@bio.mls.eng.osaka-u.ac.jp> wrote: > But you have to do solvent flattening (density modification), which people > often (unintentionally?) skip for structures solved with molecular > replacement. Please correct me if I am wrong. > > Clement > > On May 24, 2011, at 6:01 PM, herman.schreu...@sanofi-aventis.com wrote: > >> This is not my experience. Provided the solvent is featureless, I find >> that a high solvent contents leads to a lower Rfree due to a kind of >> solvent flattening effect. Of course, if a significant part of the >> molecule(s) is/are disordered, this will lead to a degradation of the >> Rfree. >> >> My 2 cents, >> Herman
