Hi Yu,

What is the real meaning of the 'wxu_scale' and 'wu'?

(scale factor for X-ray/ADP_weight: wxu_scale
ADP weight scale: wu)

see formula

Etotal = wxc_scale * wxc * Exray + wc * Egeom

in "Refinement of coordinates" chapter of phenix.refine manual:

http://phenix-online.org/documentation/refinement.htm

Same for refinement of ADPs.

During ADP refinement, it is suggested to refine the 'wxu_scale', what if I change the value of 'wu'?

It is not suggested to do at all (I mean you can do it of course but it's not something that we recommend doing routinely). The default should be just fine. However at the end of refinement you may want to tune up the weights to get the best refinement statistics (in terms of R-factors), and in that case you use "optimize_wxc=true" and/or "optimize_wxu=true". Only in some weird cases when none of the above works well, you may want to try playing with wxc_scale and wxu_scale (out of desperation, I would say).

Please let me know if it's still not clear.

Pavel.