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Hi Salameh,
there is PHENIX bulletin board where PHENIX-specific issues are discussed:
http://www.phenix-online.org/mailman/listinfo/phenixbb
Anyway, regarding your question:
> In every refinement round the wxc and wcu are out of control, 
> although I 
> modify the def file and change the values  of  wxc=1 and wxu=1 so they 
> are tightly restrained, but it failed  to fix the problem, wxc and wxu 
> values keep fluctuating,  in my latest refinement round wxc=256!! 
Without having the data (model, data and command files) I can only guess:
I presume you have a ligand with a custom CIF file that defines rediculously small 
esds for torsions and which screws up the restraints target and weights. 
If you send me the inputs I will have a closer look and tell what exactly is wrong.
> wxu=3.The Stereochemistry looks very loosely restrained and the 
> gap between 
> R-free and R-work is too big. I've been using phenix for almost 4 
> yearsand never had this problem, or once I set the values of wxc 
> and wxu that 
> will be it, never change. 
Recently we had someone with the exact same problem and my above guess was actually correct and solved the issue.
Pavel.