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.