[phenixbb] unwanted disulfids and geometry restraints

I have 2 questions: 1) I am using phenix.refine on the command line with a .eff file as input that was modified from previous GUI phenix runs. My structure has several Zn atoms and readyset creates a geometry_restraints file for the Zn interactions. I am not sure if phenix.refine gets these restraints when I run it from the command line. Do I need to read this file in some specific way? 2) The other question is: phenix refines several of the Cysteine neighbors in the Zn environment as disulfids, but they are not. How do I prevent this from happening? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220