Dear All, The default number of cycles for the Phenix refinement graphical interface is 3 (should be macro-cycles). I have done a refinement with 3 default cycles, and I get the acceptable refinement results. Then I kept everything same, except I changed the cycles of refinement from 3 to 5, however the refinement result was ugly which was unacceptable. Someone told me once I have corrected the outliers by Coot, I can have a Phenix refinement with macro-cycles as 1, in order to avoid the Ramachandran corrected ones changing backing to Ramachandran outliers (Will you please further comment whether this strategy to correct Ramachandran outliers is acceptable or not). Thus can we regard the macro-cycles of Phenix refinement as one parameter for the refinement? And why the macro-cycles of the refinement can affect the refinement result? I am looking forward to getting your reply. Smith