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 (Rfree increased).

 

The Phenix document regards 5 macrocycles refine is fine. For my situation, do you think the 3 macrocycles refine result is acceptable or not? If not acceptable, what do you suggest for improvement?

I am looking forward to getting your reply.

Smith