Hi Dialing,
When we run 3 rounds of Phenix refine, both the Rwork and Rfree are satisfactory. However if we run 5 rounds of Phenix refine with the same strategy as the above 3 rounds, in the 4th round Rfree starts to increase until the end of the 5th round.
Although by the above 3 rounds of Phenix refine we got satisfactory Rwork and Rfree, can we say the results got by that 3 rounds of Phenix refine are acceptable?
it's nearly impossible to tell what's going on given the amount of information you provided. In this case it will be much more efficient if you send me the input data and model files, and I will send you back working example with the best refinement strategy, and explain it. I will also post the summary to phenixbb. Pavel