[phenixbb] On Phenix refinement

Andreas Förster docandreas at gmail.com
Fri Feb 20 04:02:31 PST 2015

Hi Smith,

refinement shouldn't be done for three macrocycles or five but to 
convergence.  Do you think you've reached convergence?

If your refinement result is unacceptable, as you say, you have to 
change your strategy or improve your model.



On 20/02/2015 11:56, Smith Liu wrote:
> 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 (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
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