Re: [phenixbb] On Phenix refinement

Hi Smith, convergence means that the coordinates of your model (and thus R free, geometric parameters etc) have stabilized. Adding further cycles of refinement doesn't change anything, i.e. the results of a five-cycle run will be indistinguishable from those of a four-cycle run if convergence was reached after four cycles. Andreas (still very much alive) On 20/02/2015 1:39, Smith Liu wrote:

Dead Andreas, For Phenix refine, will you please tell me the definition of the convergence?

I am looking forward to getting your reply.

Smith

At 2015-02-20 20:02:31, "Andreas Förster" wrote:

...

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.

Best.

Andreas

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

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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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