Re: [phenixbb] on Rwork and Rfree

One more thing: do you mean the R-free increases by the end of refinement, or just after the water-picking step within a macrocycle? The latter is completely normal - it still needs to refine the positions and B-factors of the newly placed waters. On Tue, Feb 7, 2012 at 12:08 AM, Dialing Pretty wrote:

Dear All,

After we refine the structure of the protein to satisfactory with satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree always increases slightly after the water picking refinment.

Do you have nay idea to solve this problem or any comment?

Cheers,

Dialing

From: Nathaniel Echols

To: PHENIX user mailing list Sent: Tuesday, 7 February 2012 2:03 PM

Subject: Re: [phenixbb] on Rwork and Rfree

On Mon, Feb 6, 2012 at 7:57 PM, Dialing Pretty wrote:

...

But how about if both the Rfree and Rwork decrease, by comparing the start and final, however in the middle of the the refinement (for example the second cycle of the default3 cycles) the Rfree and Rwork are higher in comparison with the Rfree_start and Rwork_statrt?

This is okay, and not at all uncommon (especially if you use simulated annealing).

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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