[phenixbb] Low rmsd values

Pavel Afonine pafonine at lbl.gov
Wed Mar 23 04:10:10 PDT 2011

  Hi Teemu,

the statistics you quoted looks good to me. Weight optimization tries an 
array of different weights and chooses the one that brings lower Rfree 
and not yet distorted geometry (so it has upper limit on geometry 
deviations but doesn't have a lower limit).

What pleases your eye does not necessarily please the Rfree -:)

What are the Rwork/Rfree if you choose such a weight that will bring you 
the rmsds you like? What are the values if you do not optimize the weights?

All the best!

On 3/23/11 3:01 AM, Teemu Haikarainen wrote:
> Hi all,
> I am getting quite low rmsd values for my structure. I am finishing the
> refinement and I have rmsd of 0.003 Å for bonds and 0.67 for angles, with
> R/Rfree of 0.148/0.176. The resolution is 2.0 Å. I am refining with riding
> hydrogens and using the automatic weight optimization.
> I have also tried to change the weights manually, but the more “eye-pleasing”
> rmsd values always result in worse Rfree.
> Is there any reason to worry about the low rmsd values and should I always use
> the optimized weights in refinement?
> I am using the latest version of Phenix.
> Regards,
> Teemu
> --
> Teemu Haikarainen (M.Sc.)
> Turku Centre for Biotechnology
> Tykistokatu 6
> BioCity, Turku
> FIN-20521, Finland

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