[phenixbb] Low rmsd values

Teemu Haikarainen thaikara at btk.fi
Wed Mar 23 03:01:39 PDT 2011

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.


Teemu Haikarainen (M.Sc.)
Turku Centre for Biotechnology
Tykistokatu 6
BioCity, Turku
FIN-20521, Finland

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