[phenixbb] Low rmsd values

Ed Pozharski epozh001 at umaryland.edu
Wed Mar 23 09:57:22 PDT 2011

On Wed, 2011-03-23 at 12:01 +0200, Teemu Haikarainen wrote:
> I have rmsd of 0.003 Å for bonds and 0.67 for angles, with
> R/Rfree of 0.148/0.176. 

The "right" value of the bonds rmsd is a matter of debate (vigorous at
times), but 0.003A to me indicates a bit of over-restraining.  You may
want to take a closer look at how shallow the Rfree dependence on
restraint weights is (this info should be easy to extract from
log-files).  Maybe you don't need to go all the way to 0.003 to get most
of the Rfree drop.

Just to expand on this a bit, I think that the rmsd_bonds resolution
dependence is really an artifact of low resolution refinement.  Covalent
bonds are not suddenly getting stronger when the protein is in a more
disordered lattice, so one could expect that the bond length variation
will be approximately the same across (almost) all proteins.  The best
way to estimate this "natural" level of bond rmsd is from ultrahigh
resolution structures refined without restraints, and if I remember
correctly, such analysis suggests something around 0.015-0.02 A.  At
high resolution restraints can be made sufficiently weak to (hopefully)
capture the variation in bond lengths, but at lower resolution this
results in the refinement of noise, correspondingly increasing the

"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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