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