[phenixbb] occupancy refinement

Kendall Nettles knettles at scripps.edu
Tue Nov 24 19:22:48 PST 2009

Hi Maia,
I think the criteria for occupancy refinement of ligands is similar to a decision to add an alt conformation for an amino acid. I  don't refine occupancy of a ligand unless the difference map indicates that we have to. Sometimes part of the igand may be conformationally mobile and show poor density, but I personally don't think this justifies occupancy refinement without evidence from the difference map. I agree with Pavel that you shouldn't expect much change in overall statistics, unless the ligand has very low occupancy., or you have a very small protein.  We typically see 0.5-1% difference in R factors from refining with ligand versus without for nuclear receptor igand binding domains of about 250 amino acids, and we see very small differences from occupancy refinement of the ligands.

Regarding the error, I have noticed differences of 10% percent occupancy depending on what you set the starting occupancy before refinement. That is, if the starting occupancy starts at 1, you might end up with 50%, but if you start it at 0.01, you might get 40%. I don't have the expertise to explain why this is, but I also don't think it is necessarily important. I think it is more important to convince yourself that the ligand binds how you think it does. With steroid receptors, the ligand is usually planer, and tethered by hydrogen bonds on two ends. That leaves us with with four possible poses, so if in doubt, we will dock in the ligand in all of the four orientations and refine. So far, we have had only one of several dozen structures where the ligand orientation was not obvious after this procedure. I worry about a letter to the editor suggesting that the  electron density for the ligand doesn't support the conclusions of the paper, not whether the occupancy is 40% versus 50%.

You might also want to consider looking at several maps, such as the simple or simulated annealing composite omit maps. These can be noisy, so also try the kicked maps ( http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html), which I have become a big fan of.

Kendall Nettles

On 11/24/09 3:07 PM, "chern at ualberta.ca" <chern at ualberta.ca> wrote:

I am wondering what is the criteria for occupancy refinement of
ligands. I noticed that R factors change very little, but the ligand
B-factors change significantly . On the other hand, the occupancy is
refined to the second digit after the decimal point. How can I find
out the error for the refined occupancy of ligands?

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