[phenixbb] occupancy refinement

Maia Cherney chern at ualberta.ca
Wed Nov 25 07:38:14 PST 2009

Hi Pavel,

It looks like all different refined occupancies starting from different 
initial occupancies converged to the same number upon going through very 
many cycles of refinement.


Pavel Afonine wrote:
> Hi Maia,
> the atom parameters, such as occupancy, B-factor and even position are 
> interdependent in some sense. That is, if you have somewhat incorrect 
> occupancy, that B-factor refinement may compensate for it; if you 
> misplaced an atom the refinement of its occupancy or/and B-factor will 
> compensate for this. Note in all the above cases the 2mFo-DFc and 
> mFo-DFc maps will appear almost identical, as well as R-factors.
> So, I think your goal of finding a "true" occupancy is hardly achievable.
> Although, I think you can approach it by doing very many refinements 
> (say, several hundreds) (where you refine occupancies, B-factors and 
> coordinates) each refinement starting with different occupancy and 
> B-factor values, and make sure that each refinement converges. Then 
> select a subset of refined structures with similar and low R-factors 
> (discard those cases where refinement got stuck for whatever reason 
> and R-factors are higher) (and probably similar looking 2mFo-DFc and 
> mFo-DFc maps in the region of interest). Then see where the refined 
> occupancies and B-factors are clustering, and the averaged values will 
> probably give you an approximate values for occupancy and B. I did not 
> try this myself but always wanted to.
> If you have a structure consisting of 9 carbons and one gold atom, 
> then I would expect that the "second digit" in gold's occupancy would 
> matter. However, if we speak about dozen of ligand atoms (which are 
> probably a combination of C,N,O) out of a few thousands of atoms of 
> the whole structure, then I would not expect the "second digit" to be 
> visibly important.
> Pavel.
> On 11/24/09 8:08 PM, chern wrote:
>> Thank you Kendall and Pavel for your responces.
>> I really want to determine the occupancy of my ligand. I saw one 
>> suggestion to try different refinements with different occupancies 
>> and compare the B-factors.
>> The occupancy with a B-factor that is at the level with the average 
>> protein B-factors, is a "true" occupancy.
>> I also noticed the dependence of the ligand occupancy on the initial 
>> occupancy. I saw the difference of 10 to 15%, that is why I am 
>> wondering if the second digit after the decimal point makes any sence.
>> Maia
>>     ----- Original Message -----
>>     *From:* Kendall Nettles <mailto:knettles at scripps.edu>
>>     *To:* PHENIX user mailing list <mailto:phenixbb at phenix-online.org>
>>     *Sent:* Tuesday, November 24, 2009 8:22 PM
>>     *Subject:* Re: [phenixbb] occupancy refinement
>>     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),
>>     <http://www.phenix-online.org/pipermail/phenixbb/2009-September/002573.html%29,>
>>     which I have become a big fan of.
>>     Regards,
>>     Kendall Nettles
>>     On 11/24/09 3:07 PM, "chern at ualberta.ca" <chern at ualberta.ca> wrote:
>>         Hi,
>>         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?
>>         Maia
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