[phenixbb] Persistant high average B-factor.

Joseph Brock joeylives2ride at hotmail.com
Mon Jun 7 18:52:47 PDT 2010

Dear Phenix users,

I am currently using version 1.6.1-353 and I'm working on a 1.7A structure that has refined quite well using Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final R-work = 0.1776, R-free = 0.2262

However, I noticed that the average B-factor reported by polygon with these settings was quite high ( < 0.1 of other structures with a similar resolution).

Discovering I could not change the value of wxu_scale when using individual_adp+TLS, I went about trying to reduce the average B using the method described here:


However,  I still can't seem to reduce the average B-factor. I've just done a refinement with the following non-default (extreme) target weight settings:

  target_weights {
    wxc_scale = 1.5
    fix_wxc = 2
    fix_wxu = 0.1
   (wxu_scale = 1)

But if anything, reducing wxu to such low values makes the avergae B-even higher while concuretnly making the gap between R-values much worse:

Final R-work = 0.1602, R-free = 0.2457

This suggests to me that I'm obviously over fitting the data but I'm at a loss on how to proceed. Should i just accept that the automatic scaling used for Phenix TLS wxu is doing a good job and that my structure actually does have an unusually high avergae B? 

I'm fitting two ligands into density, which is at several places ambiguous, so I would like the most unbiased difference density possible.

Many thanks in advance,


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