[phenixbb] Persistant high average B-factor.

[Pavel Afonine]

Hi Joe,

could you send me the log file (from the refinement run giving the best 
Rw/Rf) for some quick diagnostics ? Please send the files to my email 
(and not to the list).

If you send model and data I will have a closer look.

Pavel.


On 6/7/10 6:52 PM, Joseph Brock wrote:
> 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:
>
> http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html
>
> 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,
>
> Joe.
>
>
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