Quoting Dale from an older post
"It's also true that the Wilson B calculation assumes that all the B
factors in the crystal are the same - which is also far from the true in
most macromolecular crystals. A person who holds to the practice of
aggressively building water molecules and loops will create a model with a
higher average B than one who uses the same data but is more restrained.
The Wilson B will, of course, be unchanged.
If you have a protein that is equally ordered throughout and you do not
build in weak water molecules and the crystal diffracts high enough to
allow a reasonably accurate calculation of the Wilson B, your average B and
and the Wilson B should be close to each other. If your protein has mobile
loops, which most lower resolution crystals do (and most higher resolution
crystals for that matter) then your average B will be larger than your
Wilson B."

This kinda agrees with my scenario I think... Wilson B is 83 A*2 and Av B
98 A*2, the discrepancy contributed by mobile loops? (3.0 A resolution).
Refinement with group B factors (two per residue) brought the av B down to
80 A*2. TLS, PDB_REDO etc did not help much.
I got the model by Mol Rep, have not tried PROSMART...
And I agree with Phoebe...The aa's are fully there! Lowering the occupancy
may work with Hetatms, but doesn't make sense to do it with residues!

On Fri, Oct 14, 2016 at 9:08 PM, Phoebe A. Rice <pr...@uchicago.edu> wrote:

> Interesting way to look at it.  But those loop residues are really in the
> crystal with an occupancy of 1, so wouldn't letting the B factor fly give a
> clearer description of what's in the crystal?  Especially as many people
> know to color the structure by B factors to get a feel for which bits are
> wiggly, but they'll never think to color it by occupancy.
> ------------------------------
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthias
> Barone [bar...@fmp-berlin.de]
> *Sent:* Friday, October 14, 2016 8:00 AM
> *Subject:* [ccp4bb] Antw: Re: [ccp4bb] High B factor
> Picking up the mail of Pavel, Phenix refines occupancies..
> If you expect the loops to be disordered, did you try to lower the
> occupancy of these residues, following Ethan Merritt statement that
> "general uncertainty [...] is represented better by occupancy <1 rather
> than an arbitrary large B factor" (To B or not to B,
> doi:10.1107/S0907444911028320).
> If this attempt does not bring the B-factors down, it will surely make the
> model more accurate, as the atom coordinates of the loops may not be
> correct at all, no?
> matthias
> >>> Pavel Afonine <pafon...@gmail.com> 14.10.16 9.36 Uhr >>>
> If you are still worry about your Bfactor, you could try TLS,
> Or NCS, but SA with MLHL might be better.
> (A joke).

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