Hi Sue,
It seems to me that it means that the refinement strategy isn't stable
in summary, in that email I wrote that there are two ways of how you can handle the total B-factor and one of its components (Bcryst). You can subtract the trace of Bcryst and add it to individual ADPs (what CNS does, for example) or you can keep Bcryst as it is. Both ways do not change the Fmodel and therefore the R-factors. So I can't see how you conclude from this about refinement stability. These are purely formatting/convention things. Regarding the physics of this phenomenon (why truly total ADP (and not "the total ADP minus Ucryst") may be higher than Wilson B), Paul Adams just commented on this which I copy-paste here and which I totally agree with: """I think it might be worth looking at the distribution of ADPs in the structure. Is there one part of the structure with a average around 27 and another part significantly higher. The problem with the Wilson analysis is that, I think, it will tend to give you the average B-factor for the best diffracting part of structure. However, when you solve the structure and calculate the average B-factor it will be across the whole structure including the more disordered parts. Hence the average B from the structure could be higher than the observed Wilson B.""" Regarding the refinement stability... I think I mentioned this a few times before. Just repeating: If you run 100 identical refinements where the only difference is the random seed you will get an ensemble of slightly different results, and the difference is more significant as lower the resolution you have. At low resolution you may end up with 1-2% difference in R-factors... See slides #9-10 here: http://www.phenix-online.org/presentations/latest/pavel_validation.pdf that illustrate the grounds for this. Why random seed makes it different? This is because the X-ray/Restraints weight calculation is done after some random shaking of the coordinates, and therefore the weight can come out slightly different, which is enough for refinement to take a different path to a different local minimum. Nothing magic here. Similar logic applies to the ways of handling total ADP and Bcryst. By doing one way or another, numerically it might provide enough of difference to result in sightly different R-factors.
the contributions from the overall Baniso and the individual B factors are not being (and prossibly can not be) separated properly
Decomposing total B-factor Utotal = Ucrystal + Ugroup + Ulocal, where Ugroup = Utls + Ulib (see recent PHENIX Newsletter for definitions) into individual components properly is much complex problem than it may appear. An attempt to solve it partially for a specific case is sketched here (especially page 9): http://www.ccp4.ac.uk/newsletters/newsletter45/articles/Tmax-CCP4_Afonine-Ur... Do you know a proper (or at least better) solution for a more general case? All the best! Pavel.