[phenixbb] high B Factor after real space refinement against a cryoEM map
pafonine at lbl.gov
Thu Oct 17 00:44:04 PDT 2019
> I am trying to do the real space refinement for my model against a 5.0
> angstrom cryoEM map. All parameters look pretty good except the B
> factor. The mean of the B factor is close to 400. I am just wondering
> whether the low resolution makes the B factor this high.
> Does anyone have any idea or suggestion on the high B factor during
> real space refinement? Is it possible to reduce it? What is the actual
> meaning of this B factor?
given how much cryo-EM maps are 'massaged' along the way, B factors are
not necessarily very meaningful. They are refined though to provide the
best match between model and cryo-EM maps to give you realistic
Apart from this, refining Bs at this resolution may result in large
numbers to compensate for the lack of density for side chains, for example.
Bottom line, I don't think this is something to worry about.
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