Hi,

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 map-model correlations.
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.

Pavel