If I am not wrong, I remember that someone proposed to standardize B-factors of protein atoms as “BS = B - Bave”, where Bave is the average B-factor of the protein.

This will make some of BS negative (if B<Bave). Are you ok with this?

Perhaps you can apply histogram equalization here (rank scaling I guess the other name is), which is a simple and reversible transformation that will map all values into 0-1 range.

Pavel