First, Thank you all for the help and suggestions, it
truly resolved the issue.
First I reset the B factors to something close to the
Wilson B average (53). Then making sure the
B-solvent contribution flag was set and refining
isotropic b-factor I reran the job. The B-factors now
are reasonable and the negative density issues have
been resolved. Using Babinet instead of simple
scaling also brought down the R and Rfree though it
did make the maps a little less defined and increased
the B factors to a higher average B. Much more
refining to do but I'm in a much better position now.
Not to mention that my maps are a lot more
interpretable.
Thanks
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