Dear community,

I am refining a crystal structure of my protein of interest at 2.3A. After molecular replacement using Phaser MR and first round of refinement, I am seeing a few red blobs (negative Fo-Fc) density sitting in space (where the solvent would be?), with no atoms in it. I tried using several different starting model for molecular replacement, and they all yielded similar maps showing empty red blobs at particular places. Because of this, my R factors are suffering even though rest of the model looks correct, fitting the density. I also tried shrinking bulk solvent mask, which only made R factors worse without making the blobs go away.

Can you tell me why this happens and what I should try?

I am attaching a screenshot of my case (Fo-Fc map contour level 3.0RMSD, 2Fo-Fc 1.0RMSD). Would be super grateful for any help or explanation!

Best wishes,

Steven