Presence of negative density in Sim Omit map

Hi Phenixbb,

We would appreciate your advice regarding an odd problem that has cropped up with one of our crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine residue in a loop, the Sim Omit map showed the positive density expected from the omission of the loop (contour level 3 sigma, colored green in attached pics). However, flanking the positive density, there is a complimentary negative density (in red). We are puzzled as to the cause of the appearance of the negative density. Can you help us?

Renu