Active site contains iron (FE2) coordinated by three histidines. 

After Phaser the active site does not contain un-explained green density.

After Refinement blobs of various shapes appear in the vicinity  and upto 3-4A of active site iron.

Refinement is done using occupancy and anomalous of iron options.

Buffers do not contain molecules that could fit in those blobs.

Any suggestions?

Thank you

Egor