On Mon, Jun 23, 2014 at 9:35 PM, Egor Tchesnokov <etchesnokov@chemistry.otago.ac.nz> wrote:

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.

Phaser resets all heteroatoms to zero occupancy unless you specifically request otherwise, and I don't think refinement will magically take care of that. If you're using the GUI, click the button labeled "Modify start model" in the middle configuration tab, choose occupancies, and enter 1 for the new occupancy. (The occupancy refinement will still take place.) Or you can just do this manually in PDBtools or the PDB editor.

-Nat