Versions of PHENIX prior to May 8, 2008 (prior to version 1.3-rc2) had a bug in the AutoBuild OMIT procedure in which OMIT maps fail to omit ligands or waters in the omit region (it only omitted the protein atoms, or DNA/RNA if the wizard was building them instead). This should no longer be an issue starting with version 1.3-rc2. I'm sorry for this error.
-Tom T
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545