Hi Yuri,
The pdb did have anisou records for H's. I believe that is because in some previous runs I had only selected chain 'A' - I left out "and not elemnt H" - which I believe caused the H's to get refined anisotropically.
Ok, that would be the explanation.
I am trying to get rid of the ANISOU records and Ill run refinement again.
Good.
ps. I am getting ready to deposit the coordinates and I dont want to keep hydrogens in the model, how can I get rid of them? I ve been using pyMol to remove them, but pymol gets rid of all the info -including symmetry -that phenix adds...
Any post-refinement changes to the model are very bad. By doing so you invalidate the reported in REMARK 3 statistics, such as R-factors, atom counts, etc. This is explained in details here: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010). In general, phenix.pdbtools is the tool to manipulate PDB files: phenix.pdbtools model.pdb remove="element H" will remove all H atoms. If you do so then re-run the refinement so you get correct numbers. More examples of PDB tools usage: http://www.phenix-online.org/documentation/pdbtools.htm Pavel.