here is a solution, not nice though:
step 1: get a pdb file with chain in question:
phenix.pdbtools model.pdb keep="chain A"
output.file_name="chain_A.pdb"
step 2: then this will give you average B
phenix.pdbtools chain_A.pdb model_statistics=true
Other suggestions (by David & Christian) might work too, but I
have no idea how these programs handle TLS contribution to ADP and
ANISOU records. Though since phenix.refine outputs total ADPs I
guess this should be just fine.
Since this question has come up before, I've added a window for displaying this in the GUI. Clicking the magnifying glass icon next to any PDB file will already open a panel showing an overview of the model contents, and now there will also be a button labeled "B-factors by chain" for any file with multiple chains. Clicking this button will display the isotropic B-factors statistics by chain. Under the circumstances, I'm assuming the B-factor field in the PDB file is already the total B-factor.
This will be available in the next nightly build.
-Nat