Hi Carsten,
1.The maps look great for the residues were some of the B-factors are 0.
To me it looks very weird. I have no explanation for this. Again, this goes to the point where I need to play with the refinement myself to be able to say more.
3. OK, I'll play around with that. Any idea what target I should use? Minimize R-free or just push all Bs above 0?
Does anyone know a publication which covers theoretical B-factor distributions?
Here are a few links related to your question that came to my mind first: D. E. Tronrud J. Appl. Cryst. (1996). 29, 100-104 Knowledge-Based B-Factor Restraints for the Refinement of Proteins F. L. Hirshfeld Acta Cryst. (1976). A32, 239-244 Can X-ray data distinguish bonding effects from vibrational smearing? S. PARTHASARATHY AND M.R.N. MURTHY Analysis of temperature factor distribution in high-resolution protein structures Protein Science (1997), 6:2561-2567. http://www.ysbl.york.ac.uk/ccp4bb/2003/msg00432.html http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=ccp4bb&T=0&F=&S=&P=52510 J.D. DUNITZ and D.N.J. WHITE Non-rigid-body thermal-motion analysis. Acta Cryst. (1973). A29, 93 Cheers, Pavel.