Hi, I am looking over a number of models from the PDB but have been unable to reproduce the R-factors for any model that was refined with Refmac and contains TLS parameters. I usually can't get within 5% of the reported value. On the other hand, I usually do pretty well for models w/o TLS.
An example is the model 1nkz. The PDB header gives an R value of 17% but even when I use tlsanal in CCP4i to generate a PDB with anisotropic B's that mimic the TLS parameters I get an R value of 22.4% using SFCheck. (I'm not implying that I suspect any problem with 1nkz, in fact I have every reason to believe this is the great model its published stats indicate.) I've found a CCP4 BB letter that stated that SFCheck does not pay attention to anisotropic B's but that letter was dated 2002. I hope this limitation has been removed, or at least the output would mention this limitation. Setting up a refinement in Refmac involves a large overhead, since even for zero cycles of refinement the program insists on a complete stereochemical definition for the strange and wondrous groups in this model. I would just like to verify the R factor and calculate a proper map for inspection in Coot. Since I have many models I would like to look at, I would like a simple procedure. I did set up a Refmac run for another model, for which I do have all the .cif's required, but even after refinement I was not close to the reported R. I see that the models I'm interested in are not present in the Electron Density Server, so I suspect I'm not alone in fighting this battle. Any advice would be appreciated, Dale Tronrud
