I am refining a structure at 2.25 A using Phenix.refine. I
am using TLS parameters for refinement but as i use TLS, phenix does
individual anisotropic refinemnt also.
No, it doesn't: it does not do "individual anisotropic refinement"
unless you specifically asked for this.
It does, however, print out individual ANISOU records at the end of refinement - but these are extracted from the TLS groups, not refined individually. If you absolutely must get rid of them, "grep -v ANISOU refined_file.pdb > new_file.pdb" will do the trick, but personally, I always like to look at the ellipsoids in PyMOL or Coot anyway, to see what the TLS groups are doing.
-Nat
