Dear CCP4 users, I refined my final model (protein-RNA complex) using TLS refinement in Refmac but when i am validating the coordinates I am having an issue with Bond Distances and Bond Angles of some of the bases of RNA, these values for some of the bases are higher ( >6 times) then the standard values. I figured that it happened only after REFMAC refinement. The coordinates before the REFMAC (the last CNS refined coordinates) were found to be acceptable by the same validation program. So my guess is something wierd is happening with RNAs only during REFMAC refinement. Although, Rfree improved by almost 1.5% with REFMAC.
In an attempt to fix this, I ommitted both chains of the RNAs during the REFMAC (.tls file contains only protein monomers) but that did not resolve the isssue either. Is there any way to fix this problem or a way to restrain particular RNA bases/chains during TLS refinement? Thanks for your time and help. Happy Holidays Yogesh -- Yogesh K. Gupta, Ph.D. Post Doctoral Fellow Molecular Physiology & Biophysics Mount Sinai School of Medicine 1425, Madison Av. (East Bldg. 16-26) Box 1677, New York, NY 10029-6574 Tel:+1 212-659-8639 Fax:+1 212-849-2456 E-mail: [EMAIL PROTECTED] -----------------------------------------
