Dear all, I have a question about how PBDREDO and REFMAC treat the geometry weight (gw). In particular, I have a structure with a N-terminal CXM bound to a HIS as a second residue. After complete refinement, I run PDBREDO to choose the most appropriate gw. Let’s say best results are found using gw = 0.1. I run REFMAC using that value, but the carbonyl carbon of CXM detaches from the amidic N of HIS (distance 1.84 A). If i run the same job using a gw of 0.2, 0.3 and so on, that distance decreases and the C-N bond is restored. By the way, increasing the gw Rfree increases as well as the difference between Rfactor and Rfree. Any idea on how to solve the problem? Should I keep higher Rfree and worse stats with still having a peptide bond there?
Thank you, Luca Luca Mazzei - PhD Department of Pharmacy and Biotechnology University of Bologna Viale Giuseppe Fanin, 40 - 40127 Bologna - Italy ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
