Hi, Nick, An R-factor of 0.16 seems low for a model refined against 2.4 A data. What are you using for the MATRIX weight in REFMAC? Here's a guide for selecting a proper MATRIX weight http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-10/msg00592.html For refinement against a 2.4 A data set, I usually use a MATRIX weight of 0.1. CNS automatically determines a proper weighting, which is probably why the spreads between your residuals with CNS refinement look more reasonable. I would also use a 5% R-free set. When I started reading your post, my first thought was that your Ramachandran plot must look like a blast of buckshot. But if the stereochemistry looks good by PROCHECK, I don't think there's anything fundamentally wrong with your methods. Good luck,
Hidong Nicholas Noinaj <[EMAIL PROTECTED]> Sent by: CCP4 bulletin board <[email protected]> 03/09/2007 06:22 PM Please respond to [EMAIL PROTECTED] To [email protected] cc Subject [ccp4bb] Differences in R and Rfree Hi, I am working on a 2.4 angstrom structure that is in its final stages of refinement and finding that REFMAC5 is giving a large difference between R and Rfree (10%), 0.16 and 0.29, respectively. 2Fo-Fc maps looks great and there is very little density in the difference maps. My model covers the entire protein sequence, except for ~5 residues on N-term and 3 residues on C-term. I then used the model for refinement (annealing) within CNS, and found that R and Rfree are relatively similar, 0.2 and 0.28, but in better agreement. I have read other posts addressing similar questions, but still unsure what my problem could be, if there is one. While I don't mind repeating things in CNS, I would really like to learn to be completely reliable on CCP4 Suite as much as possible, since i really like the REFMAC5 - Coot duo. I would appreciate any suggestions or comments you might offer. Given how nice the density maps look and that the model passes procheck analysis with very few suggestions for further investigations, i am unsure when to go from here. Thanks in advance for all feedback! Cheers, Nick
