Hi, from your description you seem to be doing the right things but the Rfree-Rwork gap is indeed rather large than expected at this resolution. If you send me model and data (off list) then there is a good chance I figure out what's happening and offer a solution (if any ligand cif files involved -- send them too). Pavel On 5/24/19 08:51, Pham, Hang wrote:
Dear all,
I am refining my structures at 2.5 A. The model is well fitting in the electron density. I already add water and ligands. I’m trying these options (XYZ coordinates, real-space, TLS parameters, Individual B-factors, Optimize X-ray/stereochemistry weight, Optimize X-ray/ ADP weight, Reference model restraints, Use secondary structure restraints, Simulated annealing (Cartesian), Automatically correct N/Q/H errors) to refine the structure but the R-free still be high. The reference model is 98% identity with the structure that I’m building. After refining, the R-work always decrease while R-free increase. My last values for R-work is 0.2501 and for R-free is 0.3246.
I’m lost and don’t know what to try more. Can anyone could explain me what happens here ? What others options that I could use to optimize R-free value ?
Thank you in advance !
Hang Pham