?Hi,
I have seen this type of behavior happen often, albeit in phasing runs with Buccanneer and/or Phenix. Check the model statistics immediately after phasing, and compare them to the model statistics after refinement in Refmac. When I have observed this phenomenon, it's likely due to the fact that the model statistics after phasing are not great--poor Ramachandran and bond and angle statistics, and places with poor fit to the electron density. After a round of positional refinement, it's not uncommon to see the model geometry improve and then the R-free go up. It doesn't have to mean that your phasing model is incorrect, it just means you need to inspect your electron density. Maybe you just need to fix the obvious problems with side chains, incorrect portions of the model in loops with weak density, etc., to improve the model and lower the Rfree. Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: Saturday, April 21, 2018 1:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rfree going up after refinement I really need more information to comment properly. However just check that you are using the same reflections for both Rfree calculations. An Rfree of 26% seems low to me from a Se met phased structure at 2.1A - there are usually small corrections to be made, What is the Rwork? Maybe attach the REFMAC log file? Eleanor On 21 April 2018 at 03:24, ??? <21620150150...@stu.xmu.edu.cn<mailto:21620150150...@stu.xmu.edu.cn>> wrote: Dear all I have got my se-phase structure with ccp4-CRANK2-SAD, and its Rfree is 0.26 when CRANK2 output, but the Rfree is higher to 0.36 when I refine it with refmac or phenix-refinement. does it mean I got a wrong phase, or I didn't got the right parameters when refinement.BTW, the resolution is 2.1A.THANKS A LOT Best Regards shijun ________________________________ UT Southwestern Medical Center The future of medicine, today.
