I guess the molecular replacement model has never been refined against this data set, so there is no reason why the Rfree should be better or worse than the Rfactor. The difference is larger than I would expect, but it may just be a statistical fluke. That the Rfree goes up significantly during refinement is what I would expect and suggests that the model needs significant rebuilding and refinement. Similar, the Rfactor going slightly up may indicate that the model is moving out of a false local minimum.
I would just continue rebuilding and refinement and see what happens. Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Eleanor Dodson Gesendet: Mittwoch, 8. April 2020 15:36 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> Well - there is something funny about your first Rfree - it shouldnt be significantly lower than R? I suspect there is some muddle over the assignment of Rfree - one used for Phaser and a different value for REFMAC? And of course at low resolution especiall Rfactors are very sensitive to scaling procedures.. Eleanor On Wed, 8 Apr 2020 at 14:08, Kyle Gregory <00003632e92fcc15-dmarc-requ...@jiscmail.ac.uk<mailto:00003632e92fcc15-dmarc-requ...@jiscmail.ac.uk>> wrote: Hello, I haven't seen this before but doing a round of refinment with REFMAC, after molecular replacement with phaser, my R factor and R free have increased? Also is it weird that my Rfree is smaller than my R factor? Result: Initial Final R factor 0.3621 0.3761 R free 0.3108 0.4733 Rms BondLength 0.0076 0.0057 Rms BondAngle 1.6504 1.5193 Rms ChirVolume 0.0600 0.0526 My map was ok(ish) but there was indication of anistropy so I attempted to improve it by using STARANISO and re-ran phaser with the output, and this is the results I see following REFMAC. Thanks, Kyle ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=HlwIywlnVCEYkSzvp_-_ccaKmZ8CA8xqZ-E4qEM1EQM&s=zZRt-jd3LFyRUJNTwo1f2rCLUWxOrh0NCUIksNNS4PI&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=HlwIywlnVCEYkSzvp_-_ccaKmZ8CA8xqZ-E4qEM1EQM&s=zZRt-jd3LFyRUJNTwo1f2rCLUWxOrh0NCUIksNNS4PI&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
