In addition, REFMAC has tightened your model's geometry which can cause a slight increase in the working R. A one percent increase in while in the upper thirties is slight.
Dale Tronrud On 4/8/2020 7:30 AM, Schreuder, Herman /DE wrote: > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
