The R factor and Rfree will always diverge during refinement; the model
is being modified to fit the working set, and not theFree set..
A largish difference at such a resolution is not surprising really.
Your rebuilding has improved the FreeR but it isnt surprising thatit has
not fallen below 38%
Eleanor
Sravanti Vaidya wrote:
Hello CCP4i GURUs,
I am working on a 3A resolution structure and I recently got a solution from
Phaser. I have just started building and refining the structure. I started
with Rfree-43 , R-41.7 and the first round of building and refining gave me
Rfree- 40 and Rfac- 35.5. The Rfree and R do not decrease to the same extent
during refinement (Refmac5). Further rounds of refinement increases the
difference between R and Rfree (Rfree-38 Rfac- 30)
I am worried that since this is just the beginning further rounds of
building and refinement might drastically increase the gap between R and
Rfree. On the positive note the FOM is increasing with refinement and the
maps look better. I also see new density at several regions where I can
build into.
I tried to change the weighting factor and geometric parameters after I read
the earlier posts here. The references noted earlier were extremely helpful.
Here are some other details of my structure which might help you
Space group- P1 21 1
Resolution- 3A
Solvent content- 39%
unit cell parameters- 63.3, 90.72 , 86.11, angles- 90, 91.5 , 90
Please enlighten me with your suggestions. Is it fine to go ahead with this
refinement or is there a way I can reduce this difference between R and Rfree??
Your help will be greatly appreciated. As this is my first structure I am
excited about it!!!
Thank you
Sravanti
