Hi Careina,
Your starting R/Rfree values seem just fine. The reason for the large disparity after refinement is because the weighting factor is way too large during the first rounds of refinement. For each round of refinement, have a few different runs which test weighting factors between 0.01-0.2. I have found that during the first round of refinement, running sequential rounds of 1 cycle refinements with gradually increasing weighting terms (0.01, 0.015, 0.02, 0.025, etc), works really well. This is a similar approach to how BALBES does its initial refinement. The smaller the weighting factor, the smaller the amount of change you will see between R/Rfree... at the expense of decreasing the amount that R/Rfree go down during each refinement. Another thing you could try if you are using Refmac is to switch from "Simple" to "Babinet" scaling. Hope this helps
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Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907
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From: "Careina Edgooms" <
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To: [log in to unmask]Sent: Wednesday, July 13, 2011 11:38:38 AM
Subject: [ccp4bb] large R-Rfree difference in "final" structure
Dear ccp4 bulletin board
I just have a slight concern regarding my Rwork Rfree difference. I have a structure that I have solved. I am reasonably content that it is complete because it has refined well, it no longer has bad geometries and contacts and all the rotamers, ramachandra, bond lengths etc are good. It gives favourable scores on molprobity and procheck. My only concern is the R factor difference. The resolution of the structure is 2.3A. The R factor is 0.24 after refinement but the Rfree is 0.33 which seems to me to be rather high. Should I be concerned?
During refinement Rfree only drops from about 0.36 to 0.33 while the R factor drops from 0.31 to 0.24.. I have removed automatic weighting in refmac in order to constrain my
bond lengths and angles during a couple of rounds of refinement. This did not have any effect on the R factors, however. I am fairly content that the space group I have chosen is correct so I am not sure what else could cause the big difference in R factors? There is no twinning.
Can I be satisfied that my structure is correct despite the high R free or should I be doing other checks/ trying other things before I can submit this structure?
Thank you for any help
Careina
