Hi, In order to do a paired refinement you need 2 sets of Rwork/Rfree at each resolution. The first is just the normal figures from refinement, the second is from the structure refined at higher resolution but with the R/Rfree calculated at the lower resolution. You can calculate this using something like phenix.model_vs_data and setting a high resolution cutoff, or I believe running Refmac with 0 rounds of refinement will do the same thing.
e.g. refinement at 2.7 refinement at 2.6 with r/rfree calculated using only the reflections to 2.7 That way you can directly compare the two and see if including the extra data to 2.6 has made your structure better. Usually this means either Rfree goes down, or Rfree stays the same but Rwork goes up (indicating less overfitting). Cheers, Jason. -- Dr Jason Busby Laboratory of Structural Biology School of Biological Sciences The University of Auckland Thomas Building 110 3A Symonds St Private Bag 92019 Auckland Mail Centre Auckland New Zealand ph: +64 9 3737599 ext 88958 On 2/07/2015, at 11:15 am, Eric Karg <0000052044071b36-dmarc-requ...@jiscmail.ac.uk<mailto:0000052044071b36-dmarc-requ...@jiscmail.ac.uk>> wrote: Hi all, I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm trying to do "paired refinement" to determine the optimal resolution cutoff. Here is what I get at different resolutions set in Phenix: Final Rfree/Rwork: 2.7—> 0.2498/0.2027 2.6—> 0.2519/0.2009 2.5—> 0.2567/0.2025 2.4 —> 0.2481/0.2042 2.3 —> 0.2493/0.2075 The geometry of all output structures are similar. 1. What is the high resolution cutoff based on these data? I know that Rfree/Rwork at different resolution should not be compared, but is there a simple way to do the test as described in the K&D 2012 Science paper using Phenix GUI? 2. For refining a structure at a lower resolution (lower than the initial dataset), do I simply set the resolution limit in the refinement or I need to reprocess the data starting from the images? Do I need to do anything with Rfree flags? Based on the discussions on this forum I know I should deposit the highest resolution dataset but my question is about the mtz file which will be used for refinement. Thank you very much for your help!
