[phenixbb] Problem with R-free assignment

Pavel Afonine pafonine at lbl.gov
Thu Sep 1 09:49:10 PDT 2011

Hi Jose,

DANO and SIGDANO are not used in refinement.

Resetting ADPs to an average value, and performing ~5 macro-cycles of 
refinement with SA and weights optimization typically should be 
sufficient. Make sure you are using the latest PHENIX version from 
nightly builds:

Let me know if you have any questions.


On 9/1/11 9:25 AM, Jose Arcadio wrote:
> Dear phenix.refine community:
> I am solving a protein structure using experimental phasing. In order 
> to do that I combined two derivative isomorphous datasets into a 
> double SAD experiment (to increase the individual weak anomalous power 
> from each dataset) using SHARP.My resolution is 3.2 A, and the space 
> group is C2221.
> I managed to build a model using the density-modified phases from 
> SHARP. Then I started refining against one of my derivative datasets 
> because my native dataset is non-isomorphous due to the heavy meal 
> soaking.Then I made two mistakes :(
> 1. I did not realize at the beginning of my refinement-building rounds 
> that I was refining against the dataset that showed the worst statistics.
> 2. I was using a dataset with only FP and SIGFP but not DANO and 
> SIGDANO. I used the phases from my SHARP map (also the experimental 
> phase restraints)
> Now I did a new run of refinement using my best dataset (better 
> statistics) and also including the anomalous data FP, SIGFP, DANO and 
> SIGDANO. Obviously, my R-work and R-free got pretty much better.
> Nevertheless, the R-free was better than R-work at the beginning of 
> the run, at the end of the refinement R-free and R-work inverted as 
> usually (being R-free worst than R-work)  r_work = 0.2582  r_free = 
> 0.2888 . Certainly, there was a mistake with a new assignment of the 
> free set of reflections. Now I am aware that the set of free 
> reflections has to be the same all over the refining procedure.
> Here are the questions
> How can I be sure that my R-free is still a safe cross validation of 
> the correctness of my structure?
> Is it useful to perform a round of simulated annealing in order to 
> erase any wrong information in my model and start the refinement 
> rounds again?
> Do you have any suggestions?
> All the best
> Jose Farias
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> phenixbb at phenix-online.org
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