[phenixbb] Problem with R-free assignment
jose.farias at tuebingen.mpg.de
Thu Sep 1 09:25:27 PDT 2011
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
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
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