Hi Tobias,

Dear PHENIXBB community,

i have come across a strange behavior in Phenix:

I copied Rfree-flags from a dataset with very slightly different unit cell

Refined the previously refined model against the new data

Rfactors in first round were good

Second round in refinement Rfree was up by 10 % just from the start during bulk solvent modeling and scaling

In another round Rfree was high in the beginning, and then dropped by those 10 % during bulk solvent modelling and scaling.

In yet another round Rfree started 10% lower than the previous round during bulk solvent modeling in the first cycle and then it jumps up again in the second cycle.

What could be wrong?

If I take a random structure from PDB:

phenix.fetch_pdb 1f8t --mtz

and run a default phenix.refine job:

phenix.refine 1f8t.{pdb,mtz}

then look at the log file, I see:

For the first macro-cycle:

(...)
start: r(all,work,free)=0.3064 0.3018 0.3435 n_refl.: 27466 re-set all scales: r(all,work,free)=0.3064 0.3018 0.3435 n_refl.: 27466 remove outliers: r(all,work,free)=0.3061 0.3016 0.3435 n_refl.: 27464 overall B=0.38 to atoms: r(all,work,free)=0.3096 0.3050 0.3470 n_refl.: 27464bulk-solvent and scaling: r(all,work,free)=0.1839 0.1798 0.2213 n_refl.: 27464 remove outliers: r(all,work,free)=0.1839 0.1798 0.2213 n_refl.: 27464(..)

Here:
- "start" means no any solvent modeling and scaling was yet done;
- last line shows R values after all corrections.

Now, for the second macro-cycle we see:

()
start: r(all,work,free)=0.1798 0.1754 0.2195 n_refl.: 27464 re-set all scales: r(all,work,free)=0.3200 0.3151 0.3607 n_refl.: 27464 remove outliers: r(all,work,free)=0.3200 0.3151 0.3607 n_refl.: 27464overall B=-2.56 to atoms: r(all,work,free)=0.2961 0.2912 0.3366 n_refl.: 27464bulk-solvent and scaling: r(all,work,free)=0.1783 0.1739 0.2183 n_refl.: 27464 remove outliers: r(all,work,free)=0.1783 0.1739 0.2183 n_refl.: 27464()

Here, "start" shows values obtained by the end of 1st macro-cycle, second line (re-set all scale) shows values after all scales were discarded, and the last line shows values R values after all scales were re-calculated again.

So.. if this is what you observe, then there is nothing wrong. Otherwise, please send me the log file and I will have a closer look.

Pavel