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.: 27464 bulk-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.: 27464 overall B=-2.56 to atoms: r(all,work,free)=0.2961 0.2912 0.3366 n_refl.: 27464 bulk-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