Hi,
I reran that (same refmac version) but I cannot reproduce the output.
Of course, you cannot reproduce the output. This is most likely because the H atoms were used internally in all calculations but they were not deposited in PDB (like in most of cases). So, to reproduce the numbers reported in PDB file header you need to re-do exactly same refinement as the authors of that structure did.
This is why it's not too bad idea to not remove H atoms from the PDB file if these hydrogens were used in calculations. In phenix.refine we keep hydrogens for exactly this reason. This costs nothing but results in easier reproducible results.
Cheers, Pavel.
