[phenixbb] Hydrogens on modified residues -- ReadySet

Dear all, ReadySet encounters some issues when adding hydrogens to modified residues. I used the 7k00 ribosome structure as a test. I noticed missing hydrogens on G7M, 4OC, UR3, MA6, 6MZ, 2MA, OMU, 2MG. Additionally, hydrogens are missing on IAS and on the NH groups of D2T, MS6 and 4D4. An amino hydrogen is also missing on 4D4. When using Coot on this file, everything looks much better except that some hydrogens are added to amino acid backbones of modified residues that need to be removed by hand. Any ideas ? Thanks a lot, Pascal