the difference is most likely because of H atoms, indeed (deferent
"ideal" values used by phenix.reduce and Monomer Library that is  
used in
phenix.refine). In the next version of phenix.refine the geometry of H
atoms will always be regularized (unless free refinement is  
requested at
ultra-high resolution), so it will be always consistent with the  
Monomer
Library definitions.


Why not just the same value to start with?

Because some programs tend to distort hydrogen's geometry completely (for example, COOT after doing local RS fit) so you start refinement with nonsense H positions. And since in riding model X-H distances are fixed you keep having wrong values. Many users reported this problem.

Pavel.

I