Re: [phenixbb] geometry in phenix.refine

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?

Also, I think H atoms should be excluded from geometry statistics calculations if riding model is used. I will add this as well.

Then you need to change the geometry statistics output by phenix.refine when riding H atoms are present. Jianghai