[phenixbb] Phenix.refine distorts geometry during rigid body refinement

I am bringing a PDB refined in Refmac back to phenix.refine. After an initial rigid body refinement to compare numbers (one chain per group), the geometry (specifically the bond length rmsd) had surprisingly increased. Phenix.validate confirmed the Refmac (initial) geometry numbers and then afterwards confirmed the distorted geometry. What is strange is that when opened in COOT, the initial and final models are completely super imposed. REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768 REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019 can you help me figure out what is going on here? These are the final few refinements of a 4.1 A structure. Thanks, Ian