I am facing some problem when I am refining my structure. My data is of resolution 2.1. The R and Free R for the structure is 23 / 28 and the rms bond angle is 1.496 and  rms bond length is 0.0103. During the initial phase of refinement, the R/ Free R decreased upto 23/ 28. But now as I am refining my structure, the R/ free R is geting

increased instead of decrease along with increment in bond angle. What should I do to decrease the R / free R or can I deposit my data as it is. The native structure for the protein is well refined and already deposited. This structure is a complex structure of the same protein with some ligand.