When can I consider high values of RMSD as a good result in docking?

hello all users… Recently I ran MD for a complex (hormone-receptor), receptor has a pdb code while the ligand has been constructed.
the outputs like energies, Rg were ok but I confused about RMSD which was higher than 2 A … RMSF showed that there were some fluctuations (at loops rejoin)…
I asked few experts about this issue, they said that the results were ok due to using crystal structure which has loops… is it correct? is there any academic evidence ? in case of complex stability, how can I interpret the results of RMSD with Rg?