Calculation of RMSD in Evaluation

[SebastianHeid]

How exactly is the RMSD calculated for the evaluation. As far as I understood one matches the crystal waters from the ground truth with the predicted crystal waters in order to determine the coverage. Is then just the RMSD between the matched water molecules computed? Or are all predicted water molecules considered?
Furthermore, could you point me to the line where this is implemented? I could not find it.

Thanks a lot for your help!