Good morning,

I have conducted a superposition between two of the same protein where one was obtained by X ray and the other was predicted by alphafold. I wanted to use the RMSD value of the alignment rather then just have qualitative results but I am unsure of how to interpret the values given by chimera.  

When I get the output of for example: RMSD between 189 pruned atom pairs is 1.164 angstroms; (across all 553 pairs: 10.750),  what exactly do these two outputs mean, which one should I be using and how exactly do I interpret this?

Kind regards,

Munira