how to “rescore” the models using lowest energy model from rosetta run as native, for RMSD vs Score plot?

Dear Friends, 

I am running ab initio structure prediciton of a 382 long protein sequence. I have got some 2000 models generated till now, and I would like to see the RMSD vs Score plot for these models. Since there si no native pdb availbale for this, when following the tutorial:rosettacommons.org/demos/latest/tutorials/…; it says ” However, if no related structure is known, you would use e.g. the lowest energy model (and rescore the top models with e.g. -native best_E.pdb).” Can you let me know how can I “rescore” the models? I mean the command line. Thanks