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I don’t know what it means by “rosetta format” – Rosetta uses the PDB format that everyone else does. There are some minor issues that come up (usually odd atom names and 0-occupancy atoms) which I can help you with if there’s a problem.
By missing residues, I assume it means that your CS rosetta prediction only predicts for regions where you had NMR data. Look at the structure you have now (that you want to refine) and decide if you want it to have more residues in it or not. How to add those residues is dependent on how you want to do the refinement; I can think of ways to add residues but none that sound right for you.
Idealizing geometry is done with the idealize executeable: http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_idealization.html