The discussion resulting from my question has been most interesting & most helpful! I'm saving it for future reference. The protein I'm working on almost has a missing loop - that is, someone finally managed to get crystals in which the previously missing residues were resolved. But someday, that won't be the case.

I have a 2.33GHz linux box, and I started my 514-residue dimeric protein on Rosetta relax a short time after lunch on Friday. The job finished sometime Saturday night or the early hours of Sunday morning. The MolProbity score was 1.93.

Thanks so much!

Irene