You have zero occupancies in some of the heavy atoms in your structure (particularly the R1A residues). Default behavior by Rosetta is to throw away those atoms and rebuild them. The rebuilt location will not necessarily match the input location. Furthermore, Rosetta also tends to repack residues which have missing atoms on loading (because, generally speaking, the rebuilt-from ideal positions will not be compatible with the rest of the protein structure. The way it does this permits movement of sidechain atoms, including atoms which may have specified coordinates. (You won’t see movement of the CB atoms, because rebuilding and packing of those atoms will always place them in the same spot, given the same backbone atoms.)
You can change the behavior towards the zero occupancy atoms by passing the commandline parameter “-ignore_zero_occupancy false” when you do your Rosetta initialization. I don’t believe you can change the repacking on incomplete reside behavior, so you’ll want to make sure that you include input coordinates for all (heavy) atoms. Keep in mind that Rosetta bases presence/absence on atom names, so the names you use in the input PDB must match up with those Rosetta expects.
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