There is something wrong with the PDB, but the chain lettering was a red herring. Your occupancy column (the next-to-last column) is zero. Set it to something nonzero (1.00 is fine). Rosetta is deleting your protein as it reads it in because the 0 occupancy is a signal that those regions should be ignored.
The same text tools I mentioned before apply; there’s a post somewhere these forums with a sed or awk command to do it.
For future reference – the forum mangles PDB spacing formatting – it is better to attach PDBs as text files rather than paste them into the box (there should be an attachment button below the reply window).