Dear Chris, this is not an answer to your question but may be helpful anyway. I checked your glycan with pdb-care at http://www.glycosciences.de/tools/pdbcare/ and found what I already assumed from looking at the image you had sent: Some of your residues feature a wrong anomer. BMA303B is an alpha-Mannose but should be beta at that position, whereas MAN304B is beta-Mannose but should be alpha to match the conserved N-glycan core structure. These are frequent problems in PDB N-glycans, so please don't feel offended - I just want to raise attention to this kind of error by pointing this out.
Best regards Thomas
