They are just warning messages of the the type usually seen for polymer terminii, and may not be real problems. The real test is can you minimize the structure, or at least evaluate the energy w/o errors.
You may need to check your "necessary revisions" more carefully.
Finally, the example illustrates one way to read only the atoms with existing coords, which was all I needed for a quick look at the subunit contact surfaces. For a more detailed study, one should probably define the residues for the disordered loop in subunit A, and use some model building approaches to define coordinates for these atoms.