The TNT sequence file contains information about your model which other crystallographic packages either store in the coordinate file or simply assume from hints in the coordinate file. For example, a Protein Databank file contains the the amino acid type of each residue in your protein but does not explicitly state which residues are connected by peptide bonds, which are connected by other types of links, or which are not connected at all.
The sequence file contains the type of each residue and all the information required to describe the links between residues. There are only three statement types used for this purpose -- CHAIN, LINK, and RESIDUE. Since models with a single chain are so common they have been treated as a special case.