PDB to mmCIF converted files do not validate for the PDBx/mmCIF dictionary

[bienchen]

The mmCIF files converted from PDB input to not validate against the PDBx/mmCIF dictionary. They are missing some essential categories. Raised the issue also with Gemmi: project-gemmi/gemmi#178

Output of CifCheck:

ERROR - In block "P38398_1jm7.1.A_1_103", parent category "entity_poly_seq", of category "atom_site", is missing.
++ERROR - In block "P38398_1jm7.1.A_1_103", parent category "pdbx_poly_seq_scheme", of category "atom_site", is missing.

entity_poly_seq appears when gemmi convert is invoked using -s. But then entity_poly is still missing.