[phenixbb] links and REMARK 3 record in the final PDB

[Ralf W. Grosse-Kunstleve]

To add to Pavel's reply, I decided not to read or write LINK records
since this would generate redundant information and may lead to
confusion (which one is used?).
Unfortunately, LINK records don't have space for all the information
for the restraints (ideal distance, esd), which forced us to move
the information into the .def file. (I didn't want/dare to venture
into extending the pdb format.)
Ralf