Clean up merged Tholes.

Terminus patching modifies Thole screening within residues, so the
clean_tholes() function now prunes the list appropriately to use the
entries from the .tdb rather than the .rtp; issues remain because some
residues have special Thole factors on CB.  This function will have to
be extended to take this into account.

Change-Id: Iabf454b10e2a5dd36850edac35a5dc187f731797