Fix problems manually

[danieleongari]

This fix operates on top of #6.
Some of these overlap with the corrections in #5.

The problems I'm fixing here come from very basic parsing of the databese:

• Missing geometry xyz file for a certain fragment's label
• Mismatching number of atoms in the header of the XYZ
• rename some databases where the suffix _ALL is not consistent: MB08-165_ALL should be MB08-165 because there are no other databases, and MetalsEE_Por21 should be MetalsEE_Por21_ALL because it is a combination of the systems in the PorBE10 and PorSS1