Create a proper super cell from cif file

Hi all,
I want to build a supercell of 333 from the attached .cif
file. I am using super cell option in avogadro. When I build and download
pdb file, I see some broken molecules (not complete structures). As this
broken molecules create trouble in generating input for MD runs. Could you
please suggest, how to create a proper complete supercell from .cif file.
I could not solve this from many days. I would highly appreciate your help.

Thanks & Regards,