Have a look at these examples - with the only difference that you should run this on a cluster machine, i.e. after
clusterme module load ccp4-workshop
For the 5Z5U example, you could also try and use the 5z5u_all.mtz file (data to 1.1 A resolution) instead of the default 1.6 A 5z5u.mtz. It is not quite clear why the structure was refined only against 1.63 A data, but intensities to 1.1A were deposited). This might be related to the severe anisotropy of the data:
Diffraction limits & principal axes of ellipsoid fitted to diffraction cut-off surface:
1.846 1.0000 0.0000 0.0000 a*
1.197 0.0000 1.0000 0.0000 b*
1.298 0.0000 0.0000 1.0000 c*
We could upload that high-resolution MTZ file (containing intensities) to the STARANISO server in order to create a new MTZ file after anisotropy analysis and correction: see job output here.