Have a look at these examples - with the only difference that you should run this on a cluster machine, i.e. after

      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.