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Main keywords:

-p; input pdb file

-m; input mtz file

-d <subdir>; to save all files in a subdirectory <subdir>.

-L; unmodelled ligand is present/unknown location. 

-Lpdb <pdb file>; pdb file of unmodelled ligand.

-RB [<rigid.dat>]; rigid body.
-B <B-ref type>; the default B-factor refinement is automatically determined, options are "individual", "group-res", "group-mcsc", "None" or "user".
-autoncs; detects NCS and restraints.
-TLS [<tls.dat>]; do TLS refinement with the definition of TLS-groups in the specified file.
-M TLSbasic (to use with keyword -M in front, being TLSbasic a macro); uses any TLS decomposition which is recorded in the input PDB file, and constructs a straightforward one (each chain modelled as a single rigid body) if there isn't one in the PDB file to start with.
-WAT <ncyc>; water updating switched on, optionally only after cycle <ncyc>.

-R <reslow> <reshigh>; low- and high-resolution limits for refinement, the default is to use all data present in the MTZ file.

-target <file.pdb>; this is to use LSSR (or structural similarity restraints, basically when you have an high-resolution structure against which you can/want to refine your low resolution one, see here

-target_weight <number>; option to use with LSSR, usually not necessary to change the default value (1.0), but in cases where the -target option increases R-free then it is advised to try reducing this number.

Other useful parameters and keywords to know:

 (the default value is 2.0)
GeometryWeight_angle=x (the default value is 2.0)

Useful links: