| -symmetrize C5 | Apply point group symmetry. | 
| -verbose 7 | Verbosity of output. | 
| -datatype u | Force writing of a new data type. | 
| -resolution 35,15.5,1.5 | Resolution limit start, end and step (default 30,20,1). | 
| -iterations 80 | Iterations (default 1). | 
| -exit 0.1 | Exit condition based on amplitude RMSD (default 0.01). | 
| -output 5 | Number of iterations between writing output maps (default 100). | 
| -Reference file.map | File to generate amplitudes from (default amplitudes from input map). | 
| -Amplitudes file.map | File with amplitudes (default amplitudes from input map). | 
| -Mask mask.tif | Mask file. |