| -type fsc | Output type of criterion: cc, r, fsc, dpr. |
| -preference -10 | Homogenous preference for clustering. |
| -verbose 7 | Verbosity of output. |
| -resolution 15.3 | Resolution limit (angstrom). |
| -cutoff 0.5,45 | Resolution cutoffs for FSC and DPR. |
| -lambda 0.6 | Damping factor for clustering (default 0.5). |
| -output file.star | Output parameter file. |
| -matrix mat.dat | Output comparison matrix file. |