You may find the graph below useful in selecting the number of groups. Often there is a 'dogleg' or 'elbow' point in the curve to the right of which adding more TLS groups does not significantly reduce the least squares residual. The number of TLS groups at that point is a reasonable number to select.

Refmac5:
Given the number of TLS groups you would like to use for each chain, TLSMD will generate a special coordinate file (PDBIN) and TLS tensor file (TLSIN) that you can use for input to Refmac5. These files are generated specifically for Refmac5 refinement by splitting the temperature factor magnitude of each atom between the TLS model and individual atomic temperature factors. Because of this, the starting B factors for further refinement are different from the ones used for motion analysis.

PHENIX:
Given the number of TLS groups you would like to use for each chain, TLSMD will generate a single file for input to PHENIX that describes the residues making up each group. PHENIX does not currently allow you to input a starting model for the TLS parameters themselves.