*FLG section specifies the ZEN flag for an upward path through a plane parallel atmosphere, and the TRA flag to output the transmittance spectrum.
The *GAS section specifies that H2O, O3, N2O and F12 (CFC-12) are to be included, while the *(12) adds any other gases that might be significant in this spectral range (from rfm.runlog it can be seen that it chooses to add CH4, F22 (HCFC-22), F11 (CFC-11) and CO2). Although N2O is included because it was explicitly specified by the user, the RFM wouldn't have added it itself.
Since this is a plane parallel atmosphere calculation, the path is specified by the *SEC section marker (although *TAN would also be acceptable) and the value of 1.0 gives the secant of the slant angle, ie 0 degrees so a vertical path.
*HDR 15AUG13 RFM Example: zenith transmittance *FLG ZEN TRA *SPC 1100 1110 0.1 *GAS H2O O3 N2O F12 *(12) *ATM ../atm/usa.atm *SEC 1.0 *HIT ../hit/hitran_2012.bin *XSC ../xsc/*.xsc *END