Rigid End Zones:
Whether or not to consider the effects of rigid end zones is declared in the Rigid End Zone box. You may choose to ignore these effects by clicking the Ignore Effects option button. If you choose to include the effects and click on the Include Effects option, you can either enter a percent reduction (between 0 and 100%) in the edit box or accept the default value of 0%. See the RAM Frame manual [Section 6.11 Joint Face Distance and Rigid End Zones] for further discussion of Rigid End Zones.

Deciding how much, if any, of the column panel zone to consider rigid is an important engineering decision that affects drift, member forces, connection design, etc. It's also a topic of discussion that's too lengthy for a simple answer.

To help, here is a link to the NEHRP Seismic Design Technical Brief No. 2, Seismic Design of Steel Special Moment Frames: A Guide for Practicing Engineers. Our rule of thumb with RAM Frame is simply that engineers should not consider rigid end zones unless there is justification for it. Using a centerline analysis may not be conservative in all regards, but it is for drift at least.

Furthermore, the rigid end zone setting has an impact on the Ram Frame - Steel mode joint checks. 

Two different equation sets are presented in AISC when performing panel zone checks. The first set of equations is applicable when panel-zone deformation is not considered in the analysis (full REZ, case 2 above). The second set of equations is applicable where panel-zone deformation is considered in the analysis (cases 1 or 3 above).