he frequency option is not available in 2016.4 GUI. It has been added in 2017.1
In 2016.4, you can set the frequency from the XSCT console in the GUI. Here're the steps
connect
jtag targets <cable id> (select the target corresponding to jtag cable)
jtag freq <new freq> (you can get the list of supported frequencies by running jtag frequency -list)
