create a .Xmodmap file in your home directory paste the following:
clear control
clear mod4
keycode 105 =
keycode 206 =
keycode 133 = Control_L NoSymbol Control_L
keycode 134 = Control_R NoSymbol Control_R
keycode 37 = Super_L NoSymbol Super_L
add control = Control_L
add control = Control_R
add mod4 = Super_L
then create a script to run xmodmap ~/.Xmodmap on startup.