Boxiness is a notorious kick drum problem. It’s usually resolved by cutting the middle frequencies around 300 Hz but if that doesn’t work try looking in the 400 and up to 600 Hz area.
Multiple cuts work differently than one large one so be sure to experiment to find the right sound
for your song.
In this week's One Minute EQ Trick video you can hear how the kick tightens up when I cut the mids out. It becomes more defined since we're accenting the lows of the drum as well as the hit of the beater while taking out all the garbage in between.
You'll cut more or less of the boxy mids depending on the
style and genre of the song. For The Long Wait that has a more natural sounding "folk-rock" sound I wouldn't drastically scoop the mids, while the "alternative-metal" band I'm about to mix today will probably get a more heavy-handed treatment.
Check the video below for the audio example.