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Phase transitions in molecular crystals are often determined by intermolecular interactions. The cage complex of [Co(C12H30N8)](3+) . 3 NO3- is reported to undergo a disorder-order phase transition at T-c1 approximate to 133 K upon cooling. Temperature-dependent neutron and synchrotron diffraction experiments revealed satellite reflections in addition to main reflections in the diffraction patterns below T-c1. The modulation wave vector varies as function of temperature and locks in at T-c3 approximate to 98 K. Here, we demonstrate that the crystal symmetry lowers from hexagonal to monoclinic in the incommensurately modulated phases in T-c1<T<T-c3. Distinctive levels of competitions: trade-off between longer N-H...O and shorter C-H...O hydrogen bonds; steric constraints to dense C-H...O bonds give rise to pronounced modulation of the basic structure. Severely frustrated crystal packing in the incommensurate phase is precursor to optimal balance of intermolecular interactions in the lock-in phase.