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The relevant parts of the microstructure participating in the plastic deformation of glassy polystyrene are identified. This is achieved by performing quasi-static deformation simulations of an atomistic representation of polystyrene, within a thermodynamic framework, under experimentally realistic boundary conditions (controlled compressive strain, atmospheric pressure in the lateral directions, and room temperature). In particular, it is shown that discontinuities in the free energy in the course of deformation are representative of microscopic plastic events, which are strongly correlated with the heterogeneous non-affine deformation of the phenyl-rings. However, despite the induced anisotropy during deformation, the phenyl-rings do not show any preferred orientation during deformation. The rearrangements of the microstructure during the discontinuities are analyzed further in terms of a local best-fit deformation gradient tensor (a modified version of the procedure introduced by Falk and Langer in 1998) as well as the stretch- and rotation-components of the local deformation of clusters of atoms that show significant non-affine deformation. This analysis shows that the local deformation is highly heterogeneous, and locally the strains and rotations can be orders of magnitude larger than the imposed deformation, giving rise to plastic deformation of the material.