The shear flow induced deformations of a nematic liquid crystal layer have been modelled numerically for the case of flow-aligning nematics. The director deviation from the plane of shear, which was predicted earlier for special surface orientation angles, has been confirmed. This deformation takes a form of director rotation about the axis perpendicular to the layer plane. As a result, transverse flow of the nematic arises. The rotation angle is close to pi at sufficiently strong shear stress, and the director is oriented at the usual flow alignment angle in a significant part of the layer. The director coming out of the shear plane should not be treated as a separate effect taking place during the flow, but rather as a way in which the usual flow-aligned structure is achieved.