We present the partition function of the refined Chern-Simons theory on S3 with arbitrary A, B, C, D gauge algebra in terms of multiple sine functions. For B and C cases this representation is novel. It allows us to conjecture duality to some refined and orientifolded versions of the topological string on the resolved conifold, and carry out the detailed identification of different contributions. The free energies for D and C algebras possess the usual halved contribution from the A theory, i.e. orientable surfaces, and contributions of non-orientable surfaces with one cross-cup, with opposite signs, similar as for the non-refined theories. However, in the refined case, both theories possess in addition a non-zero contribution of orientable surfaces with two cross-cups. In particular, we observe a trebling of the Kähler parameter, in the sense of a refinement and world-sheet (i.e. the number of cross-cups) dependent quantum shift. For B algebra the contribution of Klein bottles is zero, as is the case in the non-refined theory, and the one-cross-cup terms differ from the D and C cases. For the (refined) constant maps terms of these theories we suggest a modular-invariant representation, which leads to natural topological string interpretation. We also calculate some non-perturbative corrections.
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