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Using Bayesian inference, we determine probabilistic constraints on the parameters describing the fluctuating structure of protons at high energy. We employ the color glass condensate framework supplemented with a model for the spatial structure of the proton, along with experimental data from the ZEUS and H1 Collaborations on coherent and incoherent diffractive J/ψ production in e+p collisions at HERA. This data is found to constrain most model parameters well. This work sets the stage for future global analyses, including experimental data from e+p, p+p, and p+A collisions, to constrain the fluctuating structure of nucleons along with properties of the final state.