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We are developing a dual panel breast-dedicated PET system using NOVA RENA-3 ASICs. The coincidence timing resolution of the RENA-3 ASIC can be improved with list mode calibration. We treat the calibration problem as a convex optimization problem and use the RENA-3’s analog based timing system to correct the measured data for time dispersion effects from correlated noise, position sensitive avalanche photodiode (PSAPD) signal delays and varying signal amplitudes. The direct solution to the optimization problem involves a matrix inversion that grows order (n2) with the number of parameters. An iterative method using single-coordinate descent to approximate the inversion grows only order (n). The system calibration method is demonstrated with measured pulser data as well as with two LSO-PSAPD detectors in electronic coincidence. After applying the algorithm, the 511keV photopeak paired coincidence time resolution from the LSO-PSAPD detectors under study improved by 57%, from raw value of 16.3±0.07 ns FWHM to 6.92±0.02 ns FWHM (11.52±0.05 ns to 4.89±0.02 ns for unpaired photons).