The charge recombination lifetime of photosynthetic reaction centers (RCs) increases significantly upon lengthy illumination, revealing nonequilibrium structural transitions in the protein cofactor system. This paper analyzes the charge recombination kinetics measured in isolated RCs following a systematic variation of actinic illumination times (pulses) from 0.1 s to hundreds of seconds. The maximum entropy method (MEM) was utilized for optimizing the fitting procedure to retrieve the relaxation spectrum from the experimental recombination kinetics curves. The MEM-assisted analysis reveals that each relaxation curve contains at least three peaks in the relaxation time-distribution domain. Two peaks are always observed, one near 0.1 s and the other near 1 s recombination times. A third peak appears after prolonged photoexcitation with a relaxation time significantly greater than 1 s, and the time of this peak increases further in recombination time as the photoexcitation pulse duration is increased. In addition to the shifts of the time constant distributions, the amplitudes of the distributions in the time domain spectrum demonstrate a variation in the quinone occupancy of the RCs. The results reported here support our previous claim that accumulation of slow conformational changes, triggered by charge separation events in the RCs, controls system dynamics and favors stabilization of more efficient functioning regimes of the RCs.