Experimental difference maps near the p-coumaric acid (pCA) chromophore in PYP averaged through various time intervals and at various temperatures and contoured at ±3σ in blue and red and ±4σ in cyan and white, respectively. Averaging was performed solely to enhance the appearances of the maps and to illustrate signature features of the intermediate states. (a) Average difference map obtained from the eight earliest difference maps from 2 to 8 ns at T < 263 K. Features of three intermediates, IT, ICT and pR1, contribute to the same set of maps. (b) Average difference map obtained from 20 difference maps at T < 263 K from 256 ns to 64 µs. Features of two intermediates, pR1 and pR2, contribute. Feature α is the strongest in all maps at up to 12σ above the noise. It denotes the displacement of the Cys69 S atom in pR2. (c) Average difference map obtained from 20 difference maps in the millisecond time range at 303 < T < 323 K. Main features are found near the chromophore and on the distal loop.