Hi Philipp,

The two FFTs introduce a scale factor equivalent to the number of grid points. Please try adding this code:

  x = abs(new_array).data()
  y = abs(very_new_array).data()
  lc = flex.linear_correlation(x, y)
  lc.show_summary()
  lr = flex.linear_regression(x, y)
  lr.show_summary()

The correlation coefficient should be 1.0 exactly, and the linear-regression slope is the same as the "total number of grid points" shown in the output:

total number of grid points: 345600
...
is_well_defined: True
mean_x: 43.9292797741
mean_y: 15181959.0899
coefficient: 1.0
is_well_defined: True
y_intercept: 5.1687812285e-07
slope: 345600.0

Ralf