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number of reflection pairs

CORRECT.LP and XSCALE.LP do not explicitly state the number of reflection pairs that were used to calculated CC1/2.

However, the number can be calculated from the numbers available, for each resolution shell: there is the NUMBER OF UNIQUE REFLECTIONS (X), the NUMBER OF OBSERVED REFLECTIONS (Y), and the number of COMPARED reflections (Z) - the latter number is the total number of unmerged observations that contributed to the CC1/2 and the R-value calculations.

The number of reflections pairs that were used for the CC1/2 calculation can therefore be obtained as follows: Y-Z gives the number of unique reflections that have a single observation. The remaining (X-Y+Z) unique reflections have multiple observations, i.e. there were (X-Y+Z) reflection pairs that went into CC1/2.

why CC1/2 can be negative

There is a mathematical reason, explained in §4.1 of Assmann, G., Brehm, W. and Diederichs, K. (2016) Identification of rogue datasets in serial crystallography (2016) J. Appl. Cryst. 49, 1021-1028.