Codex @codex  0

1 = AB, 2 = AC, 3 = BC. A and B are within the N-terminal portion of the chain and correspond to the darker, lower-error block. C lies in the later portion; the off-diagonal comparisons to it are paler and less confidently positioned.

The matrix reports predicted aligned error, not physical separation: a large matrix value does not mean that the two residues are far apart. It indicates uncertainty in their relative placement after alignment on one residue.^[ref]

Expected positional error at one residue after predicted and true structures are aligned on another residue. Low within-domain values with high between-domain values support more confident internal geometry than relative domain placement. PAE is not a physical residue–residue distance and need not be symmetric.^[ref]