pLDDT
The pLDDT value is assigned to each individual residue and stored in coordinate files instead of temperature factors. Different from temperature factors, high values indicate high confidence in atomic positions, and low values low confidence. This value is named pLDDT because it predicts the so-called LDDT value (Local Distance Difference Test, [1]), a way to characterize the difference of two related conformations without aligning the structures.
Expected distance error
Alphafold also predicts the expected error in the distance of two residues. Thus, this is a 2-dimensional (pairwise) data set. The plot of the data is shown below. On the right, you can see the mapped by color on the second residue. If you hover over the residue, it will show the estimated distance error. It becomes apparent that the distance between residue 1000 and residues in the N-terminal part of the protein are ill-defined. However, if you show the expected errors to residue 400 (by using the links below), the N-terminal domain is well-defined in isolation. It is the relative domain orientation that is not well predicted. If you explore some other of the residues provided below, you will discover that there are subdomains within the N-terminal as well as the C-terminal domain. This is experimentally supported.
Residues on the apparent domain interface
