As noted in comments, some nonbonded atoms in model 6R7M have more than 0.4 Angströms overlap, but are not tagged as clashing, e.g. the sidechain oxygens of THR29 and TYR73. This is because these overlaps are not unfavorable; that is, molprobity predicts hydrogen bonding between them. I couldn't find any specifics about how molprobity determines if a particular overlap is unfavorable. The best description I found is in the documentation of the chimera tool findclash:
The Clash/Contact Parameters control what will be considered a clash or contact. The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:
overlapij = rVDWi + rVDWj – dij – allowanceij
Find atoms with VDW overlap >=[ cutoff ] angstroms - pairs of atoms with overlap ≥ cutoff will be identified. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can also identify favorable contacts.
Subtract [ allowance ] from overlap for potentially H-bonding pairs - an allowance > 0 reflects the observation that atoms sharing a hydrogen bond can come closer to each other than would be expected from their VDW radii. The allowance is only subtracted for pairs comprised of a donor (or donor-borne hydrogen) and an acceptor. This is equivalent to using smaller radii to characterize hydrogen-bonding interactions (for example, see Li and Nussinov, Proteins 32:111 (1998)). As in FindHBond, possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair.
