The second section of the WHAT_CHECK output deals with a series of administrative problems that WHAT_CHECK, in principle, can cope with, but that are complicated enough to make it a wise thing to study yourself.
Sometimes we observe covalent bonds between independent chains. This is most common, and not at all unexepected for cysteine bridges. But in 1AAR we find something that, although most likely totally correct, might confuse WHAT_CHECK.
JRNL AUTH W.J.COOK,L.C.JEFFREY,M.CARSON,Z.CHEN,C.M.PICKART JRNL TITL STRUCTURE OF A DIUBIQUITIN CONJUGATE AND A MODEL JRNL TITL 2 FOR INTERACTION WITH UBIQUITIN CONJUGATING ENZYME (E2).
In this file the authors have observed a covalent bond between the backbone O (the OXT?) of the C-terminal glycine of the A chain and a the Nζ of lysine 48 of the B chain:
LINK C GLY A 76 NZ LYS B 48 1555 1555 1.31
Figure 4. The inter-chain glycine-lysine bond in 1AAR.
By the way, we do not yet have software in place to check the name of the remaining backbone O in the glycine. This is mainly because I don't know what are the rules for such cases.
All ocurrences of this error have been removed from the PDB in recent years. We leave the check in WHAT_CHECK to avoid that the error pops up again in the future.
The alternate atom related checks in WHAT_CHECK aren't as advanced yet as they should be. We are still working on it. If you get alternate atom related warnings, you better switch on your brain and do some visual inspection. If you use the YASARA WHAT IF TwinSet software, you can use the WHAT IF colouring options to separate the alternates and look by eye for inconsistencies.