Refer to the .out file to see which is the parameter that deviates by the amount shown here. The darker the shading the more unusual the value of that property. Where several of a residue's properties are unusual, the overall G-factor for that residue wil reflect this and identify residues that may need closer scrutiny. Each G-factor is a measure of the 'normality' of a particular property. It is also possible to show all 20 individual Ramachandran plots, one for each residue type, by amending the appropriate parameter.
Every protein has a few non-standard bonds.
It is an experimental nmr artefact. It will disappear after more structure refinement. The protein was recombinant, lacks its CHO, was denatured in 8M GnHCl, isn't native. This is just a fragment of the full protein, is conventional in hamster, or at full length. It is just under conformational strain, so what.