The Model-by-model violations shows each residue's upper- and lower-bound distance violations for each model in the ensemble.
The plots shows:-
The secondary structure plot shows a schematic representation of the Kabsch & Sander (1983) secondary structure assignments. The key just below the picture shows which structure is which. Beta strands are taken to include all residues with a Kabsch & Sander assignment of E, helices corresponds to both H and G assignments, while everything else is taken to be random coil.
The shading behind the schematic picture gives an approximation to the residue accessibilities. The approximation is a fairly crude one, being based on each residue's Ooi number (Nishikawa & Ooi, 1986). An Ooi number is a count of the number of other Calpha atoms within a radius of, in this case, 14Å of the given residue's own Calpha. Although crude, this does give a good impression of which parts of the structure are buried and which are exposed on the surface. Future versions of PROCHECK will include an accurate calculation of residue accessibility.
This histogram shows a simple representation of the numbers of distance restraints that each residue has. The number at the top of the stack gives this number. Intra-residue restraints are counted once only to give this number, and how many there are of them is shown in brackets just below.
The highlighted regions illustrate the degree of violation of each residue's restraints. The regions are made up of bars stacked on top of one another, the number of bars corresponding to the number of restraints that are violated. The width of each bar is proportional to the number of models in which the restraint is violated. The lower bars are those violated in all models, and these stretch the full width of the residue's histogram bar. The higher bars correspond to those restraints violated in fewer and fewer numbers of models, and so stretch across only part of the width.
The plot for each model shows all the restraint violations for each residue.
The shape of each data point corresponds to the type of distance restraint, as follows:-
The colour of each data point corresponds to the class of distance restraint, as defined in the General parameters. The restraints are also labelled L, M or S according to this class (ie Long, Medium or Short).
Positive values correspond to upper-bound violations, while negative values correspond to lower-bound violations.
The main options for the Model-by-model violations are:-
These options can be altered by editing the parameter file, procheck_nmr.prm, as described here.