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PROCHECK Operating Manual
Appendix D - Residue-by-residue listingAn example of a residue-by-residue listing is given here. The different parts of it are described in detail below. Some of the key figures are shown on a separate summary page.Part 1. Residue informationThe first part of the residue-by-residue listing (the .out file) deals with a number of stereochemical parameters, as will be described below.Explanatory notes. The first page gives some explanatory notes about the stereochemical parameters used. These notes include the "ideal" values, and corresponding standard deviations, against which the values calculated for your structure are compared. The "ideals" used here come from an analysis of 118 high-resolution structures performed by Morris et al. (1992), and are listed in Table 1 of Appendix A. Note that, the printing of this explanatory text can be suppressed, if required, by amending the parameter file procheck.prm (see Customizing the PROCHECK plots). Residue-by-residue information. The explanatory text is followed by an analysis of each of the stereochemical parameters for each residue in the structure. Each value is highlighted by asterisks and plus-signs if it deviates from the "ideal" by more than 1 standard deviation. An asterisk represents one standard deviation, and a plus-sign represents half a standard deviation. So, a highlight such as +*** indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal. Where the deviation is more than 4.5 standard deviations, its numerical value is shown instead: for example, *5.5* represents 5.5 standard deviations. The appearance of the listing can be altered to some extent by editing the parameter file procheck.prm (see Customizing the PROCHECK plots). This allows you to show, say, only the asterisks and not have the values themselves printed. You can also include only those values that are more than a given number of standard deviations from the ideal. The information shown for each residue is as follows:
Part 2. Main-chain bond lengths and bond anglesThe second part of the listing analyses the main-chain bond lengths and bond angles of your protein structure. As before, any deviations in the actual bond-lengths and bond angles from the "ideal" values are highlighted with asterisks and plus signs.At the end of this print-out, the different bond lengths and bond angles are summarised in two tables giving the minimum, maximum, and mean values of each type, together with their standard deviations. The "ideal" values used are given at the head of the listing (though the printing of these can be suppressed by amending the parameter file procheck.prm). The ideals are as determined from the analysis of small-molecule data by Engh & Huber (1991) and are shown in Table 2 of Appendix A.
Part 3. Bad contacts listingThe bad contacts listing shows the atom-pairs involved, the type of contact, and the separation between the two atoms. As already mentioned, bad contacts are defined here as any pair of non-bonded atoms that are at a distance of <=2.6Å from one another.
Part 4. Summary statistics and quality assessmentThe final part of the print-out reproduces the statistics printed on Plots 1, 4 and 5 (Sample Plots). It also gives an overall assessment of the structure's quality using the Morris et al. (1992) stereochemical classification scheme. Here a number from 1 to 4 is assigned to the structure for each of three separate stereochemical parameters (1 being the best and 4 the worst score). Finally, it prints an analysis of the various overall G-factors calculated for the structure. Any G-factors below -1.0 may indicate properties that need to be investigated more closely.
PROCHECK Operating Manual |