I found that one can get RSRZ to go way down by loosening the geometry restraints. The result is a crappy structure and I don't recommend doing that, but it does get all the atoms crammed into some sort of density.
RSRZ, in my most humble of opinions, seems like one of those statistics that is far more useful in theory than reality. Particularly for medium-resolution structures, the fit of each entire side chain to the density is likely to be imperfect because the density is imperfect, especially toward the tips of those side chains. Then again, it can be a good flag for bits of the structure worth a second look in rebuilding. ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Matthew Bratkowski [mab...@cornell.edu] Sent: Tuesday, November 22, 2016 10:12 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports Hello all, I was wondering if anyone knew how the RSRZ score was calculated in the protein data bank validation reports and how useful of a metric this actually is for structure validation? I am trying to improve this score on a structure that I am working on, but I'm not really sure where to begin. From my understanding, the score is based on the number of RSRZ outliers with a score >2. In my case, I have several residues with scores between 2 and 4, but at least by eye, fit to the electron density does not look that bad. Hence, I can't justify deleting them to try to improve the score. If the score is just based on percent of outlier residues, then for instance wouldn't a structure with say 20 residues modeled with no corresponding electron density have the same score as a structure with 20 residues with RSRZ values of say 2.5? I was also wondering how the resolution of the structure relates to the score? Glancing through several pdb validation reports, I noticed some structure with low resolution (3.5 A or lower) with relatively high scores, while others with high resolution (2 A or higher) getting low scores. It is reasonable to assume that a structure of lower than 3.5 A would be missing several side chains and may also have some ambiguous main chain electron density, which should in theory increase the RSRZ score. While of course every structure is different and the quality of it due to the rigor of the person building the model, I was wondering if there were any general trends related to resolution and RSRZ score. Thanks, Matt
