What is a good MolProbity score?
A value -4 < x < 2 is considered appropriate for normal structures. This pre-print provides more details: Link. Molprobity score: Combines all the geometric scores into a single value to suggest quality. Lower values and higher percentiles are better.
What does MolProbity score mean?
“[The MolProbity score] is a log-weighted combination of the clashscore, percentage Ramachandran not favored and percentage bad side-chain rotamers, giving one number that reflects the crystallographic resolution at which those values would be expected.
What is a poor Rotamer?
Above the 1% level sets of χ values are assigned to named rotamers; below 1% they are designated as poor rotamers, not outliers, since they are disfavored but quite possible if stabilized by tight packing or a couple of good hydrogen bonds.
What are favored rotamers?
In the new system developed here, a score of <0.3% qualifies as a rotamer outlier – its score is worse than 99.7% of the good data. Scores ≥ 0.3% and < 2.0% are considered allowed while those ≥ 2.0% are considered favored, as is traditional for Ramachandran criteria [18, 28].
What are RSRZ outliers?
The RSR Z-score (RSRZ) is a normalisation of RSR specific to a residue type and a resolution bin (Kleywegt et al., 2004). RSRZ is calculated only for standard amino acids and nucleotides in protein, DNA and RNA chains. A residue is considered an RSRZ outlier if its RSRZ value is greater than 2.
What is a Ramachandran outlier?
Ramachandran outliers are those amino acids with non-favorable dihedral angles, and the Ramachandran plot is a powerful tool for making those evident. Most of the time, Ramachandran outliers are a consequence of mistakes during the data processing.
How do you cite MolProbity?
Cite MolProbity: Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography.
What is RSRZ?
The RSR Z-score (RSRZ) is a normalisation of RSR specific to a residue type and a resolution bin (Kleywegt et al., 2004). RSRZ is calculated only for standard amino acids and nucleotides in protein, DNA and RNA chains. This metric is calculated as the average score of all nucleotides in the entry.
What does the Ramachandran plot tell us?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
What is CaBLAM outlier?
As a general rule, CaBLAM outliers usually indicate a problem with the orientations for one or more peptide planes. Look for a way to reorient the peptide either to remove clashes or establish hydrogen bonds.