This is an interactive, graphical report of a variety of MolProbity(1) validation metrics. This data was generated using a version of MolProbity 4.02 (non-cctbx version) modified to run on HTCondor with DAGMan at the BMRB.

The bar chart shows the distribution of the percentile scores for the different metrics for a given model. Percentiles are calculated using either the percent outliers or with the raw score (i.e. for clashscore and MolProbity score).

Click on one of the score bars to see how each model scores against a given metric.

Click on one of the model bars to see how that model compares against all models for a given metric.

Three versions of MolProbity scores are available: "original hydrogens", "MolProbity hydrogens with flip corrections", and "MolProbity hydrogens without flip corrections". For the latter two versions, hydrogens were removed from the structures and re-added using MolProbity. They were added using nuclear hydrogen bond lengths for NMR structures, and using electron cloud lengths for X-ray structures. "Flip corrections" indicate whether Asn/Gln/His sidechain orientations were corrected. Note that for structures without deposited hydrogens, the clashscore and MolProbity score for "original hydrogens" will be artificially and incorrectly low.

Core residues are calculated using the CYRANGE(2) program. Core scores are only available for protein ensembles.

For all of the scores that are shown as a percent, lower percent outliers is better.

The clashscore metric indicates how many steric clashes per 1000 atoms are present in the model. Lower clashscore is better.

The Rama metric indicates whether the phi-psi backbone dihedral angles of a protein backbone fall within acceptable ranges.

The rotamer metric indicates whether the chi dihedral angles of a protein sidechain fall within acceptable ranges.

The MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution. A lower MolProbity score in general means a "higher quality" structure.

The C-beta deviation metric is a measure of how tetrahedral the angles are around the C-alpha atom. A C-beta deviation of 0.25 A is considered an outlier.

The bad bonds and angles metrics indicates whether the bond lengths or bond angles are within acceptable ranges. Any bond length or angle that is greater or less than 4 standard deviations from the average are considered outliers.

The RNA pucker metric indicates whether the RNA backbone sugar puckers are modeled in a non-standard conformation.

The RNA backbone metric indicates whether the RNA backbone dihedral angles fall within ranges of a defined set of RNA backbone "rotamers".

This server is running the High Throughput Computing version of MolProbity 4.02.

References:
1) Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21.

2) Kirchner, Güntert. (2011) Objective identification of residue ranges for the superposition of protein structures. BMC Bioinformatics 12:170.