Validation of non-protein/non-NA atomic structures #69
Description
Entry 215 presented a challenge for the validation pipeline. Because it's a full-atom structure, we used standard Molprobity analysis. However, because there were no proteins or nucleic acids the report came out essentially blank (no Ramachandran or side-chains outliers).
============================ Molprobity validation ============================
Geometry Restraints Library: GeoStd + Monomer Library
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.224 6.733 80239 Z=16.757
Angle : 6.278 97.518 108743 Z= 2.093
Chirality : 0.122 0.709 28044
Planarity : 0.104 0.326 460
Dihedral : 13.506 149.932 132182
Min Nonbonded Distance : 1.194
Molprobity Statistics.
All-atom Clashscore : None
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
Max deviation from planes:
Type MaxDev MeanDev LineInFile
=================================== Summary ===================================
Ramachandran outliers = 0.00 %
favored = 0.00 %
Rotamer outliers = 0.00 %
C-beta deviations = 0
RMS(bonds) = 0.2235
RMS(angles) = 6.28
MolProbity score = -1.00
Moreover, the clashscore calculation also failed:
Bad Clashes >= 0.4 Angstrom:
Sorry: PROBE output is empty. Model is not compatible with PROBE.
One way to approach such entries in the future might be to treat them as CG and do an excluded volume calculation. To do that we have to figure out two issues:
-
choose an appropriate atomic radii database, because
atom_sitetable doesn't provide radii -
tune the performance of the excluded volume calculation algorithm, because it wasn't designed to handle 250k+ particles systems.