The lDDT score
calculates the differences of the inter-atomic distances in model and target.
RMSD - Root-mean-square deviation for the subset of CA atoms from the model that correspond to the residues from target structure or a subdomain in the sequence-independent LGA superposition.
GDT_TS - GlobalDistanceTest_TotalScore
GDT_TS = (GDT_P1 + GDT_P2 + GDT_P4 + GDT_P8)/4,
where GDT_Pn denotes percent of residues under distance cutoff <= nÅ
TMscore measures the similarity of two protein structures.
(ref:Scoring function for ...)
Molprobity Clash Score - the number of all-atom steric overlaps > 0.4Å per 1000 atoms.
A good quality structure typically has clash-score < 20.
Cross-correlation coefficient (0-1) between a model and target density map values inside a mask calculated around the macromolecule.
CC(peaks): cross-correlation coefficient (0-1) between a model and target density map regions with the highest density values. The regions are defined by the N highest value points in the model-calculated map and the N highest value points in the experimental map.
MI: (Mutual Information) is a statistical measure that quantifies the extent of register between two binned densities relative to their background distributions.
SMOC (Segment Mander’s Overlap Coefficient) is a per-residue model-to-map fit measure, which calculates the Mander’s overlap coefficient for overlapping residue fragments and assigns the score to the central residue in the fragment. The score is in [0-1] range with higher values indicating a better fit (Note: The score can also take negative values when the density values in one of the maps are negative). The SMOC score is also calculated for the whole structure by averaging the per-residue scores.
Atom Inclusion reports the fraction of atoms within the target map contour. An atom is within the contour if its position in the map has a density value above the current threshold. Several variants of the score are calculated: AI:Orig.Model is calculated on all atoms present in the submitted model.
AI score calculated on backbone atoms only.