SPACI score report for 2qy9 in ASTRAL 2.07:

PDB Entry: 2qy9
SPACI score: 0.48
AEROSPACI score: 0.48

Experiment type: XRAY
Resolution: 1.9
R-factor: 0.188
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.569
WCK2 WHAT_CHECK Ramachandran: 0.033
WCK3 WHAT_CHECK Chi angles: 0.265
WCK4 WHAT_CHECK Backbone: -0.352

Note: Here are links to pages about PROCHECK and WHAT_CHECK.

Here is the full WHAT_CHECK report on this protein (linked from the WHAT_CHECK site).