SPACI score report for 3qz9 in ASTRAL 2.06:

PDB Entry: 3qz9
SPACI score: 0.38
AEROSPACI score: 0.38

Experiment type: XRAY
Resolution: 2.4
R-factor: 0.186
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.031
WCK2 WHAT_CHECK Ramachandran: -0.454
WCK3 WHAT_CHECK Chi angles: -0.171
WCK4 WHAT_CHECK Backbone: 3.087

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).