SPACI score report for 3s9z in ASTRAL 2.06:

PDB Entry: 3s9z
SPACI score: 0.53
AEROSPACI score: 0.53

Experiment type: XRAY
Resolution: 1.79
R-factor: 0.178
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.93
WCK2 WHAT_CHECK Ramachandran: -1.211
WCK3 WHAT_CHECK Chi angles: -0.054
WCK4 WHAT_CHECK Backbone: 3.157

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).