SPACI score report for 3d9c in ASTRAL 2.03:

PDB Entry: 3d9c
SPACI score: 0.34
AEROSPACI score: 0.34

Experiment type: XRAY
Resolution: 2.3
R-factor: 0.218
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.474
WCK2 WHAT_CHECK Ramachandran: -0.976
WCK3 WHAT_CHECK Chi angles: -1.634
WCK4 WHAT_CHECK Backbone: 0.282

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).