SPACI score report for 3n9r in ASTRAL 2.01:

PDB Entry: 3n9r
SPACI score: 0.56
AEROSPACI score: 0.56

Experiment type: XRAY
Resolution: 1.8
R-factor: 0.162
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 1
WCK1 WHAT_CHECK Packing: -0.391
WCK2 WHAT_CHECK Ramachandran: 0.056
WCK3 WHAT_CHECK Chi angles: -0.345
WCK4 WHAT_CHECK Backbone: 0.601

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).