SPACI score report for 1yj9 in ASTRAL 2.06:

PDB Entry: 1yj9
SPACI score: 0.25
AEROSPACI score: 0.25

Experiment type: XRAY
Resolution: 2.9
R-factor: 0.184
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 3
WCK1 WHAT_CHECK Packing: -4.056
WCK2 WHAT_CHECK Ramachandran: -4.144
WCK3 WHAT_CHECK Chi angles: -2.352
WCK4 WHAT_CHECK Backbone: 1.863

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).