SPACI score report for 2yx9 in ASTRAL 2.06:

PDB Entry: 2yx9
SPACI score: 0.49
AEROSPACI score: 0.49

Experiment type: XRAY
Resolution: 1.68
R-factor: 0.245
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.165
WCK2 WHAT_CHECK Ramachandran: -1.452
WCK3 WHAT_CHECK Chi angles: 0.313
WCK4 WHAT_CHECK Backbone: -0.562

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).