SPACI score report for 1y9z in ASTRAL 2.07:

PDB Entry: 1y9z
SPACI score: 0.66
AEROSPACI score: 0.66

Experiment type: XRAY
Resolution: 1.4
R-factor: 0.197
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.042
WCK2 WHAT_CHECK Ramachandran: -0.972
WCK3 WHAT_CHECK Chi angles: -0.343
WCK4 WHAT_CHECK Backbone: -0.539

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).