SPACI score report for 1y09 in ASTRAL 2.07:

PDB Entry: 1y09
SPACI score: 0.42
AEROSPACI score: 0.42

Experiment type: XRAY
Resolution: 2.25
R-factor: 0.161
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 1
WCK1 WHAT_CHECK Packing: -0.119
WCK2 WHAT_CHECK Ramachandran: -1.302
WCK3 WHAT_CHECK Chi angles: -2.378
WCK4 WHAT_CHECK Backbone: 1.013

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).