SPACI score report for 1ya9 in ASTRAL 2.07:

PDB Entry: 1ya9
SPACI score: 0.4
AEROSPACI score: 0.4

Experiment type: XRAY
Resolution: 2.09
R-factor: 0.215
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 1
WCK1 WHAT_CHECK Packing: 0.418
WCK2 WHAT_CHECK Ramachandran: -0.451
WCK3 WHAT_CHECK Chi angles: -2.88
WCK4 WHAT_CHECK Backbone: 0.205

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).