SPACI score report for 1yz9 in ASTRAL 2.07:

PDB Entry: 1yz9
SPACI score: 0.4
AEROSPACI score: 0.4

Experiment type: XRAY
Resolution: 2.1
R-factor: 0.208
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.391
WCK2 WHAT_CHECK Ramachandran: -0.533
WCK3 WHAT_CHECK Chi angles: -0.603
WCK4 WHAT_CHECK Backbone: 0.506

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).