SPACI score report for 3jya in ASTRAL 2.07:

PDB Entry: 3jya
SPACI score: 0.39
AEROSPACI score: 0.39

Experiment type: XRAY
Resolution: 2.1
R-factor: 0.234
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: 0.118
WCK2 WHAT_CHECK Ramachandran: -0.544
WCK3 WHAT_CHECK Chi angles: -0.145
WCK4 WHAT_CHECK Backbone: -0.313

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).