SPACI score report for 1ygd in ASTRAL 2.08:

PDB Entry: 1ygd
SPACI score: 0.28
AEROSPACI score: 0.28

Experiment type: XRAY
Resolution: 2.73
R-factor: 0.198
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.574
WCK2 WHAT_CHECK Ramachandran: -4.282
WCK3 WHAT_CHECK Chi angles: -3.565
WCK4 WHAT_CHECK Backbone: 0.727

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).