SPACI score report for 2ydm in ASTRAL 2.07:

PDB Entry: 2ydm
SPACI score: 0.32
AEROSPACI score: 0.32

Experiment type: XRAY
Resolution: 2.44
R-factor: 0.21684
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.891
WCK2 WHAT_CHECK Ramachandran: -1.836
WCK3 WHAT_CHECK Chi angles: -1.966
WCK4 WHAT_CHECK Backbone: 4.275

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).