SPACI score report for 2yd8 in ASTRAL 2.07:

PDB Entry: 2yd8
SPACI score: 0.45
AEROSPACI score: 0.45

Experiment type: XRAY
Resolution: 2.05
R-factor: 0.1965
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 1
WCK1 WHAT_CHECK Packing: -2.454
WCK2 WHAT_CHECK Ramachandran: -1.696
WCK3 WHAT_CHECK Chi angles: -0.843
WCK4 WHAT_CHECK Backbone: 1.783

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).