SPACI score report for 3d39 in ASTRAL 2.03:

PDB Entry: 3d39
SPACI score: 0.27
AEROSPACI score: 0.27

Experiment type: XRAY
Resolution: 2.81
R-factor: 0.201
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.235
WCK2 WHAT_CHECK Ramachandran: -2.785
WCK3 WHAT_CHECK Chi angles: -3.916
WCK4 WHAT_CHECK Backbone: 2.058

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).