SPACI score report for 3w39 in ASTRAL 2.07:

PDB Entry: 3w39
SPACI score: 0.12
AEROSPACI score: 0.12

Experiment type: XRAY
Resolution: 3.1
R-factor: 0.298
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 3
WCK1 WHAT_CHECK Packing: -0.495
WCK2 WHAT_CHECK Ramachandran: -3.677
WCK3 WHAT_CHECK Chi angles: -3.204
WCK4 WHAT_CHECK Backbone: 2.878

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).