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new PDB depositions vs. their blind AlphaFold predictions — a running test of "is folding solved?"

31EP_A

Lon protease homolog, mitochondrial · P36776 · RCSB 31EP · AF-P36776-F1 (v6)

0.8125

TM-score

0.9218

lDDT

4.346

Cα-RMSD Å

87.93

mean pLDDT

0.2271

FRAUD score

45.9%

novelty (max id)

Per-domain breakdown

Source	Domain	Range	Residues	TM	RMSD Å	mean Cα Δ	Name
PAE	PAE:1-959	1-959	537	0.8055	4.346	3.935

All metrics

Global fold agreement

TM-score (norm. experiment)	0.8125
TM-score (norm. model)	0.4848
TM-score (norm. shorter)	0.8125
TM-score (norm. longer)	0.4848
Cα-RMSD (Å)	4.346
backbone-RMSD (Å)	4.336
all-atom-RMSD (Å)	4.531
core-RMSD (Å)	1.365
core fraction	0.246
GDT_TS	42.69
GDT_HA	18.2
MaxSub	0.9191
structural overlap (3.5 Å)	0.46

Local, superposition-free

lDDT	0.9218
contact-map Jaccard	0.8407
contact precision	0.9095
contact recall	0.9175
distance-matrix mean Δ (Å)	2.633
CAD-score (approx)	0.8563

Backbone & secondary structure

SS agreement Q3 (%)	91.43
mean Δφ (°)	12.7
mean Δψ (°)	14.2
torsion within 30° (frac)	0.8734
Rg experiment (Å)	32.8
Rg model (Å)	30.73
ΔRg (Å)	2.07

Confidence calibration

mean pLDDT	87.93
pLDDT↔lDDT Pearson	0.7052
pLDDT↔lDDT Spearman	0.5565
PAE↔observed Pearson	0.6509
PAE overconfident frac	0.0004
mean PAE (Å)	9.448
mean observed error (Å)	2.628

Context & headline

coverage of model	0.56
coverage of experiment	1.0
seq identity aligned (%)	100.0
confidently-wrong residue frac	0.4004
FRAUD score	0.2271

Deposited 2026-05-29 · released 2026-06-17 · EM · 2.54 Å · closest pre-cutoff chain: 3M6A_1