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

13FJ_A

Transforming growth factor beta-1 · P01137 · RCSB 13FJ · AF-P01137-F1 (v6)

0.7649

TM-score

0.7819

lDDT

3.187

Cα-RMSD Å

79.63

mean pLDDT

0.1265

FRAUD score

100.0%

novelty (max id)

Per-domain breakdown

Source	Domain	Range	Residues	TM	RMSD Å	mean Cα Δ	Name
PAE	PAE:1-390	1-390	112	0.7246	3.187	2.544

All metrics

Global fold agreement

TM-score (norm. experiment)	0.7649
TM-score (norm. model)	0.2536
TM-score (norm. shorter)	0.7649
TM-score (norm. longer)	0.2536
Cα-RMSD (Å)	3.187
backbone-RMSD (Å)	3.143
all-atom-RMSD (Å)	3.809
core-RMSD (Å)	0.882
core fraction	0.562
GDT_TS	61.16
GDT_HA	37.95
MaxSub	0.8552
structural overlap (3.5 Å)	0.7143

Local, superposition-free

lDDT	0.7819
contact-map Jaccard	0.6988
contact precision	0.8744
contact recall	0.7768
distance-matrix mean Δ (Å)	1.488
CAD-score (approx)	0.7971

Backbone & secondary structure

SS agreement Q3 (%)	94.64
mean Δφ (°)	16.9
mean Δψ (°)	24.4
torsion within 30° (frac)	0.7768
Rg experiment (Å)	17.85
Rg model (Å)	18.56
ΔRg (Å)	0.71

Confidence calibration

mean pLDDT	79.63
pLDDT↔lDDT Pearson	0.8578
pLDDT↔lDDT Spearman	0.8655
PAE↔observed Pearson	0.345
PAE overconfident frac	0.0
mean PAE (Å)	8.406
mean observed error (Å)	1.475

Context & headline

coverage of model	0.2872
coverage of experiment	1.0
seq identity aligned (%)	100.0
confidently-wrong residue frac	0.1161
FRAUD score	0.1265

Deposited 2026-05-04 · released 2026-06-17 · X-ray · 2.75 Å · closest pre-cutoff chain: 1KLA_1