---
title: ESMFold troubleshooting
description: Fix ESMFold failures — non-standard residues like B, J, O and X, the 10-2,500 limit, timeouts on long chains, low pLDDT, and a missing PAE artifact.
---

When [ESMFold](/docs/esmfold) fails to submit or returns a structure that looks wrong, this page covers the common failure modes — from sequence validation and length limits to long runtimes, low pLDDT confidence, and missing PAE outputs.

## Common issues and fixes

ESMFold uses the ESM-2 language model to predict structures directly from sequences. Understanding common issues can help you get better predictions and interpret results appropriately.

## Sequence validation failures

- Ensure only the 20 standard amino acids are present; remove `B`, `J`, `O`,
  `U`, `X`, or `Z`.
- Remove whitespace, numbers, and FASTA comments inside the sequence body.
- Check that sequence length is within the supported limit (10-2,500 residues).

## Long runtimes or timeouts

- Split very long sequences into domains if biological context allows.
- Reduce batch size to one sequence per job for long proteins.
- Verify cluster capacity and retry during lower-traffic windows if queues are
  long.

## Low pLDDT or high PAE

- Flag low-confidence regions (<50 pLDDT) as disordered instead of forcing rigid
  models.
- Consider trimming long unstructured tails and re-running to improve core
  confidence.
- Use external secondary structure or disorder predictors to corroborate
  low-confidence zones.
- Remember that ESMFold's pLDDT scores are calibrated to correlate with structural accuracy; consistently low scores often indicate genuinely disordered regions rather than model failure.

## Novel or designed sequences

Because ESMFold does not use MSA, it can predict structures for sequences without homologs. However:

- Designed proteins or de novo sequences may have lower confidence if they differ significantly from natural protein distributions
- Synthetic peptides with non-natural features may produce unreliable predictions
- For engineered proteins, focus on high-pLDDT regions and validate experimentally when possible

## Missing PAE artifacts

- Ensure `returnPaE` is enabled; it is `true` by default.
- If outputs are still missing, re-run with a smaller sequence to rule out
  memory constraints.

## Still stuck?

- Provide the job ID, FASTA header, sequence length, and any custom parameters
  (`maxTokens`, `seed`, `returnPaE`).
- Share whether the issue is validation, runtime, or confidence-related to speed
  up support.

## Read next