run nac-before-opus-1
transcript /Users/yue/.claude/projects/-Users-yue-rietx-agent-runs-2026-10-01-wp1504-figure-work-nac-before-opus-1/14734043-6d5b-4a7f-a0e9-18f7f690882b.jsonl

   #  offset    dur    chars     tool       head
   1     3.3    3.3     5578     Bash       ls; head -60 nac.cif; P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/befor
   2    10.3    0.1     9396     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/lib/python3.12/site-
   3    12.9    0.1    19626     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/lib/python3.12/site-
   4    18.5    0.1    10399     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/lib/python3.12/site-
   5    27.1    3.4      200     Bash       ../../venvs/before/bin/python -c "
   6    40.5    4.8       55     Bash       cat > make_figure.py <<'EOF'
   7    47.9    0.0   490765     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/nac-before-opus-1/figure.png
   8    52.6    4.9       55     Bash       sed -i '' 's/size=1600, path/hidden=("Na", "Ca"), size=1600, path/' make_figure.py && ..
   9    59.5    0.1   478237     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/nac-before-opus-1/figure.png
  10    68.0    0.0     4279     Bash       sed -n 192,215p /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/before/lib/py
  11    78.2    3.1       55     Bash       ../../venvs/before/bin/python - <<'EOF'
  12    83.6    0.0   403456     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/nac-before-opus-1/figure.png
  13    89.2    1.5       49     Bash       ../../venvs/before/bin/python -c "

13 tool calls (10 Bash, 3 Read), 0 errored
14 API calls, 1.6 min wall, 0.51 M cache-read, 43 k cache-write, 7 k output, mean context 40 k
models: claude-opus-5-5 ×14

0 traced interpreter starts, 8 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 17.1 s (0.0%)
    build                                 5      1.4 s [max_atoms, max_atoms=5000]
    render_structure                      3      2.3 s [path, polyhedra, size, polyhedra=dict, size=1600, hidden]
