run gypsum-after-opus-1
transcript /Users/yue/.claude/projects/-Users-yue-rietx-agent-runs-2026-10-01-wp1504-figure-work-gypsum-after-opus-1/d18c2cf6-3240-4eaf-aea3-be48053f1f18.jsonl

   #  offset    dur    chars     tool       head
   1     2.8    3.3     1036     Bash       ls; cat gypsum.cif; P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/b
   2     9.5   10.6     5612     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/bin/python; $P -c "im
   3    22.4    0.1     8822     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/lib/python3.12/site-p
   4    26.3    0.1    15220     Bash       D=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/lib/python3.12/site-p
   5    35.7    4.9      221     Bash       cat > draw.py <<'EOF'
   6    43.4    0.1   201044     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/gypsum-after-opus-1/figure.png
   7    49.4    3.8     2185     Bash       P=/Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/venvs/after/bin/python; $P -c "
   8    58.0    5.7      326     Bash       sed -i '' 's/bond_tolerance=s3.BOND_TOLERANCE)/bond_tolerance=s3.BOND_TOLERANCE,\n      
   9    65.7    0.0   388452     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/gypsum-after-opus-1/figure.png

9 tool calls (7 Bash, 2 Read), 0 errored
10 API calls, 1.2 min wall, 0.26 M cache-read, 31 k cache-write, 4 k output, mean context 29 k
models: claude-opus-5-5 ×10

0 traced interpreter starts, 11 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 23.6 s (0.0%)
    build                                 3      0.1 s [bond_tolerance, probability, max_atoms, centres, disorder, ligands]
    keep                                  2      0.0 s
    periodicity                           2      0.0 s
    plane                                 2      0.0 s [width]
    render_structure                      2      2.2 s [path, size, view, view=c, size=1600, size=2000]
