run nac-before-opus-2
transcript /Users/yue/.claude/projects/-private-tmp-claude-501--Users-yue-Code-rietx-0433c291-1037-42b9-8cb7-5377547150b7-scratchpad-1504-root-work-nac-before-opus-2/ce06b2ad-c779-4a2b-b847-9ed915420d24.jsonl

   #  offset    dur    chars     tool       head
   1     3.2    1.5     4624     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   2     6.9    0.0     2251     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   3    10.1    0.0     8343     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   4    14.2    0.0      740     Bash       cat nac.cif; cd ../../venvs/before/lib/python3.12/site-packages/rietx; grep -n "MAX_ATOM
   5    18.0    0.9      480     Bash       P=../../venvs/before/bin/python; $P -c "
   6    26.7    1.4       42     Bash       P=../../venvs/before/bin/python; cat > make_fig.py <<'EOF'
   7    30.1    0.0   505837     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
   8    36.7    2.0      585     Bash       P=../../venvs/before/bin/python; $P - <<'EOF'
   9    41.6    0.8      183     Bash       P=../../venvs/before/bin/python; $P - <<'EOF'
  10    44.9    0.0   461373     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
  11    45.6    0.0   456009     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
  12    51.2    0.8      600     Bash       P=../../venvs/before/bin/python; $P - <<'EOF'
  13    53.8    0.0     3063     Bash       sed -n 235,300p ../../venvs/before/lib/python3.12/site-packages/rietx/viz/figure3d/scene
  14    61.4    1.3       26     Bash       P=../../venvs/before/bin/python; rm -f try_*.png; cat > render_fig.py <<'EOF'
  15    64.9    0.0   423180     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat

15 tool calls (11 Bash, 4 Read), 0 errored
15 API calls, 1.2 min wall, 0.41 M cache-read, 32 k cache-write, 6 k output, mean context 29 k
models: claude-opus-5-5 ×15

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 7.6 s (0.0%)
    build                                 7      0.5 s [bond_tolerance, probability]
    render_structure                      4      1.9 s [boundary, path, polyhedra, size, polyhedra=dict, size=1600]
