run chains-fixed-opus-3
transcript /Users/yue/.claude/projects/-private-tmp-claude-501--Users-yue-Code-rietx-0433c291-1037-42b9-8cb7-5377547150b7-scratchpad-1504-root-work-chains-fixed-opus-3/470065cb-9581-4dd0-b407-d31b268e9b61.jsonl

   #  offset    dur    chars     tool       head
   1     2.0    0.0       22     Skill      skill
   2     6.4    0.1     7341     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   3    10.9    1.5     4732     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   4    25.9    1.8     1275     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   5    30.9    0.0    25964     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
   6    40.1    1.9      352     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   7    48.0    1.4      242     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   8    51.9    0.0    27656     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
   9    57.5    0.0    88172     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
  10    65.7    1.8      303     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
  11    70.7    0.0    27132     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
  12    73.4    0.0       21     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc

12 tool calls (7 Bash, 4 Read, 1 Skill), 0 errored
13 API calls, 1.3 min wall, 0.43 M cache-read, 31 k cache-write, 5 k output, mean context 35 k
models: claude-opus-5-5 ×13

0 traced interpreter starts, 23 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 7.1 s (0.0%)
    build                                10      0.1 s [bond_tolerance, centres, disorder, ligands, max_atoms, probability]
    keep                                  4      0.0 s [complete, complete=True]
    render_structure                      9      1.6 s [path, size, up, view, up=[0, 0, 1], boundary]
