run gypsum-fixed-opus-2
transcript /Users/yue/.claude/projects/-private-tmp-claude-501--Users-yue-Code-rietx-0433c291-1037-42b9-8cb7-5377547150b7-scratchpad-1504-root-work-gypsum-fixed-opus-2/c028322a-5a11-493c-9610-2973334eb350.jsonl

   #  offset    dur    chars     tool       head
   1     1.9    0.0       22     Skill      skill
   2     4.4    0.1     7510     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   3     9.9    1.5      779     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   4    16.7    1.6     1012     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   5    21.4    0.0    25676     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
   6    31.2    1.1      445 ERR Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   7    35.2    1.5      366     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   8    42.4    2.2      563     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
   9    46.6    0.0   105928     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
  10    53.0    1.6      537     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc
  11    56.7    0.0    93856     Read       /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/scrat
  12    59.4    0.0       29     Bash       cd /private/tmp/claude-501/-Users-yue-Code-rietx/0433c291-1037-42b9-8cb7-5377547150b7/sc

12 tool calls (8 Bash, 3 Read, 1 Skill), 1 errored
13 API calls, 1.1 min wall, 0.41 M cache-read, 29 k cache-write, 5 k output, mean context 33 k
models: claude-opus-5-5 ×13

0 traced interpreter starts, 27 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 8.0 s (0.0%)
    build                                11      0.1 s [bond_tolerance, centres, disorder, ligands, max_atoms, probability]
    keep                                  6      0.0 s [complete, complete=True]
    periodicity                           3      0.0 s
    render_structure                      5      1.5 s [size, up, view, up=b, view=c, path]
    select                                2      0.0 s [element]
