[2025-09-30T01:56:12.109731] [QUERYOME] Starting research for query 401: 'Instructions: 
 Answer the question below. First, respond with the single best option letter (A, B, C, or D). Then provide a concise reasoning (1–3 sentences). Use both the retrieved evidence and your own medical knowledge to choose the most accurate answer. 

Question:
Which of the following amino acids does not include post-translational modification? 

Options:
{'A': 'Selenocysteine', 'B': 'Triiodothyronine', 'C': 'Hydroxyproline', 'D': 'Hydroxylysine'}'
[2025-09-30T01:56:12.166530] [PI] Starting research for query: 'Instructions: 
 Answer the question below. First, respond with the single best option letter (A, B, C, or D). Then provide a concise reasoning (1–3 sentences). Use both the retrieved evidence and your own medical knowledge to choose the most accurate answer. 

Question:
Which of the following amino acids does not include post-translational modification? 

Options:
{'A': 'Selenocysteine', 'B': 'Triiodothyronine', 'C': 'Hydroxyproline', 'D': 'Hydroxylysine'}'
[2025-09-30T01:56:12.168320] Saving text to bench_final/run1/medmcqa/medmcqa_400/pi_initial_prompt.txt
[2025-09-30T01:56:12.172518] [PI] Calling o3 for initial analysis...
[2025-09-30T01:56:24.853516] [PI] Reasoning iteration 1
[2025-09-30T01:56:24.855208] [PI reasoning] **Selecting amino acids without PTM**

I need to determine which amino acid does not undergo post-translational modification. Among the options: Selenocysteine, Triiodothyronine, Hydroxyproline, Hydroxylysine. Selenocysteine is co-translationally incorporated, while Triiodothyronine results from iodination and is still considered a post-translational modification. Hydroxyproline and Hydroxylysine arise from hydroxylation of specific residues, indicating they too involve PTM. Thus, the answer is A: Selenocysteine, as it is added during translation, not modified afterwards. I should gather supporting evidence for this.
[2025-09-30T01:56:24.863493] [PI] Executing function call 1: hybrid_search
[2025-09-30T01:56:24.864991] [PI] Function arguments: {'query': 'Selenocysteine is co-translationally inserted and not a post translational modification', 'k': 5, 'faiss_weight': 0.7, 'bm25_weight': 0.3, 'use_rrf': True}
[2025-09-30T01:56:24.866950] Saving JSON to bench_final/run1/medmcqa/medmcqa_400/pi_iteration_1_tool_call_2_hybrid_search.json
[2025-09-30T01:57:23.778970] [PI] Function hybrid_search executed successfully
[2025-09-30T01:57:23.781279] Saving JSON to bench_final/run1/medmcqa/medmcqa_400/pi_iteration_1_tool_result_2_hybrid_search.json
[2025-09-30T01:57:23.787030] [PI] Continuing reasoning with 1 function responses...
[2025-09-30T01:57:26.607944] [PI] Reasoning iteration 2
[2025-09-30T01:57:26.609430] [PI] Executing function call 1: hybrid_search
[2025-09-30T01:57:26.611552] [PI] Function arguments: {'query': 'Hydroxyproline post translational modification collagen proline hydroxylation', 'k': 5, 'faiss_weight': 0.6, 'bm25_weight': 0.4, 'use_rrf': True}
[2025-09-30T01:57:26.613049] Saving JSON to bench_final/run1/medmcqa/medmcqa_400/pi_iteration_2_tool_call_2_hybrid_search.json
[2025-09-30T01:58:34.136250] [PI] Function hybrid_search executed successfully
[2025-09-30T01:58:34.138306] Saving JSON to bench_final/run1/medmcqa/medmcqa_400/pi_iteration_2_tool_result_2_hybrid_search.json
[2025-09-30T01:58:34.143669] [PI] Continuing reasoning with 1 function responses...
[2025-09-30T01:58:36.936703] [PI] Reasoning iteration 3
[2025-09-30T01:58:36.937695] [PI] Executing function call 1: hybrid_search
[2025-09-30T01:58:36.939043] [PI] Function arguments: {'query': 'Triiodothyronine formed by post translational iodination of tyrosine residues in thyroglobulin', 'k': 5, 'faiss_weight': 0.6, 'bm25_weight': 0.4, 'use_rrf': True}
[2025-09-30T01:58:36.941192] Saving JSON to bench_final/run1/medmcqa/medmcqa_400/pi_iteration_3_tool_call_2_hybrid_search.json
[2025-09-30T01:59:43.807514] [PI] Function hybrid_search executed successfully
[2025-09-30T01:59:43.808992] Saving JSON to bench_final/run1/medmcqa/medmcqa_400/pi_iteration_3_tool_result_2_hybrid_search.json
[2025-09-30T01:59:43.817624] [PI] Continuing reasoning with 1 function responses...
[2025-09-30T01:59:50.326641] [PI] Reasoning iteration 4
[2025-09-30T01:59:50.331077] [PI] No function calls found in response
[2025-09-30T01:59:50.336059] [PI] No more function calls - research complete
[2025-09-30T01:59:50.337566] Saving text to bench_final/run1/medmcqa/medmcqa_400/pi_final_answer.txt
[2025-09-30T01:59:50.341547] [QUERYOME] Query completed successfully
