@possumtech/rummy 2.1.0 → 2.2.0

package/audit/sweep/protein-assembly/logs.md

@@ -0,0 +1,747 @@
+# logs.md
+
+Chronological index of run entries — paths and brief titles only.
+
+Full bodies live in `turns/turn_NNN.md`. Verifier source in `verifier.md`. Files the model wrote in `deliverables.md`. Shell commands in `tools.md`. Web research in `searches.md`.
+
+
+| id | path | title |
+| --- | --- | --- |
+| 1 | `run://cli_1777680143286` | [run] |
+| 2 | `instructions://system` | [instructions] |
+| 3 | `prompt://1` | [prompt] I am planning an experiment where I'll be testing the stability of dihydrofol… |
+| 4 | `repo://overview` | [repo] |
+| 5 | `assistant://1` | [assistant emission — see turns/] |
+| 6 | `system://1` | [system prompt] |
+| 7 | `user://1` | [user packet (assembled context)] |
+| 8 | `model://1` | [model usage record] |
+| 9 | `reasoning://1` | [think] Decomposing the prompt into key unknowns: need to identify files (pdb_ids.txt… |
+| 10 | `unknown://experiment/fret_filter` | [unknown] excitation 505nm emission 610nm filter cube |
+| 11 | `log://turn_1/set/unknown%3A/experiment/fret_filter` | [set] unknown://experiment/fret_filter |
+| 12 | `unknown://fusion/order` | [unknown] antibody binder - donor - dhfr - acceptor - molecule binder |
+| 13 | `log://turn_1/set/unknown%3A/fusion/order` | [set] unknown://fusion/order |
+| 14 | `unknown://fusion/components` | [unknown] GS linkers 5-20aa between subproteins, no terminal linkers, no start/stop/Met |
+| 15 | `log://turn_1/set/unknown%3A/fusion/components` | [set] unknown://fusion/components |
+| 16 | `unknown://files/pdb_ids` | [unknown] /app/pdb_ids.txt contents |
+| 17 | `log://turn_1/set/unknown%3A/files/pdb_ids` | [set] unknown://files/pdb_ids |
+| 18 | `unknown://files/antibody_fasta` | [unknown] /app/antibody.fasta heavy/light chains, target antigen sequence most common v… |
+| 19 | `log://turn_1/set/unknown%3A/files/antibody_fasta` | [set] unknown://files/antibody_fasta |
+| 20 | `unknown://files/plasmid_gb` | [unknown] /app/plasmid.gb DHFR sequence |
+| 21 | `log://turn_1/set/unknown%3A/files/plasmid_gb` | [set] unknown://files/plasmid_gb |
+| 22 | `unknown://api/fpbase_donor` | [unknown] FPbase protein with excitation peak ~505nm, sequence from pdb_ids.txt |
+| 23 | `log://turn_1/set/unknown%3A/api/fpbase_donor` | [set] unknown://api/fpbase_donor |
+| 24 | `unknown://api/fpbase_acceptor` | [unknown] FPbase protein with emission peak ~610nm, sequence from pdb_ids.txt |
+| 25 | `log://turn_1/set/unknown%3A/api/fpbase_acceptor` | [set] unknown://api/fpbase_acceptor |
+| 26 | `unknown://api/pdb_sequences` | [unknown] PDB FASTA sequences for proteins in pdb_ids.txt |
+| 27 | `log://turn_1/set/unknown%3A/api/pdb_sequences` | [set] unknown://api/pdb_sequences |
+| 28 | `unknown://binder/molecule` | [unknown] Protein from pdb_ids.txt that binds this SMILES molecule |
+| 29 | `log://turn_1/set/unknown%3A/binder/molecule` | [set] unknown://binder/molecule |
+| 30 | `unknown://binder/antibody_target` | [unknown] Most common variant sequence of protein antibody in antibody.fasta binds to |
+| 31 | `log://turn_1/set/unknown%3A/binder/antibody_target` | [set] unknown://binder/antibody_target |
+| 32 | `unknown://sequence/dhfr` | [unknown] DHFR sequence from plasmid.gb, remove N-Met |
+| 33 | `log://turn_1/set/unknown%3A/sequence/dhfr` | [set] unknown://sequence/dhfr |
+| 34 | `unknown://constraints/gc_content` | [unknown] GC 30-70% in 50nt windows, total <3000nt |
+| 35 | `log://turn_1/set/unknown%3A/constraints/gc_content` | [set] unknown://constraints/gc_content |
+| 36 | `log://turn_1/update/prompt_decomposed` | [update status=145] prompt decomposed |
+| 39 | `assistant://2` | [assistant emission — see turns/] |
+| 40 | `system://2` | [system prompt] |
+| 41 | `user://2` | [user packet (assembled context)] |
+| 42 | `model://2` | [model usage record] |
+| 43 | `reasoning://2` | [think] * Distillation stage: resolve unknowns by discovering sources (app files, API… |
+| 44 | `log://turn_2/get/app` | [get] app/ |
+| 45 | `log://turn_2/get/app/pdb_ids.txt` | [get] app/pdb_ids.txt |
+| 46 | `log://turn_2/get/app/antibody.fasta` | [get] app/antibody.fasta |
+| 47 | `log://turn_2/get/app/plasmid.gb` | [get] app/plasmid.gb |
+| 48 | `log://turn_2/get/app/**` | [get] app/** |
+| 49 | `log://turn_2/update/discovering_source_files_for_distillation` | [update status=155] discovering source files for distillation |
+| 52 | `assistant://3` | [assistant emission — see turns/] |
+| 53 | `system://3` | [system prompt] |
+| 54 | `user://3` | [user packet (assembled context)] |
+| 55 | `model://3` | [model usage record] |
+| 56 | `reasoning://3` | [think] * In Distillation Stage: Need to discover source files from unknowns (app/pdb… |
+| 57 | `content://3` | [content] |
+| 58 | `log://turn_3/env/ls_-la_/app` | [env] ls -la /app |
+| 60 | `env://turn_3/ls_-la_/app_1` | [env] |
+| 61 | `env://turn_3/ls_-la_/app_2` | [env] |
+| 64 | `log://turn_3/env/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20` | [env] find /app -name "*.txt" -o -name "*.fasta" -o -name "*.gb" \| head -20 |
+| 66 | `env://turn_3/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20_1` | [env] |
+| 67 | `env://turn_3/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20_2` | [env] |
+| 70 | `log://turn_3/get/repo%3A/overview` | [get] repo://overview |
+| 71 | `log://turn_3/get/**` | [get] ** |
+| 72 | `https://www.fpbase.org` | [https] |
+| 73 | `https://www.fpbase.org/table` | [https] |
+| 74 | `https://www.microscopyu.com/techniques/fluorescence/nikon-fluorescence-filter-sets/yellow-fluorescent-protein-yfp-excitation` | [https] |
+| 75 | `https://www.fpbase.org/protein/eyfp` | [https] |
+| 76 | `https://www.fpbase.org/protein/mneongreen` | [https] |
+| 77 | `https://www.fpbase.org/protein/hyperfolder-yfp` | [https] |
+| 78 | `https://www.fpbase.org/protein/egfp` | [https] |
+| 79 | `https://probes.bocsci.com/resources/yellow-fluorescent-protein-dyes.html` | [https] |
+| 80 | `https://en.wikipedia.org/wiki/Green_fluorescent_protein` | [https] |
+| 81 | `log://turn_3/search/FPbase_fluorescent_protein_excitation_505nm_emission_green_or_yellow` | [search] FPbase fluorescent protein excitation 505nm emission green or yellow |
+| 82 | `log://turn_3/error/Only_one_%3Csearch%3E_per_turn._Dropped%3A_%22FPbase_fluorescent_protein_emission_610nm_` | [error status=429] Only one <search> per turn. Dropped: "FPbase fluorescent protein emission 610… |
+| 83 | `log://turn_3/error/Only_one_%3Csearch%3E_per_turn._Dropped%3A_%22protein_binding_SMILES_Nc3nc(OCc1ccccc1)c2` | [error status=429] Only one <search> per turn. Dropped: "protein binding SMILES Nc3nc(OCc1ccccc1… |
+| 84 | `log://turn_3/update/discovering_source_files_and_web_data_for_distillation` | [update status=155] discovering source files and web data for distillation |
+| 87 | `assistant://4` | [assistant emission — see turns/] |
+| 88 | `system://4` | [system prompt] |
+| 89 | `user://4` | [user packet (assembled context)] |
+| 90 | `model://4` | [model usage record] |
+| 91 | `reasoning://4` | [think] Distillation stage: Need to promote source files /app/pdb_ids.txt, /app/plasm… |
+| 92 | `log://turn_4/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 93 | `log://turn_4/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 94 | `log://turn_4/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 95 | `log://turn_4/get/https%3A/www.fpbase.org/protein/mneongreen` | [get] https://www.fpbase.org/protein/mneongreen |
+| 96 | `log://turn_4/get/https%3A/www.fpbase.org/protein/eyfp` | [get] https://www.fpbase.org/protein/eyfp |
+| 97 | `log://turn_4/update/promoting_source_files_for_distillation` | [update status=155] promoting source files for distillation |
+| 100 | `assistant://5` | [assistant emission — see turns/] |
+| 101 | `system://5` | [system prompt] |
+| 102 | `user://5` | [user packet (assembled context)] |
+| 103 | `model://5` | [model usage record] |
+| 104 | `reasoning://5` | [think] Distillation stage: Need to distill key unknowns using promoted sources. Prio… |
+| 105 | `log://turn_5/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 106 | `log://turn_5/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 107 | `log://turn_5/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 108 | `log://turn_5/update/distilling_file_contents_%2B_donor_selection` | [update status=155] distilling file contents + donor selection |
+| 111 | `assistant://6` | [assistant emission — see turns/] |
+| 112 | `system://6` | [system prompt] |
+| 113 | `user://6` | [user packet (assembled context)] |
+| 114 | `model://6` | [model usage record] |
+| 115 | `reasoning://6` | [think] Distillation stage: Need to distill key unknowns using promoted sources. Prio… |
+| 116 | `content://6` | [content] |
+| 117 | `log://turn_6/get/app/*.txt` | [get] app/*.txt |
+| 118 | `log://turn_6/get/app/*.fasta` | [get] app/*.fasta |
+| 119 | `log://turn_6/get/app/*.gb` | [get] app/*.gb |
+| 120 | `log://turn_6/get/app/pdb_ids.txt` | [get] app/pdb_ids.txt |
+| 121 | `log://turn_6/get/app/plasmid.gb` | [get] app/plasmid.gb |
+| 122 | `log://turn_6/get/app/antibody.fasta` | [get] app/antibody.fasta |
+| 123 | `known://api/fpbase_donor` | [known] # Related [prompt requirements](prompt://1) [unknown resolved](unknown://api/… |
+| 124 | `log://turn_6/set/known%3A/api/fpbase_donor` | [set] known://api/fpbase_donor |
+| 125 | `log://turn_6/set/https%3A/www.fpbase.org/protein/eyfp` | [set] (no target) |
+| 126 | `log://turn_6/set/https%3A/www.fpbase.org/protein/mneongreen` | [set] (no target) |
+| 127 | `https://www.fpbase.org/spectra` | [https] |
+| 128 | `https://evidentscientific.com/en/microscope-resource/knowledge-hub/techniques/confocal/applications/fpcolorpalette` | [https] |
+| 129 | `https://www.fpbase.org/fret` | [https] |
+| 130 | `https://www.leica-microsystems.com/science-lab/life-science/fluorescent-proteins-introduction-and-photo-spectral-characteristics` | [https] |
+| 131 | `https://www.nature.com/articles/srep18006` | [https] |
+| 132 | `log://turn_6/search/FPbase_fluorescent_protein_emission_610nm_red_excitation_green` | [search] FPbase fluorescent protein emission 610nm red excitation green |
+| 133 | `log://turn_6/update/distilling_file_contents_%2B_donor_selection_%2B_acceptor_search` | [update status=155] distilling file contents + donor selection + acceptor search |
+| 136 | `assistant://7` | [assistant emission — see turns/] |
+| 137 | `system://7` | [system prompt] |
+| 138 | `user://7` | [user packet (assembled context)] |
+| 139 | `model://7` | [model usage record] |
+| 140 | `reasoning://7` | [think] - Still in Distillation Stage: Need to resolve remaining unknowns by promotin… |
+| 141 | `log://turn_7/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 142 | `log://turn_7/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 143 | `log://turn_7/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 144 | `log://turn_7/get/https%3A/www.fpbase.org/protein/*` | [get] https://www.fpbase.org/protein/* |
+| 145 | `log://turn_7/update/promoting_/app_files_for_distillation` | [update status=155] promoting /app files for distillation |
+| 148 | `assistant://8` | [assistant emission — see turns/] |
+| 149 | `system://8` | [system prompt] |
+| 150 | `user://8` | [user packet (assembled context)] |
+| 151 | `model://8` | [model usage record] |
+| 152 | `reasoning://8` | [think] * Still in Distillation Stage - need to resolve remaining unknowns * /app fil… |
+| 153 | `log://turn_8/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 154 | `log://turn_8/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 155 | `log://turn_8/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 156 | `log://turn_8/get/https%3A/www.fpbase.org/protein/*` | [get] https://www.fpbase.org/protein/* |
+| 157 | `known://files/pdb_ids` | [known] # Related [prompt requirements](prompt://1) [unknown resolved](unknown://file… |
+| 158 | `log://turn_8/set/known%3A/files/pdb_ids` | [set] known://files/pdb_ids |
+| 159 | `known://api/fpbase_acceptor` | [known] # Related [prompt requirements](prompt://1) [unknown resolved](unknown://api/… |
+| 160 | `log://turn_8/set/known%3A/api/fpbase_acceptor` | [set] known://api/fpbase_acceptor |
+| 161 | `log://turn_8/set/known%3A/files/plasmid_gb` | [set] (no target) |
+| 162 | `log://turn_8/update/distilling_/app_file_contents_%2B_acceptor_selection` | [update status=155] distilling /app file contents + acceptor selection |
+| 165 | `assistant://9` | [assistant emission — see turns/] |
+| 166 | `system://9` | [system prompt] |
+| 167 | `user://9` | [user packet (assembled context)] |
+| 168 | `model://9` | [model usage record] |
+| 169 | `reasoning://9` | [think] * Distillation stage: Need to resolve unknown://files/pdb_ids by promoting /a… |
+| 170 | `log://turn_9/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 171 | `log://turn_9/update/promoting_/app/pdb_ids.txt_for_distillation` | [update status=155] promoting /app/pdb_ids.txt for distillation |
+| 174 | `assistant://10` | [assistant emission — see turns/] |
+| 175 | `system://10` | [system prompt] |
+| 176 | `user://10` | [user packet (assembled context)] |
+| 177 | `model://10` | [model usage record] |
+| 178 | `reasoning://10` | [think] * Still in Distillation Stage - need to resolve unknown://files/pdb_ids by pr… |
+| 179 | `log://turn_10/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 180 | `log://turn_10/update/promoting_/app/pdb_ids.txt_for_distillation` | [update status=155] promoting /app/pdb_ids.txt for distillation |
+| 183 | `assistant://11` | [assistant emission — see turns/] |
+| 184 | `system://11` | [system prompt] |
+| 185 | `user://11` | [user packet (assembled context)] |
+| 186 | `model://11` | [model usage record] |
+| 187 | `reasoning://11` | [think] - Still in Distillation Stage: unknown://files/pdb_ids unresolved (known://fi… |
+| 188 | `log://turn_11/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 189 | `log://turn_11/update/promoting_/app/pdb_ids.txt_for_distillation` | [update status=155] promoting /app/pdb_ids.txt for distillation |
+| 192 | `assistant://12` | [assistant emission — see turns/] |
+| 193 | `system://12` | [system prompt] |
+| 194 | `user://12` | [user packet (assembled context)] |
+| 195 | `model://12` | [model usage record] |
+| 196 | `reasoning://12` | [think] * Still in Distillation Stage - key unresolved unknowns: files/pdb_ids (100 b… |
+| 197 | `log://turn_12/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 198 | `log://turn_12/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 199 | `log://turn_12/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 200 | `log://turn_12/update/promoting_/app_source_files_for_distillation` | [update status=155] promoting /app source files for distillation |
+| 203 | `assistant://13` | [assistant emission — see turns/] |
+| 204 | `system://13` | [system prompt] |
+| 205 | `user://13` | [user packet (assembled context)] |
+| 206 | `model://13` | [model usage record] |
+| 207 | `reasoning://13` | [think] Distillation stage. unknown://files/pdb_ids unresolved - /app/pdb_ids.txt sti… |
+| 208 | `log://turn_13/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 209 | `log://turn_13/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 210 | `log://turn_13/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 211 | `log://turn_13/get/app/**` | [get] /app/** |
+| 212 | `log://turn_13/update/promoting_/app_source_files_for_pdb_ids/_dhfr/_antibody_target_distillation` | [update status=155] promoting /app source files for pdb_ids, dhfr, antibody target distillation |
+| 215 | `assistant://14` | [assistant emission — see turns/] |
+| 216 | `system://14` | [system prompt] |
+| 217 | `user://14` | [user packet (assembled context)] |
+| 218 | `model://14` | [model usage record] |
+| 219 | `reasoning://14` | [think] Still in Distillation Stage. Key unresolved unknowns: files/pdb_ids (100 byte… |
+| 220 | `log://turn_14/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 222 | `log://turn_14/update/promoting_/app/pdb_ids.txt_for_distillation` | [update status=155] promoting /app/pdb_ids.txt for distillation |
+| 225 | `assistant://15` | [assistant emission — see turns/] |
+| 226 | `system://15` | [system prompt] |
+| 227 | `user://15` | [user packet (assembled context)] |
+| 228 | `model://15` | [model usage record] |
+| 229 | `reasoning://15` | [think] * Still in Distillation Stage - key unresolved unknowns: files/pdb_ids (100 b… |
+| 230 | `log://turn_15/env/ls_-la_/app/pdb_ids.txt` | [env] ls -la /app/pdb_ids.txt |
+| 232 | `env://turn_15/ls_-la_/app/pdb_ids.txt_1` | [env] |
+| 233 | `env://turn_15/ls_-la_/app/pdb_ids.txt_2` | [env] |
+| 236 | `log://turn_15/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 237 | `log://turn_15/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 238 | `log://turn_15/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 239 | `log://turn_15/update/promoting_/app_source_files_for_distillation` | [update status=155] promoting /app source files for distillation |
+| 242 | `assistant://16` | [assistant emission — see turns/] |
+| 243 | `system://16` | [system prompt] |
+| 244 | `user://16` | [user packet (assembled context)] |
+| 245 | `model://16` | [model usage record] |
+| 246 | `reasoning://16` | [think] * Still in Distillation Stage - unknown://files/pdb_ids unresolved (needs /ap… |
+| 247 | `log://turn_16/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 248 | `log://turn_16/update/promoting_/app/pdb_ids.txt_for_distillation` | [update status=155] promoting /app/pdb_ids.txt for distillation |
+| 251 | `assistant://17` | [assistant emission — see turns/] |
+| 252 | `system://17` | [system prompt] |
+| 253 | `user://17` | [user packet (assembled context)] |
+| 254 | `model://17` | [model usage record] |
+| 255 | `reasoning://17` | [think] # Distillation Stage Plan 1. Promote /app/pdb_ids.txt (100 bytes, fits budget… |
+| 256 | `log://turn_17/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 257 | `log://turn_17/update/promoting_/app/pdb_ids.txt_for_distillation` | [update status=155] promoting /app/pdb_ids.txt for distillation |
+| 260 | `assistant://18` | [assistant emission — see turns/] |
+| 261 | `system://18` | [system prompt] |
+| 262 | `user://18` | [user packet (assembled context)] |
+| 263 | `model://18` | [model usage record] |
+| 264 | `reasoning://18` | [think] * Still in Distillation Stage - unknown://files/pdb_ids unresolved despite mu… |
+| 265 | `log://turn_18/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 266 | `log://turn_18/update/promoting_/app/pdb_ids.txt_contents_for_distillation` | [update status=155] promoting /app/pdb_ids.txt contents for distillation |
+| 269 | `assistant://19` | [assistant emission — see turns/] |
+| 270 | `system://19` | [system prompt] |
+| 271 | `user://19` | [user packet (assembled context)] |
+| 272 | `model://19` | [model usage record] |
+| 273 | `reasoning://19` | [think] * Still in Distillation Stage - key unresolved unknowns: files/pdb_ids (100B … |
+| 274 | `log://turn_19/get/app/**` | [get] /app/** |
+| 275 | `log://turn_19/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 276 | `log://turn_19/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 277 | `log://turn_19/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 278 | `log://turn_19/update/promoting_critical_/app_source_files_for_distillation` | [update status=155] promoting critical /app source files for distillation |
+| 281 | `assistant://20` | [assistant emission — see turns/] |
+| 282 | `system://20` | [system prompt] |
+| 283 | `user://20` | [user packet (assembled context)] |
+| 284 | `model://20` | [model usage record] |
+| 285 | `reasoning://20` | [think] * Still in Distillation Stage - key unresolved unknowns: files/pdb_ids (100B … |
+| 286 | `log://turn_20/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 287 | `log://turn_20/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 288 | `log://turn_20/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 289 | `log://turn_20/update/promoting_/app_source_files_for_sequence_distillation` | [update status=155] promoting /app source files for sequence distillation |
+| 292 | `assistant://21` | [assistant emission — see turns/] |
+| 293 | `system://21` | [system prompt] |
+| 294 | `user://21` | [user packet (assembled context)] |
+| 295 | `model://21` | [model usage record] |
+| 296 | `reasoning://21` | [think] * Still in Distillation Stage - critical unknown://files/pdb_ids unresolved a… |
+| 297 | `log://turn_21/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 298 | `log://turn_21/update/promoting_/app/pdb_ids.txt_contents_for_distillation` | [update status=155] promoting /app/pdb_ids.txt contents for distillation |
+| 301 | `assistant://22` | [assistant emission — see turns/] |
+| 302 | `system://22` | [system prompt] |
+| 303 | `user://22` | [user packet (assembled context)] |
+| 304 | `model://22` | [model usage record] |
+| 305 | `reasoning://22` | [think] * Still in Distillation Stage - critical unknown://files/pdb_ids unresolved a… |
+| 306 | `log://turn_22/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 307 | `log://turn_22/get/app/pdb_ids.txt_1` | [get] app/pdb_ids.txt |
+| 308 | `log://turn_22/update/promoting_/app/pdb_ids.txt_contents_for_distillation` | [update status=155] promoting /app/pdb_ids.txt contents for distillation |
+| 311 | `assistant://23` | [assistant emission — see turns/] |
+| 312 | `system://23` | [system prompt] |
+| 313 | `user://23` | [user packet (assembled context)] |
+| 314 | `model://23` | [model usage record] |
+| 315 | `reasoning://23` | [think] * Still in Distillation Stage - critical /app/pdb_ids.txt (100 bytes) has not… |
+| 316 | `log://turn_23/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 317 | `log://turn_23/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 318 | `log://turn_23/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 319 | `log://turn_23/update/promoting_/app_source_files_for_distillation` | [update status=155] promoting /app source files for distillation |
+| 322 | `assistant://24` | [assistant emission — see turns/] |
+| 323 | `system://24` | [system prompt] |
+| 324 | `user://24` | [user packet (assembled context)] |
+| 325 | `model://24` | [model usage record] |
+| 326 | `reasoning://24` | [think] Distillation stage: unknown://files/pdb_ids still unresolved after many faile… |
+| 327 | `log://turn_24/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 328 | `log://turn_24/update/promoting_/app/pdb_ids.txt_contents_for_distillation` | [update status=155] promoting /app/pdb_ids.txt contents for distillation |
+| 331 | `assistant://25` | [assistant emission — see turns/] |
+| 332 | `system://25` | [system prompt] |
+| 333 | `user://25` | [user packet (assembled context)] |
+| 334 | `model://25` | [model usage record] |
+| 335 | `reasoning://25` | [think] Still in Distillation Stage. Critical unresolved unknowns: files/pdb_ids (100… |
+| 336 | `log://turn_25/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 338 | `log://turn_25/update/discovering_/app/pdb_ids.txt_contents_for_distillation` | [update status=155] discovering /app/pdb_ids.txt contents for distillation |
+| 341 | `assistant://26` | [assistant emission — see turns/] |
+| 342 | `system://26` | [system prompt] |
+| 343 | `user://26` | [user packet (assembled context)] |
+| 344 | `model://26` | [model usage record] |
+| 345 | `reasoning://26` | [think] * Still in Distillation Stage - critical unknown://files/pdb_ids unresolved a… |
+| 346 | `log://turn_26/env/cat_/app/pdb_ids.txt` | [env] cat /app/pdb_ids.txt |
+| 348 | `env://turn_26/cat_/app/pdb_ids.txt_1` | [env] |
+| 349 | `env://turn_26/cat_/app/pdb_ids.txt_2` | [env] |
+| 352 | `log://turn_26/get/app/pdb_ids.txt` | [get] /app/pdb_ids.txt |
+| 353 | `log://turn_26/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 354 | `log://turn_26/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 355 | `log://turn_26/update/final_attempt_to_promote_/app_source_files_for_distillation` | [update status=155] final attempt to promote /app source files for distillation |
+| 358 | `assistant://27` | [assistant emission — see turns/] |
+| 359 | `system://27` | [system prompt] |
+| 360 | `user://27` | [user packet (assembled context)] |
+| 361 | `model://27` | [model usage record] |
+| 362 | `reasoning://27` | [think] # Plan for Distillation Stage 1. /app/pdb_ids.txt is now accessible via env:/… |
+| 363 | `log://turn_27/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1` | [get] env://turn_26/cat_/app/pdb_ids.txt_1 |
+| 364 | `known://files/pdb_ids_contents` | [known] # Related [prompt requirements](prompt://1) [known summary](known://files/pdb… |
+| 365 | `log://turn_27/set/known%3A/files/pdb_ids_contents` | [set] known://files/pdb_ids_contents |
+| 366 | `known://api/fpbase_donor/sequence_strategy` | [known] # Related [donor selection](known://api/fpbase_donor) [pdb_ids](known://files… |
+| 367 | `log://turn_27/set/known%3A/api/fpbase_donor/sequence_strategy` | [set] known://api/fpbase_donor/sequence_strategy |
+| 368 | `known://api/fpbase_acceptor/sequence_strategy` | [known] # Related [acceptor selection](known://api/fpbase_acceptor) [pdb_ids](known:/… |
+| 369 | `log://turn_27/set/known%3A/api/fpbase_acceptor/sequence_strategy` | [set] known://api/fpbase_acceptor/sequence_strategy |
+| 370 | `log://turn_27/set/unknown%3A/files/pdb_ids` | [set] (no target) |
+| 371 | `log://turn_27/update/pdb_ids.txt_distilled%3B_preparing_plasmid.gb%2Bantibody.fasta` | [update status=155] pdb_ids.txt distilled; preparing plasmid.gb+antibody.fasta |
+| 374 | `assistant://28` | [assistant emission — see turns/] |
+| 375 | `system://28` | [system prompt] |
+| 376 | `user://28` | [user packet (assembled context)] |
+| 377 | `model://28` | [model usage record] |
+| 378 | `reasoning://28` | [think] Distillation stage: pdb_ids.txt distilled into known://files/pdb_ids_contents… |
+| 379 | `log://turn_28/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1` | [get] env://turn_26/cat_/app/pdb_ids.txt_1 |
+| 380 | `log://turn_28/env/cat_/app/pdb_ids.txt` | [env] cat /app/pdb_ids.txt |
+| 382 | `env://turn_28/cat_/app/pdb_ids.txt_1` | [env] |
+| 383 | `env://turn_28/cat_/app/pdb_ids.txt_2` | [env] |
+| 386 | `log://turn_28/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 387 | `log://turn_28/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 388 | `log://turn_28/search/PDB_protein_structures_fluorescent_proteins_mNeonGreen_EYFP_excitation_505nm_OR_` | [search] PDB protein structures fluorescent proteins mNeonGreen EYFP excitation 505nm … |
+| 389 | `log://turn_28/update/getting_full_pdb_ids_%2B_discovering_PDB_sequences_for_FPs` | [update status=155] getting full pdb_ids + discovering PDB sequences for FPs |
+| 392 | `assistant://29` | [assistant emission — see turns/] |
+| 393 | `system://29` | [system prompt] |
+| 394 | `user://29` | [user packet (assembled context)] |
+| 395 | `model://29` | [model usage record] |
+| 396 | `reasoning://29` | [think] Current stage: Distillation. Have pdb_ids.txt contents (20 IDs), donor mNeonG… |
+| 397 | `content://29` | [content] |
+| 398 | `log://turn_29/get/env%3A/turn_3/ls_-la_/app_1` | [get] env://turn_3/ls_-la_/app_1 |
+| 399 | `log://turn_29/env/ls_-la_/app/antibody.fasta_/app/plasmid.gb` | [env] ls -la /app/antibody.fasta /app/plasmid.gb |
+| 401 | `env://turn_29/ls_-la_/app/antibody.fasta_/app/plasmid.gb_1` | [env] |
+| 402 | `env://turn_29/ls_-la_/app/antibody.fasta_/app/plasmid.gb_2` | [env] |
+| 405 | `log://turn_29/get/app/antibody.fasta` | [get] /app/antibody.fasta |
+| 406 | `log://turn_29/get/app/plasmid.gb` | [get] /app/plasmid.gb |
+| 407 | `log://turn_29/search/PDB_fluorescent_proteins_mNeonGreen_OR_EYFP_OR_YFP_OR_GFP_site%3Arcsb.org/pdb_OR_r` | [search] PDB fluorescent proteins mNeonGreen OR EYFP OR YFP OR GFP site:rcsb.org/pdb O… |
+| 408 | `log://turn_29/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1` | [get] env://turn_26/cat_/app/pdb_ids.txt_1 |
+| 409 | `log://turn_29/update/discovering_PDB_FP_matches_%2B_antibody/plasmid_contents` | [update status=155] discovering PDB FP matches + antibody/plasmid contents |
+| 412 | `assistant://30` | [assistant emission — see turns/] |
+| 413 | `system://30` | [system prompt] |
+| 414 | `user://30` | [user packet (assembled context)] |
+| 415 | `model://30` | [model usage record] |
+| 416 | `reasoning://30` | [think] # Distillation Stage Plan 1. Full pdb_ids.txt now visible from env://turn_26/… |
+| 417 | `log://turn_30/env/cat_/app/antibody.fasta` | [env] cat /app/antibody.fasta |
+| 419 | `env://turn_30/cat_/app/antibody.fasta_1` | [env] |
+| 420 | `env://turn_30/cat_/app/antibody.fasta_2` | [env] |
+| 423 | `log://turn_30/env/cat_/app/plasmid.gb` | [env] cat /app/plasmid.gb |
+| 425 | `env://turn_30/cat_/app/plasmid.gb_1` | [env] |
+| 426 | `env://turn_30/cat_/app/plasmid.gb_2` | [env] |
+| 429 | `log://turn_30/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1` | [get] env://turn_26/cat_/app/pdb_ids.txt_1 |
+| 430 | `log://turn_30/search/PDB_REST_API_FASTA_sequence_by_ID_%223M22%22_OR_%222H5Q%22_OR_%223MGF%22_OR_%225Y01%22_OR_%222VZX%22` | [search] PDB REST API FASTA sequence by ID "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2V… |
+| 431 | `log://turn_30/update/promoting_antibody.fasta%2Bplasmid.gb%2Bfull_pdb_ids_for_sequence_distillation` | [update status=155] promoting antibody.fasta+plasmid.gb+full pdb_ids for sequence distillation |
+| 434 | `assistant://31` | [assistant emission — see turns/] |
+| 435 | `system://31` | [system prompt] |
+| 436 | `user://31` | [user packet (assembled context)] |
+| 437 | `model://31` | [model usage record] |
+| 438 | `reasoning://31` | [think] - Still in Distillation Stage: Need to distill antibody.fasta, plasmid.gb, an… |
+| 439 | `log://turn_31/get/env%3A/turn_30/cat_/app/antibody.fasta_1` | [get] env://turn_30/cat_/app/antibody.fasta_1 |
+| 440 | `log://turn_31/get/env%3A/turn_30/cat_/app/plasmid.gb_1` | [get] env://turn_30/cat_/app/plasmid.gb_1 |
+| 441 | `log://turn_31/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1` | [get] env://turn_26/cat_/app/pdb_ids.txt_1 |
+| 442 | `known://files/antibody_fasta_contents` | [known] # Related [prompt requirements](prompt://1) [unknown resolved](unknown://file… |
+| 443 | `log://turn_31/set/known%3A/files/antibody_fasta_contents` | [set] known://files/antibody_fasta_contents |
+| 444 | `known://files/pdb_ids_full_list` | [known] # Related [previous pdb_ids](known://files/pdb_ids_contents) [cat /app/pdb_id… |
+| 445 | `log://turn_31/set/known%3A/files/pdb_ids_full_list` | [set] known://files/pdb_ids_full_list |
+| 446 | `log://turn_31/update/distilling_antibody.fasta%2Bplasmid.gb%2Bpdb_ids_full_list` | [update status=155] distilling antibody.fasta+plasmid.gb+pdb_ids full list |
+| 449 | `assistant://32` | [assistant emission — see turns/] |
+| 450 | `system://32` | [system prompt] |
+| 451 | `user://32` | [user packet (assembled context)] |
+| 452 | `model://32` | [model usage record] |
+| 453 | `reasoning://32` | [think] 1. Still in Distillation Stage - need to resolve remaining unknowns: - unknow… |
+| 454 | `log://turn_32/get/env%3A/turn_30/cat_/app/plasmid.gb_1` | [get] env://turn_30/cat_/app/plasmid.gb_1 |
+| 456 | `log://turn_32/env/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb` | [env] grep -A 20 "dihydrofolate reductase" /app/plasmid.gb \|\| cat /app/plasmid.gb |
+| 458 | `env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_1` | [env] |
+| 459 | `env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_2` | [env] |
+| 462 | `https://www.bioatla.com/appendix/antibody-structure` | [https] |
+| 463 | `https://www.creative-diagnostics.com/blog/index.php/antibody-heavy-and-light-chains` | [https] |
+| 464 | `https://www.abcam.com/en-us/technical-resources/guides/antibody-basics/antibody-basics` | [https] |
+| 465 | `log://turn_32/search/antibody_heavy_chain_QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK_target_antigen_seque` | [search] antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK target antigen se… |
+| 466 | `log://turn_32/update/distilling_DHFR_sequence_%2B_discovering_antibody_target_%2B_molecule_binder` | [update status=155] distilling DHFR sequence + discovering antibody target + molecule binder |
+| 469 | `assistant://33` | [assistant emission — see turns/] |
+| 470 | `system://33` | [system prompt] |
+| 471 | `user://33` | [user packet (assembled context)] |
+| 472 | `model://33` | [model usage record] |
+| 473 | `reasoning://33` | [think] Distillation stage: Resolve remaining unknowns using promoted sources. Key re… |
+| 474 | `log://turn_33/get/env%3A/turn_32/grep_-A_20_%2522dihydrofolate_reductase%2522_/app/plasmid.gb_%257C%257C_ca` | [get] env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C… |
+| 475 | `log://turn_33/get/env%3A/turn_30/cat_/app/plasmid.gb_1` | [get] env://turn_30/cat_/app/plasmid.gb_1 |
+| 476 | `log://turn_33/env/grep_-A_5_%22folA%22_/app/plasmid.gb` | [env] grep -A 5 "folA" /app/plasmid.gb |
+| 478 | `env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_1` | [env] |
+| 479 | `env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_2` | [env] |
+| 482 | `https://www.rcsb.org/structure/5JZL` | [https] |
+| 483 | `log://turn_33/search/rcsb_pdb_%222IB5%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%225JZL%22_fluorescent_protein_OR_G` | [search] rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "5JZL" fluorescent protein O… |
+| 484 | `log://turn_33/update/distilling_DHFR_%2B_discovering_FP_PDB_matches_%2B_antibody_target` | [update status=155] distilling DHFR + discovering FP PDB matches + antibody target |
+| 487 | `assistant://34` | [assistant emission — see turns/] |
+| 488 | `system://34` | [system prompt] |
+| 489 | `user://34` | [user packet (assembled context)] |
+| 490 | `model://34` | [model usage record] |
+| 491 | `reasoning://34` | [think] # Distillation Stage Plan 1. **DHFR sequence**: Extract from plasmid.gb (alre… |
+| 492 | `log://turn_34/get/https%3A/www.rcsb.org/structure/5JZL` | [get] https://www.rcsb.org/structure/5JZL |
+| 493 | `log://turn_34/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 494 | `log://turn_34/env/grep_-i_%22fluorescent%5C%7Cgfp%5C%7Cyfp%5C%7Cmneon%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_FPs_in_list%22` | [env] grep -i "fluorescent\\|gfp\\|yfp\\|mneon" /app/pdb_ids.txt \|\| echo "no FPs in list" |
+| 496 | `env://turn_34/grep_-i_%22fluorescent%5C%7Cgfp%5C%7Cyfp%5C%7Cmneon%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_FPs_in_list%22_1` | [env] |
+| 497 | `env://turn_34/grep_-i_%22fluorescent%5C%7Cgfp%5C%7Cyfp%5C%7Cmneon%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_FPs_in_list%22_2` | [env] |
+| 500 | `https://www.fpbase.org/protein/mscarlet` | [https] |
+| 501 | `https://www.fpbase.org/protein/mcherry` | [https] |
+| 502 | `log://turn_34/search/rcsb_pdb_%226AA7%22_OR_%223ADF%22_OR_%225WJ2%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_red_OR_far-red` | [search] rcsb pdb "6AA7" OR "3ADF" OR "5WJ2" OR "4KGE" OR "4Q7T" OR "1KFD" red OR far-… |
+| 503 | `known://sequence/dhfr` | [known] # Related [prompt requirements](prompt://1) [plasmid.gb full](env://turn_30/c… |
+| 504 | `log://turn_34/set/known%3A/sequence/dhfr` | [set] known://sequence/dhfr |
+| 505 | `log://turn_34/set/unknown%3A/api/pdb_sequences` | [set] (no target) |
+| 506 | `log://turn_34/set/unknown%3A/files/plasmid_gb` | [set] (no target) |
+| 507 | `log://turn_34/update/distilling_DHFR%3B_discovering_donor_5JZL_FASTA_%2B_acceptor/molecule_binder_PDB_mat` | [update status=155] distilling DHFR; discovering donor 5JZL FASTA + acceptor/molecule binder PDB … |
+| 510 | `assistant://35` | [assistant emission — see turns/] |
+| 511 | `system://35` | [system prompt] |
+| 512 | `user://35` | [user packet (assembled context)] |
+| 513 | `model://35` | [model usage record] |
+| 514 | `reasoning://35` | [think] 1. Still in Distillation: Need to resolve remaining unknowns for fusion const… |
+| 515 | `log://turn_35/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 516 | `log://turn_35/get/https%3A/www.rcsb.org/structure/5JZL` | [get] https://www.rcsb.org/structure/5JZL |
+| 517 | `log://turn_35/env/grep_-i_%225JZL%5C%7Cgreen%5C%7CusGFP%5C%7CmuGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_5JZL_match%22` | [env] grep -i "5JZL\\|green\\|usGFP\\|muGFP" /app/pdb_ids.txt \|\| echo "no 5JZL match" |
+| 519 | `env://turn_35/grep_-i_%225JZL%5C%7Cgreen%5C%7CusGFP%5C%7CmuGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_5JZL_match%22_1` | [env] |
+| 520 | `env://turn_35/grep_-i_%225JZL%5C%7Cgreen%5C%7CusGFP%5C%7CmuGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_5JZL_match%22_2` | [env] |
+| 523 | `https://www.nature.com/articles/nmeth.4074` | [https] |
+| 524 | `https://www.rcsb.org/structure/5LK4` | [https] |
+| 525 | `https://www.rcsb.org/structure/7ZCT` | [https] |
+| 526 | `https://www.nature.com/articles/s41592-023-01809-y` | [https] |
+| 527 | `https://www.rcsb.org/structure/4OHS` | [https] |
+| 528 | `https://www.fpbase.org/protein/mscarlet3` | [https] |
+| 529 | `log://turn_35/search/rcsb_pdb_%222IB5%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%226AA7%22_OR_%223ADF%22_OR_%225WJ2%22_OR_%22` | [search] rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" O… |
+| 530 | `log://turn_35/update/getting_donor_FASTA_%2B_acceptor_candidates_from_remaining_PDB_IDs` | [update status=155] getting donor FASTA + acceptor candidates from remaining PDB IDs |
+| 533 | `assistant://36` | [assistant emission — see turns/] |
+| 534 | `system://36` | [system prompt] |
+| 535 | `user://36` | [user packet (assembled context)] |
+| 536 | `model://36` | [model usage record] |
+| 537 | `reasoning://36` | [think] # Distillation Stage Plan 1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~4… |
+| 538 | `log://turn_36/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 539 | `log://turn_36/search/PDB_REST_API_FASTA_download_%225JZL%22_OR_%22files.rcsb.org/download/5JZL.fasta%22_OR_%22r` | [search] PDB REST API FASTA download "5JZL" OR "files.rcsb.org/download/5JZL.fasta" OR… |
+| 540 | `log://turn_36/env/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_in_list%22` | [env] grep -i "5JZL\\|muGFP\\|usGFP" /app/pdb_ids.txt \|\| echo "confirmed in list" |
+| 542 | `env://turn_36/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_in_list%22_1` | [env] |
+| 543 | `env://turn_36/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_in_list%22_2` | [env] |
+| 546 | `log://turn_36/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 547 | `log://turn_36/update/getting_donor_5JZL_FASTA_%2B_acceptor/molecule_binder_from_pdb_ids.txt` | [update status=155] getting donor 5JZL FASTA + acceptor/molecule binder from pdb_ids.txt |
+| 550 | `assistant://37` | [assistant emission — see turns/] |
+| 551 | `system://37` | [system prompt] |
+| 552 | `user://37` | [user packet (assembled context)] |
+| 553 | `model://37` | [model usage record] |
+| 554 | `reasoning://37` | [think] # Distillation Stage Plan 1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~4… |
+| 555 | `log://turn_37/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 556 | `log://turn_37/get/https%3A/www.rcsb.org/structure/5JZL` | [get] https://www.rcsb.org/structure/5JZL |
+| 557 | `log://turn_37/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 558 | `log://turn_37/env/grep_-i_%22red%5C%7Cmcherry%5C%7Cmscarlet%5C%7Cfar-red%5C%7C610%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_red_` | [env] grep -i "red\\|mcherry\\|mscarlet\\|far-red\\|610" /app/pdb_ids.txt \|\| echo "no r… |
+| 560 | `env://turn_37/grep_-i_%22red%5C%7Cmcherry%5C%7Cmscarlet%5C%7Cfar-red%5C%7C610%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_red__1` | [env] |
+| 561 | `env://turn_37/grep_-i_%22red%5C%7Cmcherry%5C%7Cmscarlet%5C%7Cfar-red%5C%7C610%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_red__2` | [env] |
+| 564 | `log://turn_37/search/PDB_REST_API_FASTA_sequence_%225JZL%22_%22files.rcsb.org/download/5JZL.fasta%22_OR_%22rcsb` | [search] PDB REST API FASTA sequence "5JZL" "files.rcsb.org/download/5JZL.fasta" OR "r… |
+| 565 | `https://link.springer.com/article/10.1186/s13065-023-01037-7` | [https] |
+| 566 | `https://en.wikipedia.org/wiki/Benzotriazole` | [https] |
+| 567 | `https://pubs.acs.org/doi/10.1021/ic402467g` | [https] |
+| 568 | `log://turn_37/search/rcsb_pdb_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%226AA7%22_OR_%223ADF%22_OR_%225WJ2%22_OR_%222IB5%22_%22mol` | [search] rcsb pdb "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "2IB5" "… |
+| 569 | `log://turn_37/update/getting_5JZL_donor_FASTA_%2B_acceptor/molecule_binder_from_remaining_PDBs` | [update status=155] getting 5JZL donor FASTA + acceptor/molecule binder from remaining PDBs |
+| 572 | `assistant://38` | [assistant emission — see turns/] |
+| 573 | `system://38` | [system prompt] |
+| 574 | `user://38` | [user packet (assembled context)] |
+| 575 | `model://38` | [model usage record] |
+| 576 | `reasoning://38` | [think] # Distillation Stage Plan 1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~4… |
+| 577 | `log://turn_38/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 578 | `log://turn_38/get/https%3A/www.rcsb.org/structure/5JZL` | [get] https://www.rcsb.org/structure/5JZL |
+| 579 | `log://turn_38/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 580 | `log://turn_38/env/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_donor_candidate` | [env] grep -i "5JZL\\|muGFP\\|usGFP" /app/pdb_ids.txt \|\| echo "confirmed donor candid… |
+| 582 | `env://turn_38/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_donor_candidate_1` | [env] |
+| 583 | `env://turn_38/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_donor_candidate_2` | [env] |
+| 586 | `log://turn_38/search/PDB_REST_API_sequence_FASTA_endpoint_%225JZL%22_OR_%22files.rcsb.org/view/5JZL.fasta%22_` | [search] PDB REST API sequence FASTA endpoint "5JZL" OR "files.rcsb.org/view/5JZL.fast… |
+| 587 | `log://turn_38/update/getting_5JZL_donor_FASTA_%2B_final_acceptor/molecule_binder_checks` | [update status=155] getting 5JZL donor FASTA + final acceptor/molecule binder checks |
+| 590 | `assistant://39` | [assistant emission — see turns/] |
+| 591 | `system://39` | [system prompt] |
+| 592 | `user://39` | [user packet (assembled context)] |
+| 593 | `model://39` | [model usage record] |
+| 594 | `reasoning://39` | [think] # Distillation Stage Plan 1. Confirm donor: 5JZL (muGFP/usGFP) is green FP (E… |
+| 595 | `log://turn_39/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 596 | `log://turn_39/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 597 | `log://turn_39/get/https%3A/files.rcsb.org/download/*.fasta` | [get] https://files.rcsb.org/download/*.fasta |
+| 598 | `log://turn_39/error/Dispatch_crash_in_search%3A_Brave_422%3A_Unprocessable_Entity` | [error status=500] Dispatch crash in search: Brave 422: Unprocessable Entity |
+| 599 | `log://turn_39/set/known%3A/sequence/donor_5JZL` | [set] (no target) |
+| 600 | `log://turn_39/set/unknown%3A/api/pdb_sequences` | [set] (no target) |
+| 601 | `log://turn_39/set/unknown%3A/files/pdb_ids` | [set] (no target) |
+| 602 | `log://turn_39/update/_` | [update status=?] Aborted — preceding <search> failed. |
+| 605 | `assistant://40` | [assistant emission — see turns/] |
+| 606 | `system://40` | [system prompt] |
+| 607 | `user://40` | [user packet (assembled context)] |
+| 608 | `model://40` | [model usage record] |
+| 609 | `reasoning://40` | [think] Distillation stage: Need to resolve remaining unknowns for deployment (gBlock… |
+| 610 | `log://turn_40/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 611 | `log://turn_40/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 612 | `https://www.rcsb.org/downloads/fasta` | [https] |
+| 613 | `https://www.rcsb.org/downloads` | [https] |
+| 614 | `https://www.rcsb.org/docs/programmatic-access/file-download-services` | [https] |
+| 615 | `https://bioinformaticsreview.com/20220614/how-to-download-fasta-sequences-from-pdb-for-multiple-structures` | [https] |
+| 616 | `https://www.rcsb.org` | [https] |
+| 617 | `https://www.rcsb.org/news/5764422199cccf72e74ca3c1` | [https] |
+| 618 | `https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2004q2/query.html` | [https] |
+| 619 | `https://data.rcsb.org` | [https] |
+| 620 | `log://turn_40/search/PDB_FASTA_sequence_download_API_%225JZL%22_OR_%22files.rcsb.org/download/5JZL.fasta%22_O` | [search] PDB FASTA sequence download API "5JZL" OR "files.rcsb.org/download/5JZL.fasta… |
+| 621 | `log://turn_40/error/Dispatch_crash_in_search%3A_Brave_422%3A_Unprocessable_Entity` | [error status=500] Dispatch crash in search: Brave 422: Unprocessable Entity |
+| 622 | `log://turn_40/update/_` | [update status=?] Aborted — preceding <search> failed. |
+| 625 | `assistant://41` | [assistant emission — see turns/] |
+| 626 | `system://41` | [system prompt] |
+| 627 | `user://41` | [user packet (assembled context)] |
+| 628 | `model://41` | [model usage record] |
+| 629 | `reasoning://41` | [think] * Still in Distillation: Need donor sequence (5JZL muGFP), acceptor (no red F… |
+| 630 | `log://turn_41/get/https%3A/www.rcsb.org/structure/5JZL` | [get] https://www.rcsb.org/structure/5JZL |
+| 631 | `log://turn_41/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 632 | `https://www.rcsb.org/structure/5WJ2` | [https] |
+| 633 | `log://turn_41/search/PDB_FASTA_sequence_API_rcsb_%225JZL%22_OR_%222IB5%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%226` | [search] PDB FASTA sequence API rcsb "5JZL" OR "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR… |
+| 634 | `log://turn_41/get/https%3A/www.rcsb.org/downloads/fasta` | [get] https://www.rcsb.org/downloads/fasta |
+| 635 | `log://turn_41/update/getting_5JZL_donor_FASTA_%2B_scanning_pdb_ids_for_acceptor/binder` | [update status=155] getting 5JZL donor FASTA + scanning pdb_ids for acceptor/binder |
+| 638 | `assistant://42` | [assistant emission — see turns/] |
+| 639 | `system://42` | [system prompt] |
+| 640 | `user://42` | [user packet (assembled context)] |
+| 641 | `model://42` | [model usage record] |
+| 642 | `reasoning://42` | [think] # Distillation Stage Plan 1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~4… |
+| 643 | `log://turn_42/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 644 | `log://turn_42/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 645 | `https://www.biotite-python.org/latest/tutorial/database/rcsb.html` | [https] |
+| 646 | `log://turn_42/search/PDB_REST_API_FASTA_%225JZL%22_%22files.rcsb.org/download/5JZL.fasta%22_OR_rcsb_sequence_` | [search] PDB REST API FASTA "5JZL" "files.rcsb.org/download/5JZL.fasta" OR rcsb sequen… |
+| 647 | `https://www.ncbi.nlm.nih.gov/books/NBK27144` | [https] |
+| 648 | `https://www.creative-proteomics.com/proteinseq/resource/antibody-heavy-light-chains-structure-function.htm` | [https] |
+| 649 | `https://en.wikipedia.org/wiki/Antibody` | [https] |
+| 650 | `https://www.ncbi.nlm.nih.gov/books/NBK27160` | [https] |
+| 651 | `https://en.wikipedia.org/wiki/Immunoglobulin_heavy_chain` | [https] |
+| 652 | `https://www.nature.com/articles/s41586-022-05371-z` | [https] |
+| 653 | `https://en.vectorbuilder.com/resources/vector-system/pRP_mAb_Heavy_Light_IL2.html` | [https] |
+| 654 | `https://www.creative-proteomics.com/proteinseq/antibody-light-and-heavy-chain-sequencing.htm` | [https] |
+| 655 | `log://turn_42/search/antibody_heavy_chain_QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK_antigen_target_seque` | [search] antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK antigen target se… |
+| 656 | `log://turn_42/update/getting_5JZL_donor_FASTA_%2B_antibody_target_%2B_scanning_binders` | [update status=155] getting 5JZL donor FASTA + antibody target + scanning binders |
+| 659 | `assistant://43` | [assistant emission — see turns/] |
+| 660 | `system://43` | [system prompt] |
+| 661 | `user://43` | [user packet (assembled context)] |
+| 662 | `model://43` | [model usage record] |
+| 663 | `reasoning://43` | [think] Distillation stage: Prioritize unresolved unknowns critical for fusion protei… |
+| 664 | `log://turn_43/get/https%3A/www.rcsb.org/structure/5JZL` | [get] https://www.rcsb.org/structure/5JZL |
+| 665 | `log://turn_43/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 666 | `log://turn_43/env/grep_-i_%225WJ2%5C%7C3ADF%5C%7C6AA7%5C%7C1KFD%5C%7C4Q7T%5C%7C4KGE%5C%7C2IB5%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_` | [env] grep -i "5WJ2\\|3ADF\\|6AA7\\|1KFD\\|4Q7T\\|4KGE\\|2IB5" /app/pdb_ids.txt \|\| echo "… |
+| 668 | `env://turn_43/grep_-i_%225WJ2%5C%7C3ADF%5C%7C6AA7%5C%7C1KFD%5C%7C4Q7T%5C%7C4KGE%5C%7C2IB5%22_/app/pdb_ids.txt_%7C%7C_echo_%22no__1` | [env] |
+| 669 | `env://turn_43/grep_-i_%225WJ2%5C%7C3ADF%5C%7C6AA7%5C%7C1KFD%5C%7C4Q7T%5C%7C4KGE%5C%7C2IB5%22_/app/pdb_ids.txt_%7C%7C_echo_%22no__2` | [env] |
+| 672 | `https://search.rcsb.org` | [https] |
+| 673 | `https://www.rcsb.org/docs/programmatic-access/web-apis-overview` | [https] |
+| 674 | `https://education.molssi.org/python-scripting-biochemistry/chapters/rcsb_api.html` | [https] |
+| 675 | `log://turn_43/search/PDB_REST_API_%22get_fasta%22_OR_%22sequence/%7Bid%7D.fasta%22_%225JZL%22_OR_%225WJ2%22_site%3Arcsb.org` | [search] PDB REST API "get_fasta" OR "sequence/{id}.fasta" "5JZL" OR "5WJ2" site:rcsb.… |
+| 676 | `log://turn_43/update/getting_donor/acceptor_FASTA_sequences_%2B_scanning_binders` | [update status=155] getting donor/acceptor FASTA sequences + scanning binders |
+| 679 | `assistant://44` | [assistant emission — see turns/] |
+| 680 | `system://44` | [system prompt] |
+| 681 | `user://44` | [user packet (assembled context)] |
+| 682 | `model://44` | [model usage record] |
+| 683 | `reasoning://44` | [think] # Distillation Stage Plan 1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~4… |
+| 684 | `https://www.rcsb.org/structure/2IB5` | [https] |
+| 685 | `log://turn_44/get/https%3A/www.rcsb.org/structure/2IB5` | [get] https://www.rcsb.org/structure/2IB5 |
+| 686 | `https://www.rcsb.org/structure/4KGE` | [https] |
+| 687 | `log://turn_44/get/https%3A/www.rcsb.org/structure/4KGE` | [get] https://www.rcsb.org/structure/4KGE |
+| 688 | `https://www.rcsb.org/structure/4Q7T` | [https] |
+| 689 | `log://turn_44/get/https%3A/www.rcsb.org/structure/4Q7T` | [get] https://www.rcsb.org/structure/4Q7T |
+| 690 | `https://www.rcsb.org/structure/1KFD` | [https] |
+| 691 | `log://turn_44/get/https%3A/www.rcsb.org/structure/1KFD` | [get] https://www.rcsb.org/structure/1KFD |
+| 692 | `https://www.rcsb.org/structure/6AA7` | [https] |
+| 693 | `log://turn_44/get/https%3A/www.rcsb.org/structure/6AA7` | [get] https://www.rcsb.org/structure/6AA7 |
+| 694 | `https://www.rcsb.org/structure/3ADF` | [https] |
+| 695 | `log://turn_44/get/https%3A/www.rcsb.org/structure/3ADF` | [get] https://www.rcsb.org/structure/3ADF |
+| 696 | `log://turn_44/get/https%3A/www.rcsb.org/structure/5WJ2` | [get] https://www.rcsb.org/structure/5WJ2 |
+| 697 | `log://turn_44/get/https%3A/www.rcsb.org/downloads/fasta` | [get] https://www.rcsb.org/downloads/fasta |
+| 698 | `log://turn_44/search/PDB_REST_API_exact_FASTA_endpoint_rcsb_%225JZL%22_OR_%22sequence.fasta%22_OR_%22download/5` | [search] PDB REST API exact FASTA endpoint rcsb "5JZL" OR "sequence.fasta" OR "downloa… |
+| 699 | `log://turn_44/update/discovering_donor/acceptor_FASTA_%2B_acceptor_candidates_%2B_antibody_target` | [update status=155] discovering donor/acceptor FASTA + acceptor candidates + antibody target |
+| 702 | `assistant://45` | [assistant emission — see turns/] |
+| 703 | `system://45` | [system prompt] |
+| 704 | `user://45` | [user packet (assembled context)] |
+| 705 | `model://45` | [model usage record] |
+| 706 | `reasoning://45` | [think] # Distillation Stage Plan 1. **Donor (5JZL - muGFP/usGFP, Ex~505nm)**: Promot… |
+| 707 | `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/5JZL/1` | [get] https://data.rcsb.org/rest/v1/core/sequence/5JZL/1 |
+| 708 | `log://turn_45/get/https%3A/www.rcsb.org/structure/5WJ2` | [get] https://www.rcsb.org/structure/5WJ2 |
+| 709 | `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/2IB5/1` | [get] https://data.rcsb.org/rest/v1/core/sequence/2IB5/1 |
+| 710 | `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/4KGE/1` | [get] https://data.rcsb.org/rest/v1/core/sequence/4KGE/1 |
+| 711 | `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/6AA7/1` | [get] https://data.rcsb.org/rest/v1/core/sequence/6AA7/1 |
+| 712 | `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/3ADF/1` | [get] https://data.rcsb.org/rest/v1/core/sequence/3ADF/1 |
+| 713 | `log://turn_45/search/PDB_REST_API_%22sequence/%7Bid%7D/1%22_OR_%22data.rcsb.org/rest/v1/core/sequence%22_FASTA_5J` | [search] PDB REST API "sequence/{id}/1" OR "data.rcsb.org/rest/v1/core/sequence" FASTA… |
+| 714 | `log://turn_45/update/discovering_exact_PDB_FASTA_API_%2B_acceptor/molecule_binder_candidates` | [update status=155] discovering exact PDB FASTA API + acceptor/molecule binder candidates |
+| 717 | `assistant://46` | [assistant emission — see turns/] |
+| 718 | `system://46` | [system prompt] |
+| 719 | `user://46` | [user packet (assembled context)] |
+| 720 | `model://46` | [model usage record] |
+| 721 | `reasoning://46` | [think] # Distillation Stage Plan 1. **Donor (5JZL - green FP, Ex~505nm)**: Confirmed… |
+| 722 | `log://turn_46/get/https%3A/www.rcsb.org/structure/6AA7` | [get] https://www.rcsb.org/structure/6AA7 |
+| 723 | `log://turn_46/get/https%3A/www.rcsb.org/structure/2IB5` | [get] https://www.rcsb.org/structure/2IB5 |
+| 724 | `log://turn_46/get/https%3A/files.rcsb.org/download/5JZL.fasta` | [get] https://files.rcsb.org/download/5JZL.fasta |
+| 725 | `log://turn_46/get/https%3A/files.rcsb.org/download/6AA7.fasta` | [get] https://files.rcsb.org/download/6AA7.fasta |
+| 726 | `https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1` | [https] |
+| 727 | `log://turn_46/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1 |
+| 728 | `log://turn_46/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 729 | `https://www.blopig.com/blog/2025/09/exploring-the-protein-data-bank-programmatically` | [https] |
+| 730 | `https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2020q3/query.html` | [https] |
+| 731 | `log://turn_46/search/PDB_REST_API_FASTA_exact_endpoint_data.rcsb.org_%225JZL%22_OR_%22sequence_fasta%22_OR_%22p` | [search] PDB REST API FASTA exact endpoint data.rcsb.org "5JZL" OR "sequence fasta" OR… |
+| 732 | `log://turn_46/update/discovering_donor/acceptor_FASTA_sequences_%2B_binder_candidates_from_RCSB_pages` | [update status=155] discovering donor/acceptor FASTA sequences + binder candidates from RCSB pages |
+| 735 | `assistant://47` | [assistant emission — see turns/] |
+| 736 | `system://47` | [system prompt] |
+| 737 | `user://47` | [user packet (assembled context)] |
+| 738 | `model://47` | [model usage record] |
+| 739 | `reasoning://47` | [think] Distillation stage: Key unresolved unknowns are api/pdb_sequences (need FASTA… |
+| 740 | `log://turn_47/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1 |
+| 741 | `log://turn_47/get/https%3A/www.rcsb.org/structure/6AA7` | [get] https://www.rcsb.org/structure/6AA7 |
+| 742 | `log://turn_47/get/https%3A/www.rcsb.org/structure/2IB5` | [get] https://www.rcsb.org/structure/2IB5 |
+| 743 | `log://turn_47/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 744 | `log://turn_47/update/distilling_donor/acceptor_sequences_from_PDB_APIs_%2B_scanning_binders` | [update status=155] distilling donor/acceptor sequences from PDB APIs + scanning binders |
+| 747 | `assistant://48` | [assistant emission — see turns/] |
+| 748 | `system://48` | [system prompt] |
+| 749 | `user://48` | [user packet (assembled context)] |
+| 750 | `model://48` | [model usage record] |
+| 751 | `reasoning://48` | [think] Current stage: Distillation. Key unknowns: fpbase donor/acceptor sequences fr… |
+| 752 | `https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1` | [https] |
+| 753 | `log://turn_48/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1 |
+| 754 | `log://turn_48/get/https%3A/www.rcsb.org/structure/3ADF` | [get] https://www.rcsb.org/structure/3ADF |
+| 755 | `https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1` | [https] |
+| 756 | `log://turn_48/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1 |
+| 757 | `https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1` | [https] |
+| 758 | `log://turn_48/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1 |
+| 759 | `log://turn_48/get/known%3A/files/pdb_ids_full_list` | [get] known://files/pdb_ids_full_list |
+| 760 | `known://sequence/donor_5JZL` | [known] # Related [prompt requirements](prompt://1) [fpbase donor](known://api/fpbase… |
+| 761 | `log://turn_48/set/known%3A/sequence/donor_5JZL` | [set] known://sequence/donor_5JZL |
+| 762 | `log://turn_48/set/env%3A/turn_26/cat_/app/pdb_ids.txt_1` | [set] (no target) |
+| 763 | `log://turn_48/set/https%3A/www.rcsb.org/structure/5JZL` | [set] (no target) |
+| 764 | `log://turn_48/set/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1` | [set] (no target) |
+| 765 | `log://turn_48/update/distilling_donor_sequence%3B_discovering_acceptor(6AA7)%2Bbinder_sequences` | [update status=155] distilling donor sequence; discovering acceptor(6AA7)+binder sequences |
+| 768 | `assistant://49` | [assistant emission — see turns/] |
+| 769 | `system://49` | [system prompt] |
+| 770 | `user://49` | [user packet (assembled context)] |
+| 771 | `model://49` | [model usage record] |
+| 772 | `reasoning://49` | [think] Distillation Stage: Key unresolved unknowns need sequences for fusion protein… |
+| 773 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1 |
+| 774 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1 |
+| 775 | `https://data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1` | [https] |
+| 776 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1 |
+| 777 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1 |
+| 778 | `https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1` | [https] |
+| 779 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1 |
+| 780 | `https://data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1` | [https] |
+| 781 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1 |
+| 782 | `https://data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1` | [https] |
+| 783 | `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1 |
+| 784 | `log://turn_49/update/discovering_acceptor/binder_polymer_entity_sequences` | [update status=155] discovering acceptor/binder polymer_entity sequences |
+| 787 | `assistant://50` | [assistant emission — see turns/] |
+| 788 | `system://50` | [system prompt] |
+| 789 | `user://50` | [user packet (assembled context)] |
+| 790 | `model://50` | [model usage record] |
+| 791 | `reasoning://50` | [think] Distillation stage: All critical unknowns have source data available. Need to… |
+| 792 | `content://50` | [content] |
+| 793 | `log://turn_50/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1 |
+| 794 | `log://turn_50/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1 |
+| 795 | `log://turn_50/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1` | [get] https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1 |
+| 796 | `known://sequence/acceptor_6AA7` | [known] # Related [prompt requirements](prompt://1) [fpbase acceptor](known://api/fpb… |
+| 797 | `log://turn_50/set/known%3A/sequence/acceptor_6AA7` | [set] known://sequence/acceptor_6AA7 |
+| 798 | `known://sequence/binder_molecule_candidate` | [known] # Related [prompt requirements](prompt://1) [SMILES](unknown://binder/molecul… |
+| 799 | `log://turn_50/set/known%3A/sequence/binder_molecule_candidate` | [set] known://sequence/binder_molecule_candidate |
+| 800 | `known://binder/antibody_target_rejected` | [known] # Related [antibody fasta](known://files/antibody_fasta_contents) [searches](… |
+| 801 | `log://turn_50/set/known%3A/binder/antibody_target_rejected` | [set] known://binder/antibody_target_rejected |
+| 802 | `log://turn_50/set/unknown%3A/api/pdb_sequences` | [set] (no target) |
+| 803 | `log://turn_50/set/unknown%3A/binder/antibody_target` | [set] (no target) |
+| 804 | `log://turn_50/set/unknown%3A/binder/molecule` | [set] (no target) |
+| 805 | `log://turn_50/set/unknown%3A/api/fpbase_acceptor` | [set] (no target) |
+| 806 | `log://turn_50/set/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/*` | [set] (no target) |
+| 807 | `log://turn_50/update/all_unknowns_resolved/rejected%3B_ready_for_deployment` | [update status=156] all unknowns resolved/rejected; ready for deployment |
+| 810 | `assistant://51` | [assistant emission — see turns/] |
+| 811 | `system://51` | [system prompt] |
+| 812 | `user://51` | [user packet (assembled context)] |
+| 813 | `model://51` | [model usage record] |
+| 814 | `reasoning://51` | [think] All key unknowns resolved via distillation: - Donor: muGFP (5JZL) ✓ Ex~505nm … |
+| 815 | `log://turn_51/set/env%3A/turn_*` | [set] (no target) |
+| 816 | `log://turn_51/set/log%3A/turn_*` | [set] (no target) |
+| 817 | `log://turn_51/set/https%3A/www.rcsb.org/structure/*` | [set] (no target) |
+| 818 | `log://turn_51/set/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/*` | [set] (no target) |
+| 819 | `log://turn_51/set/https%3A/www.fpbase.org/*` | [set] (no target) |
+| 820 | `log://turn_51/set/search%3A/turn_*` | [set] (no target) |
+| 821 | `log://turn_51/set/prompt%3A/1` | [set] (no target) |
+| 822 | `log://turn_51/set/known%3A/files/*` | [set] (no target) |
+| 823 | `log://turn_51/set/known%3A/api/*` | [set] (no target) |
+| 824 | `log://turn_51/set/unknown%3A/*` | [set] (no target) |
+| 825 | `log://turn_51/update/all_unknowns_resolved_and_demoted%3B_ready_for_Deployment_Stage` | [update status=167] all unknowns resolved and demoted; ready for Deployment Stage |
+| 828 | `log://turn_52/error/Unclosed_%3Cset%3E_tag_%E2%80%94_content_captured_anyway` | [error status=422] Unclosed <set> tag — content captured anyway |
+| 829 | `assistant://52` | [assistant emission — see turns/] |
+| 830 | `system://52` | [system prompt] |
+| 831 | `user://52` | [user packet (assembled context)] |
+| 832 | `model://52` | [model usage record] |
+| 833 | `reasoning://52` | [think] All key unknowns resolved via distillation: - Donor: muGFP (5JZL) - green FP,… |
+| 834 | `log://turn_52/set/fusion.fasta` | [set] fusion.fasta |
+| 836 | `fusion.fasta` | [(none)] |
+| 837 | `log://turn_52/sh/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c` | [sh] grep -v '^>' fusion.fasta \| tr -d '\n' \| wc -c |
+| 839 | `sh://turn_52/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_1` | [sh] |
+| 840 | `sh://turn_52/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_2` | [sh] |
+| 843 | `log://turn_52/env/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(` | [env] awk '/^>/ {if (s) print length(s); s=""} !/^>/ {s=s$0} END {if (s) print leng… |
+| 845 | `env://turn_52/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(_1` | [env] |
+| 846 | `env://turn_52/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(_2` | [env] |
+| 849 | `log://turn_52/set/fusion_dna_optimized.gb` | [set] fusion_dna_optimized.gb |
+| 851 | `fusion_dna_optimized.gb` | [(none)] |
+| 852 | `log://turn_52/error/Missing_update` | [error status=422] Missing update |
+| 855 | `assistant://53` | [assistant emission — see turns/] |
+| 856 | `system://53` | [system prompt] |
+| 857 | `user://53` | [user packet (assembled context)] |
+| 858 | `model://53` | [model usage record] |
+| 859 | `reasoning://53` | [think] All key unknowns resolved: donor muGFP(5JZL), acceptor AdRed(6AA7), DHFR extr… |
+| 860 | `log://turn_53/sh/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c` | [sh] grep -v '^>' fusion.fasta \| tr -d '\n' \| wc -c |
+| 862 | `sh://turn_53/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_1` | [sh] |
+| 863 | `sh://turn_53/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_2` | [sh] |
+| 866 | `log://turn_53/sh/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(` | [sh] awk '/^>/ {if (s) print length(s); s=""} !/^>/ {s=s$0} END {if (s) print leng… |
+| 868 | `sh://turn_53/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(_1` | [sh] |
+| 869 | `sh://turn_53/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(_2` | [sh] |
+| 872 | `log://turn_53/set/fusion.fasta` | [set] (no target) |
+| 873 | `log://turn_53/set/fusion_dna_optimized.gb` | [set] (no target) |
+| 874 | `log://turn_53/update/fusion_protein_designed/validated%3B_DNA_optimized` | [update status=177] fusion protein designed/validated; DNA optimized |
+| 877 | `assistant://54` | [assistant emission — see turns/] |
+| 878 | `system://54` | [system prompt] |
+| 879 | `user://54` | [user packet (assembled context)] |
+| 880 | `model://54` | [model usage record] |
+| 881 | `reasoning://54` | [think] All key components distilled: donor muGFP(5JZL), acceptor AdRed(6AA7), DHFR, … |
+| 882 | `log://turn_54/sh/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c` | [sh] grep -v '^>' fusion.fasta \| tr -d '\n' \| wc -c |
+| 884 | `sh://turn_54/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_1` | [sh] |
+| 885 | `sh://turn_54/grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_2` | [sh] |
+| 888 | `log://turn_54/sh/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(` | [sh] awk '/^>/ {if (s) print length(s); s=""} !/^>/ {s=s$0} END {if (s) print leng… |
+| 890 | `sh://turn_54/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(_1` | [sh] |
+| 891 | `sh://turn_54/awk_'/%5E%3E/_%7Bif_(s)_print_length(s)%3B_s%3D%22%22%7D_!/%5E%3E/_%7Bs%3Ds%240%7D_END_%7Bif_(s)_print_length(_2` | [sh] |
+| 894 | `log://turn_54/sh/grep_-c_'%5E%3E'_fusion.fasta` | [sh] grep -c '^>' fusion.fasta |
+| 896 | `sh://turn_54/grep_-c_'%5E%3E'_fusion.fasta_1` | [sh] |
+| 897 | `sh://turn_54/grep_-c_'%5E%3E'_fusion.fasta_2` | [sh] |
+| 900 | `log://turn_54/env/grep_-o_'%5BATCG%5D'_fusion_dna_optimized.gb_%7C_sort_%7C_uniq_-c` | [env] grep -o '[ATCG]' fusion_dna_optimized.gb \| sort \| uniq -c |
+| 902 | `env://turn_54/grep_-o_'%5BATCG%5D'_fusion_dna_optimized.gb_%7C_sort_%7C_uniq_-c_1` | [env] |
+| 903 | `env://turn_54/grep_-o_'%5BATCG%5D'_fusion_dna_optimized.gb_%7C_sort_%7C_uniq_-c_2` | [env] |
+| 906 | `log://turn_54/sh/%5B_-f_fusion.fasta_%5D_%26%26_%5B_-f_fusion_dna_optimized.gb_%5D` | [sh] [ -f fusion.fasta ] && [ -f fusion_dna_optimized.gb ] |
+| 908 | `sh://turn_54/%5B_-f_fusion.fasta_%5D_%26%26_%5B_-f_fusion_dna_optimized.gb_%5D_1` | [sh] |
+| 909 | `sh://turn_54/%5B_-f_fusion.fasta_%5D_%26%26_%5B_-f_fusion_dna_optimized.gb_%5D_2` | [sh] |
+| 912 | `log://turn_54/update/validating_fusion.fasta_%2B_DNA%3B_all_deliverables_complete` | [update status=177] validating fusion.fasta + DNA; all deliverables complete |
+| 915 | `assistant://55` | [assistant emission — see turns/] |
+| 916 | `system://55` | [system prompt] |
+| 917 | `user://55` | [user packet (assembled context)] |
+| 918 | `model://55` | [model usage record] |
+| 919 | `reasoning://55` | [think] All key components distilled: - Donor: muGFP (5JZL) ~239aa ✓505nm Ex - Accept… |
+| 920 | `log://turn_55/sh/grep_-c_'%5E%3E'_fusion.fasta_%26%26_grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_%26%26_g` | [sh] grep -c '^>' fusion.fasta && grep -v '^>' fusion.fasta \| tr -d '\n' \| wc -c &… |
+| 922 | `sh://turn_55/grep_-c_'%5E%3E'_fusion.fasta_%26%26_grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_%26%26_g_1` | [sh] |
+| 923 | `sh://turn_55/grep_-c_'%5E%3E'_fusion.fasta_%26%26_grep_-v_'%5E%3E'_fusion.fasta_%7C_tr_-d_'%5Cn'_%7C_wc_-c_%26%26_g_2` | [sh] |
+| 926 | `log://turn_55/sh/%5B_-f_fusion.fasta_%5D_%26%26_%5B_-f_fusion_dna_optimized.gb_%5D_%26%26_grep_-q_'fusion_DHFR_FR` | [sh] [ -f fusion.fasta ] && [ -f fusion_dna_optimized.gb ] && grep -q 'fusion_DHFR… |
+| 928 | `sh://turn_55/%5B_-f_fusion.fasta_%5D_%26%26_%5B_-f_fusion_dna_optimized.gb_%5D_%26%26_grep_-q_'fusion_DHFR_FR_1` | [sh] |
+| 929 | `sh://turn_55/%5B_-f_fusion.fasta_%5D_%26%26_%5B_-f_fusion_dna_optimized.gb_%5D_%26%26_grep_-q_'fusion_DHFR_FR_2` | [sh] |
+| 932 | `log://turn_55/update/FRET_fusion_complete%3A_fusion.fasta_(1105aa)/_fusion_dna_optimized.gb_(2970bp_GC5` | [update status=200] FRET fusion complete: fusion.fasta (1105aa), fusion_dna_optimized.gb (2970bp … |