@possumtech/rummy 2.0.1 → 2.2.0

package/audit/sweep/protein-assembly/turns/turn_047.md

@@ -0,0 +1,201 @@
+# turn 047
+
+tokens: prompt=65310 cached=6736 completion=538 reasoning=0 total=65848 cost=0
+created: 2026-05-02 00:08:49
+
+update: status=155 body=distilling donor/acceptor sequences from PDB APIs + scanning binders
+
+---
+
+## reasoning (think)
+
+```
+Distillation stage: Key unresolved unknowns are api/pdb_sequences (need FASTA for donor/acceptor/binder from pdb_ids.txt), binder/antibody_target (antigen sequence antibody binds), binder/molecule (protein binding SMILES from pdb_ids.txt). 
+
+From context:
+- Donor: 5JZL (muGFP/usGFP, green Ex~488-505nm) - https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1 has sequence "MRGSHHHHHHGSSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLCROVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK" (remove N-Met, tags)
+- Acceptor candidates: 6AA7 (red FP Em 612nm perfect), 2IB5 (yellow mutant), 4KGE (NIR), etc.
+- DHFR: known://sequence/dhfr has mature sequence ISLIAALAV... 
+- Antibody target/molecule binder still unknown - need to distill from PDB pages or reject if not found.
+
+Plan: 
+1. Promote 5JZL polymer_entity for donor sequence extraction
+2. Get acceptor sequences (6AA7 first - Em=612nm matches 610nm filter)
+3. Check PDB pages for antibody target (none found) and molecule binder (SMILES search failed)
+4. Distill donor/acceptor sequences into known://sequence/*
+5. Reject unresolvable unknowns (antibody target, molecule binder if no match)
+6. Demote heavy pages after distillation
+```
+
+## assistant emission
+
+```
+<think>
+Distillation stage: Key unresolved unknowns are api/pdb_sequences (need FASTA for donor/acceptor/binder from pdb_ids.txt), binder/antibody_target (antigen sequence antibody binds), binder/molecule (protein binding SMILES from pdb_ids.txt). 
+
+From context:
+- Donor: 5JZL (muGFP/usGFP, green Ex~488-505nm) - https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1 has sequence "MRGSHHHHHHGSSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLCROVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK" (remove N-Met, tags)
+- Acceptor candidates: 6AA7 (red FP Em 612nm perfect), 2IB5 (yellow mutant), 4KGE (NIR), etc.
+- DHFR: known://sequence/dhfr has mature sequence ISLIAALAV... 
+- Antibody target/molecule binder still unknown - need to distill from PDB pages or reject if not found.
+
+Plan: 
+1. Promote 5JZL polymer_entity for donor sequence extraction
+2. Get acceptor sequences (6AA7 first - Em=612nm matches 610nm filter)
+3. Check PDB pages for antibody target (none found) and molecule binder (SMILES search failed)
+4. Distill donor/acceptor sequences into known://sequence/*
+5. Reject unresolvable unknowns (antibody target, molecule binder if no match)
+6. Demote heavy pages after distillation
+</think>
+
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1" line="1" limit="20"/>
+<get path="https://www.rcsb.org/structure/6AA7" line="1" limit="50"/>
+<get path="https://www.rcsb.org/structure/2IB5" line="1" limit="50"/>
+<get path="known://files/pdb_ids_full_list"/>
+
+<update status="155">distilling donor/acceptor sequences from PDB APIs + scanning binders</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_47/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1","lineStart":1,"lineEnd":3,"totalLines":3,"action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1
+[lines 1–3 / 3 total]
+# 1
+
+{"entity_poly":{"nstd_linkage":"no","nstd_monomer":"yes","pdbx_seq_one_letter_code":"MRGSHHHHHHGSSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTL(CRO)VLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK","pdbx_seq_one_letter_code_can":"MRGSHHHHHHGSSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLXVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK","pdbx_strand_id":"A,B","rcsb_artifact_monomer_count":1,"rcsb_conflict_count":7,"rcsb_deletion_count":0,"rcsb_entity_polymer_type":"Protein","rcsb_insertion_count":0,"rcsb_mutation_count":1,"rcsb_non_std_monomer_count":1,"rcsb_non_std_monomers":["CRO"],"rcsb_sample_sequence_length":247,"type":"polypeptide(L)"},"entity_src_gen":[{"gene_src_common_name":"Jellyfish","pdbx_alt_source_flag":"sample","pdbx_beg_seq_num":1,"pdbx_end_seq_num":247,"pdbx_gene_src_gene":"gfp","pdbx_gene_src_ncbi_taxonomy_id":"6100","pdbx_gene_src_scientific_name":"Aequorea victoria","pdbx_host_org_ncbi_taxonomy_id":"469008","pdbx_host_org_scientific_name":"Escherichia coli BL21(DE3)","pdbx_host_org_strain":"BL21(DE3)","pdbx_seq_type":"Biological sequence","pdbx_src_id":1}],"rcsb_cluster_flexibility":{"avg_rmsd":0.985,"label":"Low","link":"https://pdbflex.org/cluster.html#!/5dtxA/27637/5jzlA","max_rmsd":22.53,"provenance_code":"PDBFlex"},"rcsb_cluster_membership":[{"cluster_id":67718,"identity":100},{"cluster_id":51815,"identity":95},{"cluster_id":40296,"identity":90},{"cluster_id":2258,"identity":70},{"cluster_id":1101,"identity":50},{"cluster_id":353,"identity":30}],"rcsb_entity_host_organism":[{"beg_seq_num":1,"end_seq_num":247,"ncbi_common_names":["Escherichia coli str. 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BL21(DE3)"},{"depth":10,"id":"469008","name":"Escherichia coli strain BL21(DE3)"}]}],"rcsb_entity_source_organism":[{"beg_seq_num":1,"common_name":"Jellyfish","end_seq_num":247,"ncbi_common_names":["Mesonema victoria"],"ncbi_parent_scientific_name":"Eukaryota","ncbi_scientific_name":"Aequorea victoria","ncbi_taxonomy_id":6100,"pdbx_src_id":1,"provenance_source":"Primary Data","scientific_name":"Aequorea victoria","source_type":"genetically engineered","taxonomy_lineage":[{"depth":1,"id":"131567","name":"cellular organisms"},{"depth":1,"id":"131567","name":"biota"},{"depth":2,"id":"2759","name":"Eukaryota"},{"depth":2,"id":"2759","name":"Eucarya"},{"depth":2,"id":"2759","name":"Eucaryotae"},{"depth":2,"id":"2759","name":"Eukarya"},{"depth":2,"id":"2759","name":"Eukaryotae"},{"depth":2,"id":"2759","name":"eukaryotes"},{"depth":3,"id":"33154","name":"Opisthokonta"},{"depth":3,"id":"33154","name":"Fungi/Metazoa group"},{"depth":3,"id":"33154","name":"opisthokonts"},{"depth":4,"id":"33208","name":"Metazoa"},{"depth":4,"id":"33208","name":"Animalia"},{"depth":4,"id":"33208","name":"animals"},{"depth":4,"id":"33208","name":"metazoans"},{"depth":4,"id":"33208","name":"multicellular animals"},{"depth":5,"id":"6072","name":"Eumetazoa"},{"depth":6,"id":"6073","name":"Cnidaria"},{"depth":6,"id":"6073","name":"cnidarians"},{"depth":6,"id":"6073","name":"coelenterates"},{"depth":7,"id":"6074","name":"Hydrozoa"},{"depth":7,"id":"6074","name":"hydrozoans"},{"depth":8,"id":"37516","name":"Hydroidolina"},{"depth":8,"id":"37516","name":"Hydroida"},{"depth":8,"id":"37516","name":"Hydroidomedusae"},{"depth":9,"id":"500008","name":"Leptothecata"},{"depth":9,"id":"500008","name":"Calyptoblastea"},{"depth":9,"id":"500008","name":"Leptomedusae"},{"depth":9,"id":"500008","name":"Leptothecatae"},{"depth":9,"id":"500008","name":"Thecata"},{"depth":10,"id":"128126","name":"Aequoreidae"},{"depth":11,"id":"6099","name":"Aequorea"},{"depth":12,"id":"6100","name":"Aequorea victoria"},{"depth":12,"id":"6100","name":"Mesonema victoria"}],"rcsb_gene_name":[{"provenance_source":"Primary Data","value":"gfp"}]}],"rcsb_polymer_entity":{"formula_weight":28.076,"pdbx_description":"Green 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protein","provenance_source":"UNIPROT","type":"InterPro","annotation_lineage":[{"id":"IPR009017","name":"Green fluorescent protein"}]}],"rcsb_polymer_entity_container_identifiers":{"asym_ids":["A","B"],"auth_asym_ids":["A","B"],"chem_comp_monomers":["ALA","ARG","ASN","ASP","CRO","CYS","GLN","GLU","GLY","HIS","ILE","LEU","LYS","MET","PHE","PRO","SER","THR","TRP","TYR","VAL"],"chem_comp_nstd_monomers":["CRO"],"entity_id":"1","entry_id":"5JZL","rcsb_id":"5JZL_1","uniprot_ids":["P42212"],"reference_sequence_identifiers":[{"database_accession":"P42212","database_name":"UniProt","entity_sequence_coverage":0.9473684210526315,"provenance_source":"SIFTS","reference_sequence_coverage":0.9831932773109243}]},"rcsb_polymer_entity_feature":[{"assignment_version":"V1.0","feature_id":"monomer_feature_1","name":"Parent monomer THR, TYR, GLY","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":76}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["THR"," 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binding sites","provenance_source":"Anchor2","type":"disorder_binding","feature_positions":[{"beg_seq_id":1,"values":[0.51,0.5,0.49,0.48,0.48,0.47,0.47,0.47,0.47,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.48,0.47,0.47,0.46,0.45,0.44,0.44,0.44,0.43,0.43,0.43,0.43,0.43,0.43,0.43,0.42,0.42,0.41,0.4,0.38,0.37,0.36,0.35,0.34,0.34,0.33,0.33,0.33,0.33,0.33,0.34,0.34,0.34,0.34,0.35,0.35,0.36,0.37,0.38,0.4,0.41,0.42,0.43,0.42,0.4,0.39,0.37,0.36,0.35,0.35,0.34,0.34,0.34,0.34,0.35,0.37,0.39,0.41,0.43,0.42,0.4,0.38,0.37,0.36,0.35,0.34,0.35,0.35,0.37,0.37,0.38,0.38,0.39,0.39,0.39,0.4,0.4,0.4,0.39,0.38,0.37,0.37,0.36,0.36,0.35,0.34,0.33,0.33,0.32,0.32,0.32,0.33,0.33,0.33,0.34,0.35,0.36,0.36,0.37,0.38,0.38,0.38,0.38,0.39,0.4,0.41,0.41,0.41,0.4,0.4,0.39,0.38,0.38,0.38,0.38,0.37,0.37,0.36,0.37,0.37,0.39,0.41,0.42,0.43,0.43,0.42,0.41,0.39,0.37,0.36,0.36,0.36,0.37,0.38,0.38,0.39,0.4,0.42,0.43,0.42,0.41,0.41,0.41,0.41,0.42,0.42,0.43,0.43,0.42,0.41,0.41,0.41,0.41,0.41,0.41,0.41,0.41,0.41,0.41,0.41,0.41,0.42,0.42,0.42,0.42,0.43,0.43,0.43,0.43,0.43,0.43,0.44,0.44,0.44,0.44,0.45,0.45,0.46,0.46,0.47,0.47,0.47,0.47,0.46,0.46,0.46,0.46,0.46,0.46,0.46,0.46,0.46,0.45,0.45,0.45,0.44,0.44,0.44,0.44,0.44,0.44,0.44,0.44,0.44,0.44,0.43,0.43,0.43,0.43,0.42,0.42,0.42,0.42,0.43,0.43,0.43,0.43,0.43,0.43,0.43,0.42,0.42,0.41,0.4]}]},{"name":"Disordered regions","provenance_source":"IUPred2(short)","type":"disorder","feature_positions":[{"beg_seq_id":1,"values":[0.98,0.97,0.96,0.94,0.93,0.91,0.89,0.81,0.7,0.67,0.63,0.63,0.58,0.61,0.55,0.51,0.47,0.48,0.42,0.42,0.42,0.41,0.35,0.35,0.34,0.33,0.3,0.22,0.27,0.3,0.29,0.28,0.33,0.36,0.35,0.39,0.45,0.45,0.43,0.48,0.48,0.47,0.39,0.44,0.37,0.36,0.29,0.23,0.21,0.21,0.26,0.27,0.26,0.18,0.2,0.15,0.17,0.11,0.15,0.14,0.1,0.06,0.06,0.1,0.06,0.09,0.06,0.06,0.06,0.06,0.06,0.06,0.04,0.04,0.07,0.05,0.06,0.05,0.08,0.06,0.06,0.06,0.05,0.05,0.05,0.07,0.06,0.12,0.18,0.26,0.29,0.23,0.26,0.35,0.33,0.33,0.28,0.32,0.25,0.25,0.27,0.27,0.35,0.43,0.36,0.35,0.37,0.4,0.34,0.35,0.29,0.34,0.32,0.31,0.3,0.3,0.3,0.3,0.23,0.31,0.31,0.23,0.24,0.17,0.17,0.23,0.17,0.17,0.12,0.13,0.13,0.17,0.18,0.25,0.18,0.12,0.12,0.12,0.16,0.14,0.15,0.1,0.15,0.09,0.13,0.14,0.15,0.22,0.17,0.18,0.13,0.12,0.1,0.1,0.1,0.17,0.23,0.24,0.23,0.17,0.25,0.22,0.23,0.16,0.24,0.18,0.18,0.19,0.19,0.19,0.27,0.35,0.36,0.39,0.33,0.35,0.27,0.24,0.25,0.27,0.29,0.3,0.34,0.41,0.47,0.51,0.5,0.5,0.5,0.5,0.59,0.55,0.49,0.44,0.47,0.53,0.53,0.59,0.56,0.49,0.48,0.54,0.54,0.53,0.48,0.43,0.41,0.48,0.48,0.5,0.5,0.49,0.52,0.56,0.63,0.6,0.55,0.5,0.44,0.44,0.52,0.51,0.47,0.44,0.41,0.44,0.5,0.42,0.42,0.41,0.38,0.36,0.34,0.36,0.3,0.22,0.21,0.28,0.37,0.47,0.56,0.58,0.63,0.71,0.75,0.81,0.86]}]}],"rcsb_polymer_entity_feature_summary":[{"count":1,"coverage":0.05263,"maximum_length":13,"minimum_length":13,"type":"artifact"},{"count":1,"coverage":0.00405,"type":"mutation"},{"count":1,"coverage":0.00405,"type":"modified_monomer"}],"rcsb_polymer_entity_group_membership":[{"aggregation_method":"matching_uniprot_accession","group_id":"P42212","aligned_regions":[{"entity_beg_seq_id":14,"length":234,"ref_beg_seq_id":3}]},{"aggregation_method":"sequence_identity","group_id":"40296_90","similarity_cutoff":90.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":247,"ref_beg_seq_id":103}]},{"aggregation_method":"sequence_identity","group_id":"51815_95","similarity_cutoff":95.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":247,"ref_beg_seq_id":103}]},{"aggregation_method":"sequence_identity","group_id":"2258_70","similarity_cutoff":70.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":75,"ref_beg_seq_id":443},{"entity_beg_seq_id":76,"length":172,"ref_beg_seq_id":520}]},{"aggregation_method":"sequence_identity","group_id":"1101_50","similarity_cutoff":50.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":2,"ref_beg_seq_id":480},{"entity_beg_seq_id":3,"length":73,"ref_beg_seq_id":484},{"entity_beg_seq_id":76,"length":172,"ref_beg_seq_id":559}]},{"aggregation_method":"sequence_identity","group_id":"67718_100","similarity_cutoff":100.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":247,"ref_beg_seq_id":103}]},{"aggregation_method":"sequence_identity","group_id":"353_30","similarity_cutoff":30.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":11,"ref_beg_seq_id":1010},{"entity_beg_seq_id":12,"length":64,"ref_beg_seq_id":1027},{"entity_beg_seq_id":76,"length":172,"ref_beg_seq_id":1093}]}],"rcsb_id":"5JZL_1"}
+```
+
+### `log://turn_47/get/https%3A/www.rcsb.org/structure/6AA7`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/6AA7","lineStart":1,"lineEnd":50,"totalLines":262,"action":"get"}
+
+```
+https://www.rcsb.org/structure/6AA7
+[lines 1–50 / 262 total]
+# RCSB PDB - 6AA7: Fluorescent protein from Acropora digitifera
+
+##  6AA7 | pdb\_00006aa7[](https://www.wwpdb.org/documentation/new-format-for-pdb-ids)
+
+#### Fluorescent protein from Acropora digitifera
+
+  
+
+* * *
+
+  
+
+This is version 3.0 of the entry. See complete
+[history](https://www.rcsb.org/versions/6AA7) .
+
+  
+
+#### Spectral and structural analysis of a red fluorescent protein from Acropora digitifera.
+
+[Kim, S.E.](https://www.rcsb.org/search?q=citation.rcsb_authors:Kim,%20S.E.) ,
+[Hwang, K.Y.](https://www.rcsb.org/search?q=citation.rcsb_authors:Hwang,%20K.Y.)
+, [Nam, K.H.](https://www.rcsb.org/search?q=citation.rcsb_authors:Nam,%20K.H.)
+
+(2019) Protein Sci **28**: 375-381
+
+*   **PubMed:** [30368951](https://www.rcsb.org/search?q=rcsb_pubmed_container_identifiers.pubmed_id:30368951) [Search on PubMed](http://www.ncbi.nlm.nih.gov/pubmed/?term=30368951)[Search on PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6319757)
+*   **DOI:** [https://doi.org/10.1002/pro.3540](https://doi.org/10.1002/pro.3540)
+  
+*   **PubMed Abstract:** 
+    
+    Fluorescent proteins (FPs) possess a wide variety of spectral properties that
+    make them of widespread interest as optical markers. These proteins can be
+    applied as pH indicators or metal biosensors. The discovery and characterization
+    of new fluorescent proteins is expected to further extend their application.
+    Here, we report the spectral and structural analysis of a red fluorescent
+    protein from Acropora digitifera (designated AdRed). This protein shows a
+    tetrameric state and is red emitting, with excitation and emission maxima at 567
+    and 612 nm, respectively. Its crystal structure shows the tetrameric interface
+    stabilized by hydrogen bonding and salt bridges. The electron density map of the
+    chromophore, consisting of Asp66-Tyr67-Gly68, shows the decarboxylated side
+    chain of Asp66. Ser223, located near the chromophore, has the role of bridging
+    His202 and Glu221, and is part of the hydrogen bond network. Mutated AdRed with
+    Cys148Ser reveals a blue shift in fluorescence excitation and emission. Our
+    results provide insights into understanding the molecular function of AdRed and
+    other FPs.
+    
+
+* * *
+
+**Organizational Affiliation**: 
+```
+
+### `log://turn_47/get/https%3A/www.rcsb.org/structure/2IB5`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/2IB5","lineStart":1,"lineEnd":50,"totalLines":50,"action":"get"}
+
+```
+https://www.rcsb.org/structure/2IB5
+[lines 1–50 / 50 total]
+# RCSB PDB - 2IB5: Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
+
+#### Structural Characterization of a Blue Chromoprotein and Its Yellow Mutant from the Sea Anemone Cnidopus Japonicus
+
+[Chan, M.C.Y.](https://www.rcsb.org/search?q=citation.rcsb_authors:Chan,%20M.C.Y.)
+,
+[Karasawa, S.](https://www.rcsb.org/search?q=citation.rcsb_authors:Karasawa,%20S.)
+, [Mizuno, H.](https://www.rcsb.org/search?q=citation.rcsb_authors:Mizuno,%20H.)
+,
+[Bosanac, I.](https://www.rcsb.org/search?q=citation.rcsb_authors:Bosanac,%20I.)
+, [Ho, D.](https://www.rcsb.org/search?q=citation.rcsb_authors:Ho,%20D.) ,
+[Prive, G.G.](https://www.rcsb.org/search?q=citation.rcsb_authors:Prive,%20G.G.)
+,
+[Miyawaki, A.](https://www.rcsb.org/search?q=citation.rcsb_authors:Miyawaki,%20A.)
+, [Ikura, M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Ikura,%20M.)
+
+(2006) J Biological Chem **281**: 37813-37819
+
+*   **PubMed:** [17028187](https://www.rcsb.org/search?q=rcsb_pubmed_container_identifiers.pubmed_id:17028187) [Search on PubMed](http://www.ncbi.nlm.nih.gov/pubmed/?term=17028187)
+*   **DOI:** [https://doi.org/10.1074/jbc.M606921200](https://doi.org/10.1074/jbc.M606921200)
+  
+*   **PubMed Abstract:** 
+    
+    Green fluorescent protein (GFP) and its relatives (GFP protein family) have been
+    isolated from marine organisms such as jellyfish and corals that belong to the
+    phylum Cnidaria (stinging aquatic invertebrates). They are intrinsically
+    fluorescent proteins. In search of new members of the family of green
+    fluorescent protein family, we identified a non-fluorescent chromoprotein from
+    the Cnidopus japonicus species of sea anemone that possesses 45% sequence
+    identity to dsRed (a red fluorescent protein). This newly identified blue color
+    protein has an absorbance maximum of 610 nm and is hereafter referred to as
+    cjBlue. Determination of the cjBlue 1.8 A crystal structure revealed a
+    chromophore comprised of Gln(63)-Tyr(64)-Gly(65). The ring stacking between
+    Tyr(64) and His(197) stabilized the cjBlue trans chromophore conformation along
+    the Calpha2-Cbeta2 bond of 5-\[(4-hydroxyphenyl)methylene\]-imidazolinone, which
+    closely resembled that of the "Kindling Fluorescent Protein" and Rtms5.
+    Replacement of Tyr(64) with Leu in wild-type cjBlue produced a visible color
+    change from blue to yellow with a new absorbance maximum of 417 nm.
+    Interestingly, the crystal structure of the yellow mutant Y64L revealed two
+    His(197) imidazole ring orientations, suggesting a flip-flop interconversion
+    between the two conformations in solution. We conclude that the dynamics and
+    structure of the chromophore are both essential for the optical appearance of
+    these color proteins.
+    
+
+* * *
+
+**Organizational Affiliation**: 
+
+*   Division of Signaling Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
+```
+
+### `log://turn_47/get/known%3A/files/pdb_ids_full_list`
+scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
+
+```
+known://files/pdb_ids_full_list promoted
+```
+
+### `log://turn_47/update/distilling_donor/acceptor_sequences_from_PDB_APIs_%2B_scanning_binders`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+distilling donor/acceptor sequences from PDB APIs + scanning binders
+```
+

package/audit/sweep/protein-assembly/turns/turn_048.md

@@ -0,0 +1,169 @@
+# turn 048
+
+tokens: prompt=73647 cached=8332 completion=990 reasoning=0 total=74637 cost=0
+created: 2026-05-02 00:08:58
+
+update: status=155 body=distilling donor sequence; discovering acceptor(6AA7)+binder sequences
+
+---
+
+## reasoning (think)
+
+```
+Current stage: Distillation. Key unknowns: fpbase donor/acceptor sequences from pdb_ids.txt, antibody target, molecule binder from pdb_ids.txt, pdb sequences.
+
+Progress:
+- Donor: 5JZL = muGFP (green, Ex~488nm matches 505nm filter). Full sequence extracted from https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1: "MRGSHHHHHHGSSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLCROVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK" (remove N-Met, tags).
+- Acceptor candidates: 6AA7 (red FP, Em=612nm perfect for 610nm filter, Acropora digitifera), 2IB5 (blue chromoprotein/yellow mutant, Abs=610nm).
+- DHFR: Distilled, mature sequence ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR.
+- Antibody target & molecule binder unresolved - need sequences from pdb_ids.txt proteins.
+- Need 6AA7 sequence via same API, check binders.
+
+Plan: 
+1. Get acceptor sequence for 6AA7 (best Em=612nm).
+2. Resolve antibody target/molecule binder by checking RCSB pages.
+3. Distill donor sequence (trim artifacts).
+4. Demote heavy pages, promote sequences.
+5. Continue distillation.
+```
+
+## assistant emission
+
+```
+<think>
+Current stage: Distillation. Key unknowns: fpbase donor/acceptor sequences from pdb_ids.txt, antibody target, molecule binder from pdb_ids.txt, pdb sequences.
+
+Progress:
+- Donor: 5JZL = muGFP (green, Ex~488nm matches 505nm filter). Full sequence extracted from https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1: "MRGSHHHHHHGSSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLCROVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK" (remove N-Met, tags).
+- Acceptor candidates: 6AA7 (red FP, Em=612nm perfect for 610nm filter, Acropora digitifera), 2IB5 (blue chromoprotein/yellow mutant, Abs=610nm).
+- DHFR: Distilled, mature sequence ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR.
+- Antibody target & molecule binder unresolved - need sequences from pdb_ids.txt proteins.
+- Need 6AA7 sequence via same API, check binders.
+
+Plan: 
+1. Get acceptor sequence for 6AA7 (best Em=612nm).
+2. Resolve antibody target/molecule binder by checking RCSB pages.
+3. Distill donor sequence (trim artifacts).
+4. Demote heavy pages, promote sequences.
+5. Continue distillation.
+</think>
+
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1"/>
+<get path="https://www.rcsb.org/structure/3ADF"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1"/>
+<get path="known://files/pdb_ids_full_list"/>
+
+<set path="known://sequence/donor_5JZL" summary="sequence,donor,5JZL,muGFP,green,505nm" visibility="visible">
+# Related
+[prompt requirements](prompt://1)
+[fpbase donor](known://api/fpbase_donor)
+[pdb_ids](known://files/pdb_ids_full_list)
+[pdb 5JZL page](https://www.rcsb.org/structure/5JZL)
+[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1)
+[unknown resolved](unknown://api/fpbase_donor)
+[unknown resolved](unknown://api/pdb_sequences)
+
+# Donor: muGFP (5JZL) sequence
+Monomeric ultra-stable GFP. Green FP for 505nm excitation.
+
+**Full sequence** (247aa, remove N-Met + His-tag + CRO chromophore artifact):
+KGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK
+
+**Mature coding sequence length**: ~717nt (239aa).
+</set>
+
+<set path="env://turn_26/cat_/app/pdb_ids.txt_1" visibility="summarized"/>
+<set path="https://www.rcsb.org/structure/5JZL" visibility="summarized"/>
+<set path="https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1" visibility="summarized"/>
+
+<update status="155">distilling donor sequence; discovering acceptor(6AA7)+binder sequences</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_48/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1 promoted
+```
+
+### `log://turn_48/get/https%3A/www.rcsb.org/structure/3ADF`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/3ADF","action":"get"}
+
+```
+https://www.rcsb.org/structure/3ADF promoted
+```
+
+### `log://turn_48/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1 promoted
+```
+
+### `log://turn_48/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1 promoted
+```
+
+### `log://turn_48/get/known%3A/files/pdb_ids_full_list`
+scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
+
+```
+known://files/pdb_ids_full_list promoted
+```
+
+### `log://turn_48/set/known%3A/sequence/donor_5JZL`
+scheme=log action=set attrs={"path":"known://sequence/donor_5JZL","patch":"===================================================================\n--- known://sequence/donor_5JZL\told\t\n+++ known://sequence/donor_5JZL\tnew\t\n@@ -0,0 +1,16 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[fpbase donor](known://api/fpbase_donor)\n+[pdb_ids](known://files/pdb_ids_full_list)\n+[pdb 5JZL page](https://www.rcsb.org/structure/5JZL)\n+[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1)\n+[unknown resolved](unknown://api/fpbase_donor)\n+[unknown resolved](unknown://api/pdb_sequences)\n+\n+# Donor: muGFP (5JZL) sequence\n+Monomeric ultra-stable GFP. Green FP for 505nm excitation.\n+\n+**Full sequence** (247aa, remove N-Met + His-tag + CRO chromophore artifact):\n+KGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK\n+\n+**Mature coding sequence length**: ~717nt (239aa).\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[fpbase donor](known://api/fpbase_donor)\n[pdb_ids](known://files/pdb_ids_full_list)\n[pdb 5JZL page](https://www.rcsb.org/structure/5JZL)\n[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1)\n[unknown resolved](unknown://api/fpbase_donor)\n[unknown resolved](unknown://api/pdb_sequences)\n\n# Donor: muGFP (5JZL) sequence\nMonomeric ultra-stable GFP. Green FP for 505nm excitation.\n\n**Full sequence** (247aa, remove N-Met + His-tag + CRO chromophore artifact):\nKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK\n\n**Mature coding sequence length**: ~717nt (239aa).\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":403,"summary":"sequence,donor,5JZL,muGFP,green,505nm","action":"set"}
+
+```
+# Related
+[prompt requirements](prompt://1)
+[fpbase donor](known://api/fpbase_donor)
+[pdb_ids](known://files/pdb_ids_full_list)
+[pdb 5JZL page](https://www.rcsb.org/structure/5JZL)
+[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1)
+[unknown resolved](unknown://api/fpbase_donor)
+[unknown resolved](unknown://api/pdb_sequences)
+
+# Donor: muGFP (5JZL) sequence
+Monomeric ultra-stable GFP. Green FP for 505nm excitation.
+
+**Full sequence** (247aa, remove N-Met + His-tag + CRO chromophore artifact):
+KGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLVLCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKAYFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEDVTAAGITHGMDELYK
+
+**Mature coding sequence length**: ~717nt (239aa).
+```
+
+### `log://turn_48/set/env%3A/turn_26/cat_/app/pdb_ids.txt_1`
+scheme=log action=set attrs={}
+
+```
+env://turn_26/cat_/app/pdb_ids.txt_1 set to summarized
+```
+
+### `log://turn_48/set/https%3A/www.rcsb.org/structure/5JZL`
+scheme=log action=set attrs={}
+
+```
+https://www.rcsb.org/structure/5JZL set to summarized
+```
+
+### `log://turn_48/set/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1`
+scheme=log action=set attrs={}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1 set to summarized
+```
+
+### `log://turn_48/update/distilling_donor_sequence%3B_discovering_acceptor(6AA7)%2Bbinder_sequences`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+distilling donor sequence; discovering acceptor(6AA7)+binder sequences
+```
+

package/audit/sweep/protein-assembly/turns/turn_049.md

@@ -0,0 +1,119 @@
+# turn 049
+
+tokens: prompt=88985 cached=3244 completion=375 reasoning=0 total=89360 cost=0
+created: 2026-05-02 00:09:15
+
+update: status=155 body=discovering acceptor/binder polymer_entity sequences
+
+---
+
+## reasoning (think)
+
+```
+Distillation Stage: Key unresolved unknowns need sequences for fusion protein assembly.
+
+1. **Donor (5JZL/muGFP)**: Extract clean sequence from polymer_entity API (remove His-tag, CRO, N-Met). Confirmed green FP.
+
+2. **Acceptor**: 6AA7 (red FP, Em=612nm perfect match), 2IB5 (blue chromoprotein Abs=610nm), extract sequences from APIs.
+
+3. **Antibody target**: Heavy chain CDR suggests epitope; need most common antigen sequence.
+
+4. **Molecule binder**: SMILES = 1-(benzyloxy)-1H-benzotriazole derivative; scan PDBs for binding protein.
+
+5. **DHFR**: Already distilled, mature sequence ready.
+
+6. **Fusion assembly**: Once sequences obtained, can deploy gBlock in Deployment Stage.
+
+Prioritize polymer_entity APIs for remaining FPs, then distill clean sequences.
+```
+
+## assistant emission
+
+```
+<think>
+Distillation Stage: Key unresolved unknowns need sequences for fusion protein assembly.
+
+1. **Donor (5JZL/muGFP)**: Extract clean sequence from polymer_entity API (remove His-tag, CRO, N-Met). Confirmed green FP.
+
+2. **Acceptor**: 6AA7 (red FP, Em=612nm perfect match), 2IB5 (blue chromoprotein Abs=610nm), extract sequences from APIs.
+
+3. **Antibody target**: Heavy chain CDR suggests epitope; need most common antigen sequence.
+
+4. **Molecule binder**: SMILES = 1-(benzyloxy)-1H-benzotriazole derivative; scan PDBs for binding protein.
+
+5. **DHFR**: Already distilled, mature sequence ready.
+
+6. **Fusion assembly**: Once sequences obtained, can deploy gBlock in Deployment Stage.
+
+Prioritize polymer_entity APIs for remaining FPs, then distill clean sequences.
+</think>
+
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1"/>
+
+<update status="155">discovering acceptor/binder polymer_entity sequences</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1 promoted
+```
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1 promoted
+```
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/3ADF/1 promoted
+```
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/5WJ2/1 promoted
+```
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1 promoted
+```
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/4Q7T/1 promoted
+```
+
+### `log://turn_49/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/1KFD/1 promoted
+```
+
+### `log://turn_49/update/discovering_acceptor/binder_polymer_entity_sequences`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+discovering acceptor/binder polymer_entity sequences
+```
+