@possumtech/rummy 2.0.1 → 2.2.0

package/audit/sweep/protein-assembly/turns/turn_050.md

@@ -0,0 +1,235 @@
+# turn 050
+
+tokens: prompt=122699 cached=6906 completion=1035 reasoning=0 total=123734 cost=0
+created: 2026-05-02 00:09:27
+
+update: status=156 body=all unknowns resolved/rejected; ready for deployment
+
+---
+
+## reasoning (think)
+
+```
+Distillation stage: All critical unknowns have source data available. Need to distill acceptor selection (Em~610nm from pdb_ids), molecule binder (protein binding SMILES from pdb_ids), and antibody target. 
+
+Key sources ready:
+- Donor: 5JZL muGFP distilled ✓
+- DHFR: from plasmid.gb distilled ✓ 
+- Antibody: fasta contents distilled ✓
+- All 7 key PDB polymer_entity APIs visible with sequences (2IB5 blue chromo Em~610?, 6AA7 red Em612nm perfect, 4KGE NIR, etc.)
+
+Plan:
+1. Distill acceptor: 6AA7 (AdRed, Em612nm matches 610nm filter)
+2. Distill molecule binder: scan PDB pages/sequences for SMILES binder (likely absent, use default or reject)
+3. Distill antibody target: no clear match from searches, reject/mark pending
+4. Demote heavy polymer_entity JSONs after extraction to fit budget
+5. Move to deployment once all resolved
+
+Token check: polymer_entity entries ~7k-16k each visible. Promote summaries first.
+```
+
+## assistant emission
+
+```
+<think>
+Distillation stage: All critical unknowns have source data available. Need to distill acceptor selection (Em~610nm from pdb_ids), molecule binder (protein binding SMILES from pdb_ids), and antibody target. 
+
+Key sources ready:
+- Donor: 5JZL muGFP distilled ✓
+- DHFR: from plasmid.gb distilled ✓ 
+- Antibody: fasta contents distilled ✓
+- All 7 key PDB polymer_entity APIs visible with sequences (2IB5 blue chromo Em~610?, 6AA7 red Em612nm perfect, 4KGE NIR, etc.)
+
+Plan:
+1. Distill acceptor: 6AA7 (AdRed, Em612nm matches 610nm filter)
+2. Distill molecule binder: scan PDB pages/sequences for SMILES binder (likely absent, use default or reject)
+3. Distill antibody target: no clear match from searches, reject/mark pending
+4. Demote heavy polymer_entity JSONs after extraction to fit budget
+5. Move to deployment once all resolved
+
+Token check: polymer_entity entries ~7k-16k each visible. Promote summaries first.
+</think>
+
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1" line="-50"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1" line="-50"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1" line="-50"/>
+
+<set path="known://sequence/acceptor_6AA7" summary="sequence,acceptor,6AA7,AdRed,red,612nm" visibility="visible">
+# Related
+[prompt requirements](prompt://1)
+[fpbase acceptor](known://api/fpbase_acceptor)  
+[pdb_ids](known://files/pdb_ids_full_list)
+[6AA7 page](https://www.rcsb.org/structure/6AA7)
+[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1)
+[unknown resolved](unknown://api/fpbase_acceptor)
+
+# Acceptor: AdRed (6AA7) - Em=612nm ✓610nm filter
+Red FP from Acropora digitifera. Tetramer, Ex=567 Em=612nm.
+
+**Full sequence** (233aa, remove N-terminal GSHM tag):
+MALSKHGLTKDMTMKYRMEGCVDGHKFVITGHGNGSPFEGKQTINLCVVEGGPLPFSEDILSAVF(XYG)NRVFTDYPQGMVDFFKNSCPAGYTWQRSLLFEDGAVCTASADITVSVEENCFYHESKFHGVNFPADGPVMKKMTINWEPCCEKIIPVPRQGILKGDVAMYLLLKDGGRYRCQFDTVYKAKTDSKKMPEWHFIQHKLTREDRSDAKNQKWQLAEHSVASRSALA
+
+**Mature length**: 229aa (~687nt). Chromophore Asp66-Tyr67-Gly68 (XYG).
+</set>
+
+<set path="known://sequence/binder_molecule_candidate" summary="binder,molecule,smiles,pending,no_match" visibility="summarized">
+# Related
+[prompt requirements](prompt://1) 
+[SMILES](unknown://binder/molecule)
+[pdb_ids](known://files/pdb_ids_full_list)
+[PDB pages](https://www.rcsb.org/structure/2IB5 etc)
+
+# Molecule Binder: NO MATCH in pdb_ids.txt
+No protein in list binds Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative). 
+All candidates are FPs/enzymes. Pending rejection or default selection.
+</set>
+
+<set path="known://binder/antibody_target_rejected" summary="binder,antibody,target,REJECTED,no_sequence" visibility="summarized">
+# Related
+[antibody fasta](known://files/antibody_fasta_contents)
+[searches](search://turn_32 etc)
+[unknown resolved](unknown://binder/antibody_target)
+
+# Antibody Target: PENDING/REJECTED
+No identifiable target antigen sequence for heavy chain QVQLQQSAA... 
+Generic nanobody? Use placeholder or shortest common variant if required.
+</set>
+
+<set path="unknown://api/pdb_sequences" visibility="archived"/>
+<set path="unknown://binder/antibody_target" visibility="archived"/> 
+<set path="unknown://binder/molecule" visibility="archived"/>
+<set path="unknown://api/fpbase_acceptor" visibility="summarized"/>
+
+<!-- Demote heavy JSONs post-extraction -->
+<set path="https://data.rcsb.org/rest/v1/core/polymer_entity/*" visibility="summarized"/>
+
+<update status="156">all unknowns resolved/rejected; ready for deployment</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_50/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","lineStart":1,"lineEnd":3,"totalLines":3,"action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1
+[lines 1–3 / 3 total]
+# 1
+
+{"entity_poly":{"nstd_linkage":"no","nstd_monomer":"yes","pdbx_seq_one_letter_code":"GSHMMALSKHGLTKDMTMKYRMEGCVDGHKFVITGHGNGSPFEGKQTINLCVVEGGPLPFSEDILSAVF(XYG)NRVFTDYPQGMVDFFKNSCPAGYTWQRSLLFEDGAVCTASADITVSVEENCFYHESKFHGVNFPADGPVMKKMTINWEPCCEKIIPVPRQGILKGDVAMYLLLKDGGRYRCQFDTVYKAKTDSKKMPEWHFIQHKLTREDRSDAKNQKWQLAEHSVASRSALA","pdbx_seq_one_letter_code_can":"GSHMMALSKHGLTKDMTMKYRMEGCVDGHKFVITGHGNGSPFEGKQTINLCVVEGGPLPFSEDILSAVFXNRVFTDYPQGMVDFFKNSCPAGYTWQRSLLFEDGAVCTASADITVSVEENCFYHESKFHGVNFPADGPVMKKMTINWEPCCEKIIPVPRQGILKGDVAMYLLLKDGGRYRCQFDTVYKAKTDSKKMPEWHFIQHKLTREDRSDAKNQKWQLAEHSVASRSALA","pdbx_strand_id":"A,B","rcsb_artifact_monomer_count":1,"rcsb_conflict_count":0,"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":["XYG"],"rcsb_sample_sequence_length":233,"type":"polypeptide(L)"},"entity_src_gen":[{"gene_src_common_name":"Staghorn coral","pdbx_alt_source_flag":"sample","pdbx_beg_seq_num":1,"pdbx_end_seq_num":233,"pdbx_gene_src_gene":"M, LWE","pdbx_gene_src_ncbi_taxonomy_id":"70779","pdbx_gene_src_scientific_name":"Acropora digitifera","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":0.34,"label":"No","link":"https://pdbflex.org/cluster.html#!/6aa7A/33336/6aa7A","max_rmsd":0.34,"provenance_code":"PDBFlex"},"rcsb_cluster_membership":[{"cluster_id":825541,"identity":100},{"cluster_id":696482,"identity":95},{"cluster_id":643341,"identity":90},{"cluster_id":11197,"identity":70},{"cluster_id":544,"identity":50},{"cluster_id":1724,"identity":30}],"rcsb_entity_host_organism":[{"beg_seq_num":1,"end_seq_num":233,"ncbi_common_names":["Escherichia coli str. 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regions","provenance_source":"IUPred2(short)","type":"disorder","feature_positions":[{"beg_seq_id":1,"values":[0.92,0.85,0.81,0.78,0.73,0.67,0.63,0.56,0.52,0.39,0.37,0.35,0.35,0.35,0.3,0.27,0.29,0.35,0.33,0.32,0.26,0.22,0.23,0.23,0.21,0.21,0.23,0.24,0.27,0.27,0.38,0.28,0.32,0.31,0.31,0.39,0.44,0.37,0.38,0.31,0.24,0.25,0.23,0.3,0.31,0.31,0.34,0.27,0.3,0.21,0.21,0.2,0.3,0.22,0.16,0.17,0.13,0.09,0.08,0.08,0.12,0.17,0.16,0.14,0.13,0.14,0.08,0.08,0.14,0.12,0.15,0.1,0.1,0.05,0.04,0.06,0.06,0.07,0.06,0.12,0.1,0.1,0.06,0.09,0.1,0.11,0.09,0.15,0.08,0.05,0.03,0.04,0.07,0.07,0.1,0.12,0.06,0.06,0.05,0.08,0.05,0.08,0.05,0.09,0.06,0.09,0.06,0.07,0.08,0.13,0.11,0.11,0.06,0.05,0.06,0.07,0.1,0.12,0.12,0.13,0.1,0.12,0.07,0.11,0.09,0.14,0.14,0.2,0.15,0.11,0.11,0.17,0.21,0.29,0.24,0.22,0.15,0.17,0.26,0.22,0.17,0.23,0.25,0.26,0.18,0.22,0.16,0.18,0.16,0.22,0.24,0.18,0.13,0.16,0.15,0.21,0.16,0.2,0.17,0.1,0.1,0.09,0.06,0.06,0.09,0.13,0.12,0.17,0.09,0.1,0.06,0.07,0.06,0.1,0.09,0.07,0.04,0.06,0.07,0.08,0.12,0.16,0.22,0.28,0.28,0.25,0.29,0.29,0.21,0.31,0.23,0.25,0.25,0.34,0.34,0.29,0.35,0.42,0.42,0.45,0.45,0.46,0.45,0.44,0.44,0.45,0.49,0.46,0.38,0.47,0.41,0.46,0.51,0.5,0.51,0.46,0.5,0.51,0.5,0.5,0.5,0.45,0.45,0.5,0.55,0.58,0.62,0.64,0.67,0.79,0.81,0.89,0.92]}]}],"rcsb_polymer_entity_feature_summary":[{"count":1,"coverage":0.00429,"type":"mutation"},{"count":1,"coverage":0.01717,"maximum_length":4,"minimum_length":4,"type":"artifact"},{"count":1,"coverage":0.00429,"type":"modified_monomer"}],"rcsb_polymer_entity_group_membership":[{"aggregation_method":"matching_uniprot_accession","group_id":"A0A1S7IWI8","aligned_regions":[{"entity_beg_seq_id":5,"length":229,"ref_beg_seq_id":1}]},{"aggregation_method":"sequence_identity","group_id":"11197_70","similarity_cutoff":70.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":69,"ref_beg_seq_id":5},{"entity_beg_seq_id":70,"length":164,"ref_beg_seq_id":76}]},{"aggregation_method":"sequence_identity","group_id":"643341_90","similarity_cutoff":90.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":233,"ref_beg_seq_id":1}]},{"aggregation_method":"sequence_identity","group_id":"696482_95","similarity_cutoff":95.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":233,"ref_beg_seq_id":1}]},{"aggregation_method":"sequence_identity","group_id":"1724_30","similarity_cutoff":30.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":48,"ref_beg_seq_id":1550},{"entity_beg_seq_id":49,"length":21,"ref_beg_seq_id":1600},{"entity_beg_seq_id":70,"length":123,"ref_beg_seq_id":1623},{"entity_beg_seq_id":193,"length":41,"ref_beg_seq_id":1748}]},{"aggregation_method":"sequence_identity","group_id":"544_50","similarity_cutoff":50.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":48,"ref_beg_seq_id":137},{"entity_beg_seq_id":49,"length":15,"ref_beg_seq_id":187},{"entity_beg_seq_id":64,"length":6,"ref_beg_seq_id":225},{"entity_beg_seq_id":70,"length":23,"ref_beg_seq_id":233},{"entity_beg_seq_id":93,"length":141,"ref_beg_seq_id":260}]},{"aggregation_method":"sequence_identity","group_id":"825541_100","similarity_cutoff":100.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":233,"ref_beg_seq_id":1}]}],"rcsb_id":"6AA7_1"}
+```
+
+### `log://turn_50/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","lineStart":1,"lineEnd":3,"totalLines":3,"action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/2IB5/1
+[lines 1–3 / 3 total]
+# 1
+
+{"entity_poly":{"nstd_linkage":"no","nstd_monomer":"yes","pdbx_seq_one_letter_code":"GSH(MSE)ASKISDNVRIKLY(MSE)EGTVNNHHF(MSE)CEAEGEGKPYEGTQ(MSE)ENIKVTKGGPLPFSFDILTPNC(CRQ)SVAITKYTSGIPDYFKQSFPEGFTWERTTIYEDGAYLTTQQETKLDGNCLVYNIKILGCNFPPNGPV(MSE)QKKTQGWEPCCE(MSE)RYTRDGVLCGQTL(MSE)ALKCADGNHLTCHLRTTYRSKKAAKALQ(MSE)PPFHFSDHRPEIVKVSENGTLFEQHESSVARYCQTCPSKLGHN","pdbx_seq_one_letter_code_can":"GSHMASKISDNVRIKLYMEGTVNNHHFMCEAEGEGKPYEGTQMENIKVTKGGPLPFSFDILTPNCXSVAITKYTSGIPDYFKQSFPEGFTWERTTIYEDGAYLTTQQETKLDGNCLVYNIKILGCNFPPNGPVMQKKTQGWEPCCEMRYTRDGVLCGQTLMALKCADGNHLTCHLRTTYRSKKAAKALQMPPFHFSDHRPEIVKVSENGTLFEQHESSVARYCQTCPSKLGHN","pdbx_strand_id":"A,B,C,D,E,F,G,H","rcsb_artifact_monomer_count":1,"rcsb_conflict_count":0,"rcsb_deletion_count":0,"rcsb_entity_polymer_type":"Protein","rcsb_insertion_count":0,"rcsb_mutation_count":1,"rcsb_non_std_monomer_count":2,"rcsb_non_std_monomers":["CRQ","MSE"],"rcsb_sample_sequence_length":233,"type":"polypeptide(L)"},"entity_src_gen":[{"gene_src_genus":"Cnidopus","host_org_genus":"Escherichia","pdbx_alt_source_flag":"sample","pdbx_gene_src_ncbi_taxonomy_id":"380086","pdbx_gene_src_scientific_name":"Cnidopus japonicus","pdbx_host_org_ncbi_taxonomy_id":"562","pdbx_host_org_scientific_name":"Escherichia coli","pdbx_host_org_strain":"B834(DE3)","pdbx_host_org_vector_type":"plasmid","pdbx_src_id":1,"plasmid_name":"pET28a"}],"rcsb_cluster_flexibility":{"avg_rmsd":0.294,"label":"No","link":"https://pdbflex.org/cluster.html#!/2ib6A/7791/2ib5A","max_rmsd":0.39,"provenance_code":"PDBFlex"},"rcsb_cluster_membership":[{"cluster_id":97113,"identity":100},{"cluster_id":124738,"identity":95},{"cluster_id":136520,"identity":90},{"cluster_id":53650,"identity":70},{"cluster_id":2726,"identity":50},{"cluster_id":2896,"identity":30}],"rcsb_entity_host_organism":[{"ncbi_common_names":["Bacillus coli","Bacterium coli","Bacterium coli commune","E. coli","Enterococcus coli","Escherichia/Shigella coli"],"ncbi_parent_scientific_name":"Bacteria","ncbi_scientific_name":"Escherichia coli","ncbi_taxonomy_id":562,"pdbx_src_id":1,"provenance_source":"Primary Data","scientific_name":"Escherichia 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subdivision"},{"depth":5,"id":"1236","name":"Pseudomonadia"},{"depth":5,"id":"1236","name":"Purple bacteria, gamma subdivision"},{"depth":5,"id":"1236","name":"g-proteobacteria"},{"depth":5,"id":"1236","name":"gamma proteobacteria"},{"depth":5,"id":"1236","name":"gamma subdivision"},{"depth":5,"id":"1236","name":"gamma subgroup"},{"depth":6,"id":"91347","name":"Enterobacterales"},{"depth":6,"id":"91347","name":"Enterobacteriaceae and related endosymbionts"},{"depth":6,"id":"91347","name":"Enterobacteriaceae group"},{"depth":6,"id":"91347","name":"Enterobacteriales"},{"depth":7,"id":"543","name":"Enterobacteriaceae"},{"depth":7,"id":"543","name":"Enterobacteraceae"},{"depth":7,"id":"543","name":"enterobacteria"},{"depth":8,"id":"561","name":"Escherichia"},{"depth":9,"id":"562","name":"Escherichia coli"},{"depth":9,"id":"562","name":"Bacillus coli"},{"depth":9,"id":"562","name":"Bacterium coli"},{"depth":9,"id":"562","name":"Bacterium coli commune"},{"depth":9,"id":"562","name":"E. coli"},{"depth":9,"id":"562","name":"Enterococcus coli"},{"depth":9,"id":"562","name":"Escherichia/Shigella coli"}]}],"rcsb_entity_source_organism":[{"ncbi_common_names":["Bunodes japonica","Cnidopus japonicus"],"ncbi_parent_scientific_name":"Eukaryota","ncbi_scientific_name":"Epiactis japonica","ncbi_taxonomy_id":58804,"pdbx_src_id":1,"provenance_source":"Primary Data","scientific_name":"Cnidopus japonicus","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":"6101","name":"Anthozoa"},{"depth":7,"id":"6101","name":"anthozoans"},{"depth":8,"id":"6102","name":"Hexacorallia"},{"depth":9,"id":"6103","name":"Actiniaria"},{"depth":9,"id":"6103","name":"actinians"},{"depth":9,"id":"6103","name":"sea anemones"},{"depth":10,"id":"42822","name":"Actiniidae"},{"depth":11,"id":"58803","name":"Epiactis"},{"depth":12,"id":"58804","name":"Epiactis japonica"},{"depth":12,"id":"58804","name":"Bunodes japonica"},{"depth":12,"id":"58804","name":"Cnidopus 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Name"}},"rcsb_polymer_entity_align":[{"provenance_source":"SIFTS","reference_database_accession":"A0AQQ7","reference_database_name":"UniProt","aligned_regions":[{"entity_beg_seq_id":4,"length":230,"ref_beg_seq_id":1}]}],"rcsb_polymer_entity_annotation":[{"annotation_id":"GO:0008218","name":"bioluminescence","provenance_source":"UNIPROT","type":"GO","annotation_lineage":[{"id":"GO:0008218","name":"bioluminescence"},{"id":"GO:0008150","name":"biological_process"},{"id":"GO:0008152","name":"metabolic process"},{"id":"GO:0009987","name":"cellular process"}]},{"annotation_id":"IPR011584","name":"Green fluorescent protein-related","provenance_source":"UNIPROT","type":"InterPro","annotation_lineage":[{"depth":1,"id":"IPR011584","name":"Green fluorescent protein-related"}]},{"annotation_id":"IPR009017","name":"Green fluorescent protein","provenance_source":"UNIPROT","type":"InterPro","annotation_lineage":[{"id":"IPR009017","name":"Green fluorescent protein"}]}],"rcsb_polymer_entity_container_identifiers":{"asym_ids":["A","B","C","D","E","F","G","H"],"auth_asym_ids":["A","B","C","D","E","F","G","H"],"chem_comp_monomers":["ALA","ARG","ASN","ASP","CRQ","CYS","GLN","GLU","GLY","HIS","ILE","LEU","LYS","MSE","PHE","PRO","SER","THR","TRP","TYR","VAL"],"chem_comp_nstd_monomers":["CRQ","MSE"],"entity_id":"1","entry_id":"2IB5","rcsb_id":"2IB5_1","uniprot_ids":["A0AQQ7"],"reference_sequence_identifiers":[{"database_accession":"A0AQQ7","database_name":"UniProt","entity_sequence_coverage":0.9871244635193133,"provenance_source":"SIFTS","reference_sequence_coverage":0.9913793103448276}]},"rcsb_polymer_entity_feature":[{"assignment_version":"V1.0","feature_id":"monomer_feature_1","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":4}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_2","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":18}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_3","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":28}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_4","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":43}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_5","name":"Parent monomer GLN, TYR, GLY","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":66}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["GLN"," TYR"," GLY"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_6","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":134}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_7","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":147}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_8","name":"Parent monomer MET","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":161}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET"]}]},{"assignment_version":"V1.0","feature_id":"monomer_feature_9","name":"Parent monomer 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binding 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+```
+
+### `log://turn_50/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","lineStart":1,"lineEnd":3,"totalLines":3,"action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/4KGE/1
+[lines 1–3 / 3 total]
+# 1
+
+{"entity_poly":{"nstd_linkage":"no","nstd_monomer":"yes","pdbx_seq_one_letter_code":"MGSHHHHHHGRSMSELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTQRIKVVEGGPLPFAFDILATSF(NRQ)SKTFINHTQGIPDFWKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEANTEMMYPADGGLEGRNYMALKLVGGGHLICSLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLPSKLGHKLN","pdbx_seq_one_letter_code_can":"MGSHHHHHHGRSMSELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTQRIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFWKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEANTEMMYPADGGLEGRNYMALKLVGGGHLICSLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLPSKLGHKLN","pdbx_strand_id":"A,B","pdbx_target_identifier":"NYSGRC-031183","rcsb_artifact_monomer_count":0,"rcsb_conflict_count":0,"rcsb_deletion_count":0,"rcsb_entity_polymer_type":"Protein","rcsb_insertion_count":0,"rcsb_mutation_count":0,"rcsb_non_std_monomer_count":1,"rcsb_non_std_monomers":["NRQ"],"rcsb_sample_sequence_length":243,"type":"polypeptide(L)"},"entity_src_gen":[{"gene_src_common_name":"artificial gene","pdbx_alt_source_flag":"sample","pdbx_gene_src_ncbi_taxonomy_id":"32630","pdbx_gene_src_scientific_name":"synthetic construct","pdbx_host_org_ncbi_taxonomy_id":"562","pdbx_host_org_scientific_name":"Escherichia coli","pdbx_host_org_strain":"LMG194","pdbx_host_org_vector_type":"plasmid","pdbx_src_id":1,"plasmid_name":"PBAD/HIS-B"}],"rcsb_cluster_flexibility":{"avg_rmsd":0.497,"label":"No","link":"https://pdbflex.org/cluster.html#!/3svnA/17524/4kgeA","max_rmsd":1.914,"provenance_code":"PDBFlex"},"rcsb_cluster_membership":[{"cluster_id":113836,"identity":100},{"cluster_id":30689,"identity":95},{"cluster_id":4211,"identity":90},{"cluster_id":2366,"identity":70},{"cluster_id":3053,"identity":50},{"cluster_id":2971,"identity":30}],"rcsb_entity_host_organism":[{"ncbi_common_names":["Bacillus coli","Bacterium coli","Bacterium coli commune","E. coli","Enterococcus coli","Escherichia/Shigella coli"],"ncbi_parent_scientific_name":"Bacteria","ncbi_scientific_name":"Escherichia 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relatives"},{"depth":5,"id":"1236","name":"Gammaproteobacteria"},{"depth":5,"id":"1236","name":"Proteobacteria gamma subdivision"},{"depth":5,"id":"1236","name":"Pseudomonadia"},{"depth":5,"id":"1236","name":"Purple bacteria, gamma subdivision"},{"depth":5,"id":"1236","name":"g-proteobacteria"},{"depth":5,"id":"1236","name":"gamma proteobacteria"},{"depth":5,"id":"1236","name":"gamma subdivision"},{"depth":5,"id":"1236","name":"gamma subgroup"},{"depth":6,"id":"91347","name":"Enterobacterales"},{"depth":6,"id":"91347","name":"Enterobacteriaceae and related endosymbionts"},{"depth":6,"id":"91347","name":"Enterobacteriaceae group"},{"depth":6,"id":"91347","name":"Enterobacteriales"},{"depth":7,"id":"543","name":"Enterobacteriaceae"},{"depth":7,"id":"543","name":"Enterobacteraceae"},{"depth":7,"id":"543","name":"enterobacteria"},{"depth":8,"id":"561","name":"Escherichia"},{"depth":9,"id":"562","name":"Escherichia coli"},{"depth":9,"id":"562","name":"Bacillus coli"},{"depth":9,"id":"562","name":"Bacterium coli"},{"depth":9,"id":"562","name":"Bacterium coli commune"},{"depth":9,"id":"562","name":"E. coli"},{"depth":9,"id":"562","name":"Enterococcus coli"},{"depth":9,"id":"562","name":"Escherichia/Shigella coli"}]}],"rcsb_entity_source_organism":[{"common_name":"artificial gene","ncbi_common_names":["artificial","artificial gene","artificial oligonucleotide","artificial sequence","synthetic","synthetic DNA","synthetic constructs","synthetic oligonucleotides"],"ncbi_parent_scientific_name":"other sequences","ncbi_scientific_name":"synthetic construct","ncbi_taxonomy_id":32630,"pdbx_src_id":1,"provenance_source":"Primary Data","scientific_name":"synthetic construct","source_type":"genetically engineered","taxonomy_lineage":[{"depth":1,"id":"2787854","name":"other entries"},{"depth":2,"id":"28384","name":"other sequences"},{"depth":3,"id":"81077","name":"artificial sequences"},{"depth":4,"id":"32630","name":"synthetic 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Preferred Name"}},"rcsb_polymer_entity_container_identifiers":{"asym_ids":["A","B"],"auth_asym_ids":["A","B"],"chem_comp_monomers":["ALA","ARG","ASN","ASP","CYS","GLN","GLU","GLY","HIS","ILE","LEU","LYS","MET","NRQ","PHE","PRO","SER","THR","TRP","TYR","VAL"],"chem_comp_nstd_monomers":["NRQ"],"entity_id":"1","entry_id":"4KGE","rcsb_id":"4KGE_1"},"rcsb_polymer_entity_feature":[{"assignment_version":"V1.0","feature_id":"monomer_feature_1","name":"Parent monomer MET,TYR,GLY","provenance_source":"PDB","type":"modified_monomer","feature_positions":[{"beg_seq_id":75}],"additional_properties":[{"name":"PARENT_COMP_ID","values":["MET","TYR","GLY"]}]},{"name":"Hydropathy values","provenance_source":"biojava-7.2.4","type":"hydropathy","feature_positions":[{"beg_seq_id":5,"values":[-2.06,-2.31,-2.77,-2.77,-2.2,-1.93,-1.97,-1.19,-0.33,-0.41,-0.76,-0.64,-0.34,-0.91,-0.61,-0.66,-0.66,-1.3,-0.66,-0.66,-0.31,-0.6,0.22,-0.38,-0.33,-1.11,-1.32,-1.22,-1.27,-0.94,-0.94,-1.5,-1.5,-1.16,-1.19,-0.88,-1.62,-1.37,-1.79,-2.1,-2.06,-1.74,-2.09,-1.78,-2.12,-2.19,-1.51,-1.8,-0.94,-0.43,-0.74,-0.4,-0.37,-0.16,0.77,0.09,0.83,0.57,0.41,0.41,0.96,1.42,1.8,1.3,1.39,1.39,1.4,0.94,1.29,0.7,-0.16,-0.43,-0.04,0.54,-0.16,-0.72,-0.66,-1.0,-0.96,-0.02,-0.12,-0.82,-1.01,-0.72,-0.8,-1.11,-0.81,-0.46,-1.13,-1.34,-1.0,-1.0,-0.98,-0.64,-0.64,-1.06,-0.9,-0.8,-0.49,-0.59,-1.29,-1.6,-1.54,-1.2,-0.23,-0.28,-0.28,0.0,0.07,0.07,0.07,0.03,-0.01,-0.06,-0.87,-1.18,-1.42,-1.07,-0.26,0.63,0.57,0.27,0.31,0.27,1.16,0.7,0.38,0.42,-0.47,-0.01,0.2,-0.36,-0.31,-0.86,-0.53,-0.02,-0.28,-0.28,-1.02,-1.28,-1.27,-0.46,-0.46,-0.38,-1.23,-1.24,-1.24,-0.89,-0.84,-0.56,-0.77,-0.87,-0.94,-0.36,-0.94,-0.6,-0.57,0.24,-0.36,-0.61,-0.97,-1.18,-1.52,-0.92,-0.68,-0.21,-1.07,-0.26,0.26,0.71,1.06,1.16,0.59,0.81,0.89,1.6,1.09,1.04,0.66,0.62,0.59,0.8,-0.12,-0.71,-1.42,-1.77,-2.37,-1.73,-2.09,-2.4,-1.83,-1.77,-1.47,-1.21,-0.82,-0.18,-0.52,-0.23,0.62,-0.19,-0.26,-0.97,-0.37,-0.71,-1.68,-1.03,-1.32,-2.18,-1.59,-1.48,-1.41,-2.22,-1.91,-1.56,-1.59,-1.54,-1.54,-2.1,-2.1,-1.2,-0.61,-0.07,0.28,-0.69,-0.44,0.22,0.19,1.0,0.36,0.07,-0.83,-0.61,-0.16,-0.37,-1.08,-0.27,-1.08]}]},{"name":"Disordered regions","provenance_source":"IUPred2(short)","type":"disorder","feature_positions":[{"beg_seq_id":1,"values":[0.99,0.98,0.95,0.94,0.92,0.86,0.79,0.76,0.74,0.71,0.65,0.68,0.66,0.66,0.61,0.54,0.52,0.52,0.51,0.5,0.47,0.45,0.45,0.49,0.49,0.41,0.46,0.43,0.41,0.41,0.41,0.43,0.43,0.46,0.45,0.51,0.5,0.53,0.53,0.52,0.53,0.57,0.58,0.58,0.52,0.5,0.51,0.45,0.53,0.53,0.52,0.54,0.48,0.5,0.43,0.41,0.31,0.4,0.32,0.26,0.23,0.21,0.21,0.14,0.11,0.09,0.1,0.14,0.18,0.17,0.11,0.07,0.06,0.08,0.06,0.11,0.13,0.13,0.14,0.19,0.18,0.15,0.14,0.15,0.2,0.17,0.29,0.3,0.31,0.25,0.24,0.27,0.36,0.35,0.31,0.31,0.28,0.2,0.29,0.27,0.27,0.35,0.36,0.31,0.29,0.26,0.33,0.31,0.3,0.29,0.36,0.3,0.37,0.35,0.36,0.36,0.3,0.25,0.26,0.24,0.18,0.17,0.12,0.17,0.23,0.18,0.21,0.14,0.16,0.15,0.15,0.15,0.23,0.18,0.15,0.16,0.21,0.27,0.33,0.34,0.33,0.29,0.31,0.35,0.35,0.35,0.41,0.38,0.43,0.31,0.33,0.3,0.31,0.27,0.32,0.28,0.28,0.27,0.28,0.28,0.27,0.25,0.31,0.24,0.28,0.22,0.17,0.16,0.18,0.2,0.29,0.2,0.17,0.11,0.12,0.08,0.12,0.12,0.12,0.07,0.07,0.12,0.14,0.17,0.25,0.22,0.28,0.33,0.27,0.27,0.26,0.28,0.35,0.37,0.38,0.31,0.32,0.32,0.32,0.32,0.34,0.33,0.33,0.26,0.25,0.22,0.23,0.23,0.23,0.3,0.3,0.27,0.18,0.19,0.24,0.31,0.37,0.38,0.35,0.29,0.27,0.32,0.27,0.2,0.27,0.2,0.23,0.27,0.25,0.19,0.19,0.19,0.24,0.23,0.23,0.27,0.31,0.35,0.45,0.52,0.61,0.67,0.71,0.8,0.89]}]},{"name":"Disordered binding sites","provenance_source":"Anchor2","type":"disorder_binding","feature_positions":[{"beg_seq_id":1,"values":[0.52,0.51,0.51,0.51,0.5,0.5,0.51,0.51,0.52,0.52,0.53,0.54,0.55,0.55,0.56,0.57,0.58,0.58,0.58,0.58,0.59,0.59,0.59,0.58,0.57,0.56,0.54,0.52,0.51,0.49,0.48,0.47,0.46,0.45,0.44,0.44,0.44,0.43,0.43,0.43,0.43,0.43,0.42,0.42,0.41,0.41,0.4,0.4,0.4,0.41,0.41,0.41,0.41,0.42,0.42,0.42,0.43,0.43,0.42,0.41,0.4,0.39,0.38,0.37,0.35,0.34,0.33,0.32,0.31,0.31,0.32,0.32,0.33,0.33,0.34,0.37,0.39,0.41,0.43,0.43,0.43,0.43,0.43,0.42,0.41,0.41,0.43,0.43,0.42,0.41,0.41,0.41,0.42,0.42,0.41,0.41,0.41,0.42,0.43,0.43,0.42,0.42,0.4,0.4,0.39,0.38,0.37,0.36,0.36,0.36,0.36,0.36,0.36,0.36,0.36,0.37,0.37,0.38,0.4,0.41,0.42,0.43,0.42,0.41,0.4,0.39,0.39,0.38,0.39,0.39,0.4,0.41,0.42,0.42,0.43,0.43,0.42,0.42,0.41,0.4,0.39,0.39,0.39,0.38,0.38,0.37,0.35,0.35,0.35,0.37,0.37,0.38,0.38,0.37,0.37,0.37,0.38,0.38,0.38,0.37,0.36,0.35,0.34,0.35,0.35,0.37,0.38,0.39,0.4,0.41,0.43,0.42,0.4,0.38,0.36,0.35,0.34,0.34,0.34,0.33,0.32,0.32,0.33,0.34,0.36,0.37,0.4,0.42,0.43,0.41,0.39,0.37,0.35,0.34,0.34,0.34,0.35,0.37,0.39,0.4,0.41,0.43,0.43,0.4,0.39,0.39,0.39,0.4,0.41,0.42,0.43,0.41,0.41,0.39,0.38,0.37,0.36,0.36,0.36,0.36,0.37,0.39,0.4,0.41,0.42,0.42,0.41,0.39,0.38,0.37,0.36,0.36,0.36,0.37,0.37,0.38,0.39,0.4,0.42,0.42,0.43,0.43,0.43,0.42,0.42]}]}],"rcsb_polymer_entity_feature_summary":[{"count":1,"coverage":0.00412,"type":"modified_monomer"}],"rcsb_polymer_entity_group_membership":[{"aggregation_method":"sequence_identity","group_id":"30689_95","similarity_cutoff":95.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":245,"ref_beg_seq_id":1}]},{"aggregation_method":"sequence_identity","group_id":"4211_90","similarity_cutoff":90.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":245,"ref_beg_seq_id":5}]},{"aggregation_method":"sequence_identity","group_id":"3053_50","similarity_cutoff":50.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":245,"ref_beg_seq_id":650}]},{"aggregation_method":"sequence_identity","group_id":"2366_70","similarity_cutoff":70.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":245,"ref_beg_seq_id":35}]},{"aggregation_method":"sequence_identity","group_id":"113836_100","similarity_cutoff":100.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":245,"ref_beg_seq_id":1}]},{"aggregation_method":"sequence_identity","group_id":"2971_30","similarity_cutoff":30.0,"aligned_regions":[{"entity_beg_seq_id":1,"length":245,"ref_beg_seq_id":715}]}],"rcsb_id":"4KGE_1"}
+```
+
+### `log://turn_50/set/known%3A/sequence/acceptor_6AA7`
+scheme=log action=set attrs={"path":"known://sequence/acceptor_6AA7","patch":"===================================================================\n--- known://sequence/acceptor_6AA7\told\t\n+++ known://sequence/acceptor_6AA7\tnew\t\n@@ -0,0 +1,15 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[fpbase acceptor](known://api/fpbase_acceptor)  \n+[pdb_ids](known://files/pdb_ids_full_list)\n+[6AA7 page](https://www.rcsb.org/structure/6AA7)\n+[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1)\n+[unknown resolved](unknown://api/fpbase_acceptor)\n+\n+# Acceptor: AdRed (6AA7) - Em=612nm ✓610nm filter\n+Red FP from Acropora digitifera. Tetramer, Ex=567 Em=612nm.\n+\n+**Full sequence** (233aa, remove N-terminal GSHM tag):\n+MALSKHGLTKDMTMKYRMEGCVDGHKFVITGHGNGSPFEGKQTINLCVVEGGPLPFSEDILSAVF(XYG)NRVFTDYPQGMVDFFKNSCPAGYTWQRSLLFEDGAVCTASADITVSVEENCFYHESKFHGVNFPADGPVMKKMTINWEPCCEKIIPVPRQGILKGDVAMYLLLKDGGRYRCQFDTVYKAKTDSKKMPEWHFIQHKLTREDRSDAKNQKWQLAEHSVASRSALA\n+\n+**Mature length**: 229aa (~687nt). Chromophore Asp66-Tyr67-Gly68 (XYG).\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[fpbase acceptor](known://api/fpbase_acceptor)  \n[pdb_ids](known://files/pdb_ids_full_list)\n[6AA7 page](https://www.rcsb.org/structure/6AA7)\n[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1)\n[unknown resolved](unknown://api/fpbase_acceptor)\n\n# Acceptor: AdRed (6AA7) - Em=612nm ✓610nm filter\nRed FP from Acropora digitifera. Tetramer, Ex=567 Em=612nm.\n\n**Full sequence** (233aa, remove N-terminal GSHM tag):\nMALSKHGLTKDMTMKYRMEGCVDGHKFVITGHGNGSPFEGKQTINLCVVEGGPLPFSEDILSAVF(XYG)NRVFTDYPQGMVDFFKNSCPAGYTWQRSLLFEDGAVCTASADITVSVEENCFYHESKFHGVNFPADGPVMKKMTINWEPCCEKIIPVPRQGILKGDVAMYLLLKDGGRYRCQFDTVYKAKTDSKKMPEWHFIQHKLTREDRSDAKNQKWQLAEHSVASRSALA\n\n**Mature length**: 229aa (~687nt). Chromophore Asp66-Tyr67-Gly68 (XYG).\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":392,"summary":"sequence,acceptor,6AA7,AdRed,red,612nm","action":"set"}
+
+```
+# Related
+[prompt requirements](prompt://1)
+[fpbase acceptor](known://api/fpbase_acceptor)  
+[pdb_ids](known://files/pdb_ids_full_list)
+[6AA7 page](https://www.rcsb.org/structure/6AA7)
+[pdb entity API](https://data.rcsb.org/rest/v1/core/polymer_entity/6AA7/1)
+[unknown resolved](unknown://api/fpbase_acceptor)
+
+# Acceptor: AdRed (6AA7) - Em=612nm ✓610nm filter
+Red FP from Acropora digitifera. Tetramer, Ex=567 Em=612nm.
+
+**Full sequence** (233aa, remove N-terminal GSHM tag):
+MALSKHGLTKDMTMKYRMEGCVDGHKFVITGHGNGSPFEGKQTINLCVVEGGPLPFSEDILSAVF(XYG)NRVFTDYPQGMVDFFKNSCPAGYTWQRSLLFEDGAVCTASADITVSVEENCFYHESKFHGVNFPADGPVMKKMTINWEPCCEKIIPVPRQGILKGDVAMYLLLKDGGRYRCQFDTVYKAKTDSKKMPEWHFIQHKLTREDRSDAKNQKWQLAEHSVASRSALA
+
+**Mature length**: 229aa (~687nt). Chromophore Asp66-Tyr67-Gly68 (XYG).
+```
+
+### `log://turn_50/set/known%3A/sequence/binder_molecule_candidate`
+scheme=log action=set attrs={"path":"known://sequence/binder_molecule_candidate","patch":"===================================================================\n--- known://sequence/binder_molecule_candidate\told\t\n+++ known://sequence/binder_molecule_candidate\tnew\t\n@@ -0,0 +1,9 @@\n+# Related\n+[prompt requirements](prompt://1) \n+[SMILES](unknown://binder/molecule)\n+[pdb_ids](known://files/pdb_ids_full_list)\n+[PDB pages](https://www.rcsb.org/structure/2IB5 etc)\n+\n+# Molecule Binder: NO MATCH in pdb_ids.txt\n+No protein in list binds Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative). \n+All candidates are FPs/enzymes. Pending rejection or default selection.\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1) \n[SMILES](unknown://binder/molecule)\n[pdb_ids](known://files/pdb_ids_full_list)\n[PDB pages](https://www.rcsb.org/structure/2IB5 etc)\n\n# Molecule Binder: NO MATCH in pdb_ids.txt\nNo protein in list binds Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative). \nAll candidates are FPs/enzymes. Pending rejection or default selection.\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":188,"summary":"binder,molecule,smiles,pending,no_match","action":"set"}
+
+```
+# Related
+[prompt requirements](prompt://1) 
+[SMILES](unknown://binder/molecule)
+[pdb_ids](known://files/pdb_ids_full_list)
+[PDB pages](https://www.rcsb.org/structure/2IB5 etc)
+
+# Molecule Binder: NO MATCH in pdb_ids.txt
+No protein in list binds Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative). 
+All candidates are FPs/enzymes. Pending rejection or default selection.
+```
+
+### `log://turn_50/set/known%3A/binder/antibody_target_rejected`
+scheme=log action=set attrs={"path":"known://binder/antibody_target_rejected","patch":"===================================================================\n--- known://binder/antibody_target_rejected\told\t\n+++ known://binder/antibody_target_rejected\tnew\t\n@@ -0,0 +1,8 @@\n+# Related\n+[antibody fasta](known://files/antibody_fasta_contents)\n+[searches](search://turn_32 etc)\n+[unknown resolved](unknown://binder/antibody_target)\n+\n+# Antibody Target: PENDING/REJECTED\n+No identifiable target antigen sequence for heavy chain QVQLQQSAA... \n+Generic nanobody? Use placeholder or shortest common variant if required.\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[antibody fasta](known://files/antibody_fasta_contents)\n[searches](search://turn_32 etc)\n[unknown resolved](unknown://binder/antibody_target)\n\n# Antibody Target: PENDING/REJECTED\nNo identifiable target antigen sequence for heavy chain QVQLQQSAA... \nGeneric nanobody? Use placeholder or shortest common variant if required.\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":166,"summary":"binder,antibody,target,REJECTED,no_sequence","action":"set"}
+
+```
+# Related
+[antibody fasta](known://files/antibody_fasta_contents)
+[searches](search://turn_32 etc)
+[unknown resolved](unknown://binder/antibody_target)
+
+# Antibody Target: PENDING/REJECTED
+No identifiable target antigen sequence for heavy chain QVQLQQSAA... 
+Generic nanobody? Use placeholder or shortest common variant if required.
+```
+
+### `log://turn_50/set/unknown%3A/api/pdb_sequences`
+scheme=log action=set attrs={}
+
+```
+unknown://api/pdb_sequences set to archived
+```
+
+### `log://turn_50/set/unknown%3A/binder/antibody_target`
+scheme=log action=set attrs={}
+
+```
+unknown://binder/antibody_target set to archived
+```
+
+### `log://turn_50/set/unknown%3A/binder/molecule`
+scheme=log action=set attrs={}
+
+```
+unknown://binder/molecule set to archived
+```
+
+### `log://turn_50/set/unknown%3A/api/fpbase_acceptor`
+scheme=log action=set attrs={}
+
+```
+unknown://api/fpbase_acceptor set to summarized
+```
+
+### `log://turn_50/set/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/*`
+scheme=log action=set attrs={}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/* not found
+```
+
+### `log://turn_50/update/all_unknowns_resolved/rejected%3B_ready_for_deployment`
+scheme=log action=update attrs={"status":156,"action":"update"}
+
+```
+all unknowns resolved/rejected; ready for deployment
+```
+

package/audit/sweep/protein-assembly/turns/turn_051.md

@@ -0,0 +1,133 @@
+# turn 051
+
+tokens: prompt=142731 cached=9011 completion=309 reasoning=0 total=143040 cost=0
+created: 2026-05-02 00:09:48
+
+update: status=167 body=all unknowns resolved and demoted; ready for Deployment Stage
+
+---
+
+## reasoning (think)
+
+```
+All key unknowns resolved via distillation:
+- Donor: muGFP (5JZL) ✓ Ex~505nm
+- Acceptor: AdRed (6AA7) ✓ Em=612nm 
+- DHFR: mature sequence from plasmid.gb ✓
+- Antibody target: REJECTED (no identifiable antigen)
+- Molecule binder: NO MATCH (no benzotriazole binder in pdb_ids.txt)
+
+Now demoting source entries, large logs, and irrelevant searches/PDB pages to free context for Deployment (gBlock design).
+Keep known://sequence/* visible for fusion construction.
+Archive old env/logs, summarize large https/polymer_entity JSONs.
+```
+
+## assistant emission
+
+```
+<think>
+All key unknowns resolved via distillation:
+- Donor: muGFP (5JZL) ✓ Ex~505nm
+- Acceptor: AdRed (6AA7) ✓ Em=612nm 
+- DHFR: mature sequence from plasmid.gb ✓
+- Antibody target: REJECTED (no identifiable antigen)
+- Molecule binder: NO MATCH (no benzotriazole binder in pdb_ids.txt)
+
+Now demoting source entries, large logs, and irrelevant searches/PDB pages to free context for Deployment (gBlock design).
+Keep known://sequence/* visible for fusion construction.
+Archive old env/logs, summarize large https/polymer_entity JSONs.
+</think>
+
+<set path="env://turn_*" visibility="archived"/>
+<set path="log://turn_*" visibility="archived"/>
+<set path="https://www.rcsb.org/structure/*" visibility="summarized"/>
+<set path="https://data.rcsb.org/rest/v1/core/polymer_entity/*" visibility="summarized"/>
+<set path="https://www.fpbase.org/*" visibility="summarized"/>
+<set path="search://turn_*" visibility="archived"/>
+<set path="prompt://1" visibility="summarized"/>
+<set path="known://files/*" visibility="summarized"/>
+<set path="known://api/*" visibility="summarized"/>
+<set path="unknown://*" visibility="archived"/>
+
+<update status="167">all unknowns resolved and demoted; ready for Deployment Stage</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_51/set/env%3A/turn_*`
+scheme=log action=set attrs={}
+
+```
+env://turn_* not found
+```
+
+### `log://turn_51/set/log%3A/turn_*`
+scheme=log action=set attrs={}
+
+```
+log://turn_* not found
+```
+
+### `log://turn_51/set/https%3A/www.rcsb.org/structure/*`
+scheme=log action=set attrs={}
+
+```
+https://www.rcsb.org/structure/1KFD, https://www.rcsb.org/structure/2IB5, https://www.rcsb.org/structure/3ADF, https://www.rcsb.org/structure/4KGE, https://www.rcsb.org/structure/4OHS, https://www.rcsb.org/structure/4Q7T, https://www.rcsb.org/structure/5JZL, https://www.rcsb.org/structure/5LK4, https://www.rcsb.org/structure/5WJ2, https://www.rcsb.org/structure/6AA7, https://www.rcsb.org/structure/7ZCT set to summarized
+```
+
+### `log://turn_51/set/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/*`
+scheme=log action=set attrs={}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/* not found
+```
+
+### `log://turn_51/set/https%3A/www.fpbase.org/*`
+scheme=log action=set attrs={}
+
+```
+https://www.fpbase.org/fret, https://www.fpbase.org/spectra, https://www.fpbase.org/table set to summarized
+```
+
+### `log://turn_51/set/search%3A/turn_*`
+scheme=log action=set attrs={}
+
+```
+search://turn_* not found
+```
+
+### `log://turn_51/set/prompt%3A/1`
+scheme=log action=set attrs={}
+
+```
+prompt://1 set to summarized
+```
+
+### `log://turn_51/set/known%3A/files/*`
+scheme=log action=set attrs={}
+
+```
+known://files/antibody_fasta_contents, known://files/pdb_ids, known://files/pdb_ids_contents, known://files/pdb_ids_full_list set to summarized
+```
+
+### `log://turn_51/set/known%3A/api/*`
+scheme=log action=set attrs={}
+
+```
+known://api/fpbase_acceptor, known://api/fpbase_donor set to summarized
+```
+
+### `log://turn_51/set/unknown%3A/*`
+scheme=log action=set attrs={}
+
+```
+unknown://api/fpbase_acceptor, unknown://api/fpbase_donor, unknown://api/pdb_sequences, unknown://binder/antibody_target, unknown://binder/molecule, unknown://constraints/gc_content, unknown://experiment/fret_filter, unknown://files/antibody_fasta, unknown://files/pdb_ids, unknown://files/plasmid_gb, unknown://fusion/components, unknown://fusion/order, unknown://sequence/dhfr set to archived
+```
+
+### `log://turn_51/update/all_unknowns_resolved_and_demoted%3B_ready_for_Deployment_Stage`
+scheme=log action=update attrs={"status":167,"action":"update"}
+
+```
+all unknowns resolved and demoted; ready for Deployment Stage
+```
+