Starting phenix.real_space_refine on Sat Aug 8 22:40:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.map" model { file = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i87_35240/08_2026/8i87_35240.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 143 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 19624 2.51 5 N 5205 2.21 5 O 6006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31066 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3264 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3758 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3306 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "D" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3782 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3762 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3203 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 394} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 1, 'ASP:plan': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "O" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3292 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "T" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3782 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 362 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Unexpected atoms: {' U%rna2p_pyr,OP3': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "I" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Unexpected atoms: {' U%rna2p_pyr,OP3': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 343 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 324 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Unexpected atoms: {' U%rna2p_pyr,OP3': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "S" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 390 Unexpected atoms: {' U%rna2p_pyr,OP3': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "U" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 324 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 4 "ATOM 28532 OP3 U H 1 .*. O " "ATOM 28922 OP3 U I 1 .*. O " "ATOM 29979 OP3 U L 1 .*. O " "ATOM 30369 OP3 U S 1 .*. O " Time building chain proxies: 7.55, per 1000 atoms: 0.24 Number of scatterers: 31066 At special positions: 0 Unit cell: (121.6, 166.25, 214.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 143 15.00 Mg 4 11.99 O 6006 8.00 N 5205 7.00 C 19624 6.00 sf(0) = scattering factor at diffraction angle 0. Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.