Starting phenix.real_space_refine on Tue Oct 27 20:43:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sqj_40707/10_2026/8sqj_40707.cif" } resolution = 3.06 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= 0.015 sd= 1.023 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 8242 2.51 5 N 2291 2.21 5 O 2945 1.98 5 H 12403 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26058 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 14700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 14700 Classifications: {'peptide': 929} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2823 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1138 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2842 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1688 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Unexpected atoms: {' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1122 Classifications: {'RNAv2': 35} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna3p': 34} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 538 Unexpected atoms: {' C%rna2p_pyr,HO3'': 1} Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Classifications: {'RNA': 1} Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3, 'water': 118} Link IDs: {None: 120} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4821 SG CYS A 301 31.699 89.795 112.230 1.00 31.05 S ATOM 4898 SG CYS A 306 32.877 93.103 113.297 1.00 41.25 S ATOM 4963 SG CYS A 310 33.796 89.593 115.174 1.00 30.19 S ATOM 7720 SG CYS A 487 30.320 90.929 90.907 1.00 44.18 S ATOM 10237 SG CYS A 645 30.399 94.305 92.029 1.00 38.26 S ATOM 10247 SG CYS A 646 29.184 91.934 94.440 1.00 49.04 S Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 24207 HO3' G P 35 .*. H " "ATOM 25867 HO3' C O 20 .*. H " Time building chain proxies: 4.61, per 1000 atoms: 0.18 Number of scatterers: 26058 At special positions: 0 Unit cell: (93.095, 140.725, 167.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 88 16.00 P 86 15.00 Mg 1 11.99 O 2945 8.00 N 2291 7.00 C 8242 6.00 H 12403 1.00 sf(0) = scattering factor at diffraction angle 0. Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 2 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.