Starting phenix.real_space_refine on Mon Aug 10 01:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qxe_4666/08_2026/6qxe_4666.cif" } resolution = 4.15 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= 0.000 sd= 0.005 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 24 5.49 5 S 146 5.16 5 C 13434 2.51 5 N 3700 2.21 5 O 4106 1.98 5 H 19050 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s 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: 40460 Number of models: 1 Model: "" Number of chains: 10 Chain: "M" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 933 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8141 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 9631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 9631 Classifications: {'peptide': 611} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1129 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 396 Unexpected atoms: {' G%rna3p_pur,HO3'': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "E" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8141 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 486} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 9631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 9631 Classifications: {'peptide': 611} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1129 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 396 Unexpected atoms: {' G%rna3p_pur,HO3'': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 21157 HO3' G D 12 .*. H " "ATOM 40454 HO3' G H 12 .*. H " Time building chain proxies: 6.09, per 1000 atoms: 0.15 Number of scatterers: 40460 At special positions: 0 Unit cell: (186.84, 113.4, 102.6, 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 146 16.00 P 24 15.00 O 4106 8.00 N 3700 7.00 C 13434 6.00 H 19050 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.