Starting phenix.real_space_refine on Thu Aug 6 10:20:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.map" model { file = "/net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t0n_10356/08_2026/6t0n_10356.cif" } resolution = 2.54 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 29 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 8940 2.51 5 N 2496 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 14598 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5741 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 25, 'TRANS': 678} Chain breaks: 2 Chain: "B" Number of atoms: 5972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5972 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 1 Chain: "C" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2016 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "R" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 292 Classifications: {'RNAv2': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 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: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "B" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "V" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 13752 OP3 A V 1 .*. O " Time building chain proxies: 2.62, per 1000 atoms: 0.18 Number of scatterers: 14598 At special positions: 0 Unit cell: (106.464, 119.467, 118.654, 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 92 16.00 P 29 15.00 Mg 2 11.99 O 3039 8.00 N 2496 7.00 C 8940 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: 1 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.