Starting phenix.real_space_refine on Fri Aug 7 02:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.map" model { file = "/net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t0v_10360/08_2026/6t0v_10360.cif" } resolution = 3.02 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= 0.006 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 48 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 11562 2.51 5 N 3253 2.21 5 O 3628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s 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: 18604 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5746 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5950 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5878 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 709} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "R" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 296 Unusual residues: {'GTG': 1} Classifications: {'RNAv2': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 3, '2KH': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17597 OP3 A V 1 .*. O " Time building chain proxies: 3.88, per 1000 atoms: 0.21 Number of scatterers: 18604 At special positions: 0 Unit cell: (120.28, 127.594, 116.216, 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 108 16.00 P 48 15.00 Mg 5 11.99 O 3628 8.00 N 3253 7.00 C 11562 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.