Starting phenix.real_space_refine on Thu Aug 6 12:12:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.cif Found real_map, /net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.map" model { file = "/net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6szv_10355/08_2026/6szv_10355.cif" } resolution = 2.5 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 43 5.49 5 Mg 5 5.21 5 S 92 5.16 5 C 9073 2.51 5 N 2554 2.21 5 O 3080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 14847 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5716 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 25, 'TRANS': 675} Chain breaks: 2 Chain: "B" Number of atoms: 5955 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 bond proxies already assigned to first conformer: 6052 Chain: "C" Number of atoms: 2025 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 2043 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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 200 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2KH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 27 " occ=0.60 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.40 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 13719 OP3 A V 1 .*. O " Time building chain proxies: 4.58, per 1000 atoms: 0.31 Number of scatterers: 14847 At special positions: 0 Unit cell: (103.213, 116.216, 112.965, 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 43 15.00 Mg 5 11.99 O 3080 8.00 N 2554 7.00 C 9073 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.