Starting phenix.real_space_refine on Fri Oct 30 10:45:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.map" model { file = "/net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8be0_15996/10_2026/8be0_15996.cif" } resolution = 2.34 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= 0.003 sd= 0.028 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: 7 Type Number sf(0) Gaussians P 47 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 11444 2.51 5 N 3155 2.21 5 O 3657 1.98 5 H 17924 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.16s 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: 36361 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 11538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11538 Classifications: {'peptide': 722} Link IDs: {'PTRANS': 26, 'TRANS': 695} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 11413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 726, 11402 Classifications: {'peptide': 726} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 691} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 726, 11402 Classifications: {'peptide': 726} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 691} Chain breaks: 2 bond proxies already assigned to first conformer: 11501 Chain: "C" Number of atoms: 11882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 11882 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 28, 'TRANS': 702} Chain breaks: 2 Chain: "V" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "R" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 388 Unexpected atoms: {' U%rna2p_pyr,HO3'': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 473 Classifications: {'RNAv2': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Classifications: {'RNAv2': 2} Modifications used: {'rna2p_pyr': 2} Link IDs: {'rna2p': 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS B 483 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS B 483 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 34856 OP3 A V 1 .*. O " "ATOM 35607 HO3' U R 19 .*. H " Time building chain proxies: 6.60, per 1000 atoms: 0.18 Number of scatterers: 36361 At special positions: 0 Unit cell: (121.26, 127.065, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 132 16.00 P 47 15.00 Mg 2 11.99 O 3657 8.00 N 3155 7.00 C 11444 6.00 H 17924 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.