Starting phenix.real_space_refine on Thu Aug 6 07:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.map" model { file = "/net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8omr_16976/08_2026/8omr_16976.cif" } resolution = 3.3 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7626 atoms to isotropic. 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 Zn 2 6.06 5 P 75 5.49 5 S 48 5.16 5 C 4520 2.51 5 N 1341 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 7626 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 3000 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368} Conformer: "B" Number of residues, atoms: 390, 3000 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368} bond proxies already assigned to first conformer: 3053 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3014 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1589 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 75} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' ZN': 1, '9DG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2336 SG CYS A 317 50.960 46.783 79.155 1.00 71.53 S ATOM 2349 SG CYS A 319 48.135 45.426 76.966 1.00 57.96 S ATOM 2369 SG CYS A 322 51.015 47.274 75.471 1.00 66.05 S ATOM 5496 SG CYS B 351 26.013 26.939 71.448 1.00 61.72 S ATOM 5508 SG CYS B 353 27.602 29.987 72.683 1.00 70.08 S ATOM 5532 SG CYS B 356 24.182 29.011 73.915 1.00 67.56 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 335 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 335 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 6047 OP3 A C 1 .*. O " Time building chain proxies: 1.58, per 1000 atoms: 0.21 Number of scatterers: 7626 At special positions: 0 Unit cell: (72.54, 99.06, 124.8, 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) Zn 2 29.99 S 48 16.00 P 75 15.00 O 1640 8.00 N 1341 7.00 C 4520 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.