Starting phenix.real_space_refine on Fri Aug 7 01:02:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pth_17871/08_2026/8pth_17871.map" } resolution = 2.73 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= 0.001 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 Zn 1 6.06 5 P 27 5.49 5 S 54 5.16 5 C 5715 2.51 5 N 1629 2.21 5 O 1819 1.98 5 H 8991 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 18236 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7856 Classifications: {'peptide': 509} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2868 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Unexpected atoms: {' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain breaks: 1 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 47.327 53.573 19.817 1.00 43.06 S ATOM 4472 SG CYS A 282 45.157 52.027 16.924 1.00 58.28 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17821 HO3' G D 40 .*. H " Time building chain proxies: 3.11, per 1000 atoms: 0.17 Number of scatterers: 18236 At special positions: 0 Unit cell: (89.88, 94.92, 126.84, 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) Zn 1 29.99 S 54 16.00 P 27 15.00 O 1819 8.00 N 1629 7.00 C 5715 6.00 H 8991 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: 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.