Starting phenix.real_space_refine on Fri Aug 7 17:13:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2026/8qz8_18772.cif" } resolution = 3.13 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= 0.002 sd= 0.072 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7113 2.51 5 N 2035 2.21 5 O 2292 1.98 5 H 11077 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 22629 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7910 Classifications: {'peptide': 512} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 491} Chain breaks: 1 Chain: "C" Number of atoms: 6696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6696 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain: "V" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1046 Unexpected atoms: {' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 17, 'rna3p': 15} Chain breaks: 1 Chain: "P" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unexpected atoms: {' A%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 47.930 47.016 19.706 1.00 76.37 S ATOM 4473 SG CYS A 282 45.639 45.224 17.052 1.00 87.29 S ATOM 18195 SG CYS C 233 21.177 52.353 108.814 1.00129.37 S ATOM 18219 SG CYS C 235 21.445 54.226 105.382 1.00120.87 S ATOM 16861 SG CYS C 146 9.859 61.301 88.729 1.00133.35 S ATOM 17049 SG CYS C 159 9.623 64.497 90.979 1.00131.26 S ATOM 17105 SG CYS C 163 12.623 62.252 91.247 1.00119.92 S ATOM 17115 SG CYS C 164 12.238 64.813 88.738 1.00123.42 S Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 22297 HO3' G V 40 .*. H " "ATOM 22586 HO3' A P 32 .*. H " Time building chain proxies: 3.69, per 1000 atoms: 0.16 Number of scatterers: 22629 At special positions: 0 Unit cell: (92.19, 101.848, 125.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 45 15.00 Mg 1 11.99 O 2292 8.00 N 2035 7.00 C 7113 6.00 H 11077 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.