Starting phenix.real_space_refine on Tue Aug 4 17:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2026/8aw3_15690.cif" } resolution = 3.6 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= 0.011 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 Zn 2 6.06 5 P 73 5.49 5 S 26 5.16 5 C 2899 2.51 5 N 903 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5059 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Unexpected atoms: {' G%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 73} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "2" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1341 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "3" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2159 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" 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 2293 SG CYS 2 136 45.404 41.101 78.006 1.00 52.15 S ATOM 2315 SG CYS 2 139 46.023 40.789 81.160 1.00 49.74 S ATOM 4670 SG CYS 3 291 40.792 29.700 77.854 1.00 52.47 S ATOM 4691 SG CYS 3 294 44.534 28.750 76.195 1.00 55.91 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 24 OP3 G 1 1 .*. O " Time building chain proxies: 0.93, per 1000 atoms: 0.18 Number of scatterers: 5059 At special positions: 0 Unit cell: (76.14, 76.95, 115.83, 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 26 16.00 P 73 15.00 O 1156 8.00 N 903 7.00 C 2899 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.