Starting phenix.real_space_refine on Fri Aug 7 03:00:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2026/6z8k_11118.cif" } resolution = 3.02 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= 0.002 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 44 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 11707 2.51 5 N 3120 2.21 5 O 3600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s 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: 18587 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "X" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNAv2': 4} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNAv2': 11} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "T" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 17631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2158, 17631 Classifications: {'peptide': 2158} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 2087} Chain breaks: 10 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17114 SG CYS A2064 86.345 101.656 90.538 1.00 77.50 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 23 OP3 A C 1 .*. O " Time building chain proxies: 3.84, per 1000 atoms: 0.21 Number of scatterers: 18587 At special positions: 0 Unit cell: (120.596, 133.812, 148.68, 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 114 16.00 P 44 15.00 Mg 1 11.99 O 3600 8.00 N 3120 7.00 C 11707 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.