Starting phenix.real_space_refine on Fri Aug 7 12:15:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.map" model { file = "/net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qx3_4661/08_2026/6qx3_4661.cif" } resolution = 3.79 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= 0.007 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 P 14 5.49 5 S 79 5.16 5 C 6857 2.51 5 N 1884 2.21 5 O 2107 1.98 5 H 10646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 21587 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 329 Unexpected atoms: {' A%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 6} Chain: "G" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unexpected atoms: {' U%rna2p_pyr,HO3'': 1} Classifications: {'RNAv2': 4} Modifications used: {'rna2p_pyr': 4} Link IDs: {'rna2p': 3} Chain: "O" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1799 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 9750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9750 Classifications: {'peptide': 615} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 586} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 8157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8157 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 487} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1430 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 322 HO3' A D 10 .*. H " "ATOM 445 HO3' U G 12 .*. H " Time building chain proxies: 3.84, per 1000 atoms: 0.18 Number of scatterers: 21587 At special positions: 0 Unit cell: (103.68, 102.6, 120.96, 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) S 79 16.00 P 14 15.00 O 2107 8.00 N 1884 7.00 C 6857 6.00 H 10646 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.