Starting phenix.real_space_refine on Thu Aug 6 16:45:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo1_26637/08_2026/7uo1_26637.map" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 1.000 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 Ca 10 9.91 5 P 454 5.49 5 S 2 5.16 5 C 4934 2.51 5 N 1993 2.21 5 O 3301 1.98 5 H 5894 0.53 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: 16588 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 12071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 12071 Unexpected atoms: {' C%rna3p_pyr,HO3'': 1, ' G%rna3p_pur,HO5'': 1} Classifications: {'RNAv2': 373} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 26, 'rna3p_pur': 191, 'rna3p_pyr': 128} Link IDs: {'rna2p': 51, 'rna3p': 321} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 2622 Unexpected atoms: {' A%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 82} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 73} Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1885 Classifications: {'peptide': 112} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CA': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 46 residue: pdb=" P C B 20 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 20 " occ=0.00 residue: pdb=" P C B 21 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 21 " occ=0.00 residue: pdb=" P G B 22 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 22 " occ=0.00 residue: pdb=" P C B 23 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 23 " occ=0.00 residue: pdb=" P U B 24 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 24 " occ=0.00 residue: pdb=" P U B 25 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 25 " occ=0.00 residue: pdb=" P C B 26 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 26 " occ=0.00 residue: pdb=" P G B 27 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 27 " occ=0.00 residue: pdb=" P U B 28 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 28 " occ=0.00 residue: pdb=" P C B 29 " occ=0.00 ... (29 atoms not shown) pdb=" H6 C B 29 " occ=0.00 residue: pdb=" P G B 30 " occ=0.00 ... (32 atoms not shown) pdb=" H22 G B 30 " occ=0.00 residue: pdb=" P U B 31 " occ=0.00 ... (28 atoms not shown) pdb=" H6 U B 31 " occ=0.00 ... (remaining 34 not shown) Number of atoms with unknown nonbonded energy type symbols: 3 "ATOM 32 HO5' G B 1 .*. H " "ATOM 12064 HO3' C B 373 .*. H " "ATOM 14686 HO3' A C 77 .*. H " Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 16588 At special positions: 0 Unit cell: (99.6826, 116.048, 196.39, 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) Ca 10 19.99 S 2 16.00 P 454 15.00 O 3301 8.00 N 1993 7.00 C 4934 6.00 H 5894 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: 3 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.