Starting phenix.real_space_refine on Thu Aug 6 06:08:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.map" model { file = "/net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8as7_15608/08_2026/8as7_15608.cif" } resolution = 2.6 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= 0.005 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 39 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 8364 2.51 5 N 2339 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 13431 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12586 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1575, 12550 Classifications: {'peptide': 1575} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1515} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1575, 12550 Classifications: {'peptide': 1575} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1515} Chain breaks: 4 bond proxies already assigned to first conformer: 12775 Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 12} Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 49 Unusual residues: {' MG': 2, '2KH': 1, 'EPE': 1} Classifications: {'undetermined': 4, 'water': 3} Link IDs: {None: 6} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 13333 OP3 A G 1 .*. O " Time building chain proxies: 4.31, per 1000 atoms: 0.32 Number of scatterers: 13431 At special positions: 0 Unit cell: (102.85, 107.95, 129.2, 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 73 16.00 P 39 15.00 Mg 2 11.99 O 2614 8.00 N 2339 7.00 C 8364 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.