Starting phenix.real_space_refine on Sat Aug 8 21:21:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1m_0592/08_2026/6o1m_0592.map" } resolution = 3.15 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= 0.004 sd= 0.050 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 34 5.49 5 S 48 5.16 5 C 9894 2.51 5 N 2777 2.21 5 O 2923 1.98 5 H 15371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 31047 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "D" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "E" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "F" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "G" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "H" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "I" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "K" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1081 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "L" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1095 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain: "M" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1114 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "N" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1100 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "O" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Unexpected atoms: {' A%rna2p_pur,HO5'': 1, ' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 3} Link IDs: {'rna2p': 17} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Unexpected atoms: {' A%rna2p_pur,HO5'': 1, ' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 3} Link IDs: {'rna2p': 17} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Chain: "S" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Number of atoms with unknown nonbonded energy type symbols: 4 "ATOM 21560 HO5' A O 1 .*. H " "ATOM 22111 HO3' G O 18 .*. H " "ATOM 22149 HO5' A P 1 .*. H " "ATOM 22700 HO3' G P 18 .*. H " Time building chain proxies: 5.37, per 1000 atoms: 0.17 Number of scatterers: 31047 At special positions: 0 Unit cell: (101.37, 122.08, 107.91, 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 48 16.00 P 34 15.00 O 2923 8.00 N 2777 7.00 C 9894 6.00 H 15371 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: 4 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.