Starting phenix.real_space_refine on Fri Aug 7 01:04:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.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/6qct_4512/08_2026/6qct_4512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qct_4512/08_2026/6qct_4512.cif" } 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 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= 0.003 sd= 0.026 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 41 5.49 5 Mg 2 5.21 5 S 132 5.16 5 C 11414 2.51 5 N 3150 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 18266 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5793 Classifications: {'peptide': 722} Link IDs: {'PTRANS': 26, 'TRANS': 695} Chain: "B" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5774 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 700} Chain breaks: 1 Chain: "C" Number of atoms: 5832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5832 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 700} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 284 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "R" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "M" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 313 Unusual residues: {'GTG': 1} Classifications: {'RNAv2': 12, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" A M 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17422 OP3 A V 1 .*. O " Time building chain proxies: 3.63, per 1000 atoms: 0.20 Number of scatterers: 18266 At special positions: 0 Unit cell: (122.172, 127.989, 120.509, 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 132 16.00 P 41 15.00 Mg 2 11.99 O 3527 8.00 N 3150 7.00 C 11414 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.