Starting phenix.real_space_refine on Sun Aug 9 15:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bf5_16013/08_2026/8bf5_16013.cif" } resolution = 2.96 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= 0.001 sd= 0.017 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 P 43 5.49 5 Mg 3 5.21 5 S 131 5.16 5 C 11254 2.51 5 N 3105 2.21 5 O 3472 1.98 5 H 17699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 35707 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 11187 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 26, 'TRANS': 670} Chain breaks: 1 Chain: "B" Number of atoms: 11418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 11418 Classifications: {'peptide': 726} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 692} Chain breaks: 2 Chain: "C" Number of atoms: 11827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 11827 Classifications: {'peptide': 729} 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: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "R" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 392 Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "M" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 405 Unexpected atoms: {' A%rna3p_pur,HO3'': 1} Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 11} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 34455 OP3 A V 1 .*. O " "ATOM 35614 HO3' A M 20 .*. H " Time building chain proxies: 5.95, per 1000 atoms: 0.17 Number of scatterers: 35707 At special positions: 0 Unit cell: (121.929, 125.015, 115.755, 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) S 131 16.00 P 43 15.00 Mg 3 11.99 O 3472 8.00 N 3105 7.00 C 11254 6.00 H 17699 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.