Starting phenix.real_space_refine on Sun Oct 25 22:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1f_14240/10_2026/7r1f_14240.map" } resolution = 2.58 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= 0.015 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 47 5.49 5 Mg 3 5.21 5 S 136 5.16 5 C 11458 2.51 5 N 3161 2.21 5 O 3567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18372 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5776 Classifications: {'peptide': 720} Link IDs: {'PTRANS': 26, 'TRANS': 693} Chain: "B" Number of atoms: 5762 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 728, 5715 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 693} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 728, 5715 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 693} Chain breaks: 2 bond proxies already assigned to first conformer: 5777 Chain: "C" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5836 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 28, 'TRANS': 700} Chain breaks: 1 Chain: "V" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 262 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: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 259 Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 373 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} 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} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG B 239 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 239 " occ=0.50 residue: pdb=" N AMET B 408 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 408 " occ=0.50 residue: pdb=" N AMET B 409 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 409 " occ=0.50 residue: pdb=" N AMET B 410 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 410 " occ=0.50 residue: pdb=" N AGLY B 411 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 411 " occ=0.50 residue: pdb=" N AMET B 412 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 412 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17397 OP3 A V 1 .*. O " Time building chain proxies: 4.57, per 1000 atoms: 0.25 Number of scatterers: 18372 At special positions: 0 Unit cell: (120.834, 124.122, 120.834, 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 136 16.00 P 47 15.00 Mg 3 11.99 O 3567 8.00 N 3161 7.00 C 11458 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.