Starting phenix.real_space_refine on Sun Oct 25 22:47:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0e_14222/10_2026/7r0e_14222.cif" } resolution = 2.51 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 53 5.49 5 Mg 2 5.21 5 S 127 5.16 5 C 11420 2.51 5 N 3224 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 18554 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 bond proxies already assigned to first conformer: 5865 Chain: "B" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5778 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 692} Chain breaks: 3 Chain: "C" Number of atoms: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5784 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 29, 'TRANS': 699} Chain breaks: 1 Chain: "M" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 293 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 12} 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNAv2': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "R" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 377 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 6, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 15} Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} 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} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 508 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 508 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 18103 OP3 A V 1 .*. O " Time building chain proxies: 4.93, per 1000 atoms: 0.27 Number of scatterers: 18554 At special positions: 0 Unit cell: (115.78, 128.185, 124.877, 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 127 16.00 P 53 15.00 Mg 2 11.99 O 3728 8.00 N 3224 7.00 C 11420 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.