Starting phenix.real_space_refine on Fri Aug 7 02:41:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.map" model { file = "/net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tw1_10603/08_2026/6tw1_10603.cif" } resolution = 2.7 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= 0.000 sd= 0.005 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 45 5.49 5 Mg 4 5.21 5 S 108 5.16 5 C 11508 2.51 5 N 3231 2.21 5 O 3731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 18627 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5733 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 25, 'TRANS': 677} Chain breaks: 2 Chain: "B" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5879 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 30, 'TRANS': 709} Chain: "V" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 703 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 14, 'rna3p': 18} Chain breaks: 1 Chain: "M" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17560 OP3 A V 1 .*. O " Time building chain proxies: 3.12, per 1000 atoms: 0.17 Number of scatterers: 18627 At special positions: 0 Unit cell: (121.092, 122.718, 119.467, 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 108 16.00 P 45 15.00 Mg 4 11.99 O 3731 8.00 N 3231 7.00 C 11508 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.