Starting phenix.real_space_refine on Thu Aug 6 13:52:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.cif Found real_map, /net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.map" model { file = "/net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6szu_10354/08_2026/6szu_10354.cif" } resolution = 2.41 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= 0.006 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 56 5.49 5 Mg 6 5.21 5 S 92 5.16 5 C 9213 2.51 5 N 2605 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s 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: 15245 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 bond proxies already assigned to first conformer: 5860 Chain: "B" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5964 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Chain: "C" Number of atoms: 2022 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} bond proxies already assigned to first conformer: 2040 Chain: "V" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 929 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 44} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 12, 'rna3p_pyr': 15} Link IDs: {'rna2p': 17, 'rna3p': 26} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} 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: "V" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "M" 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: 2 residue: pdb=" N AARG A 491 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 491 " occ=0.50 residue: pdb=" N AHIS C 27 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 13770 OP3 A V 1 .*. O " Time building chain proxies: 4.41, per 1000 atoms: 0.29 Number of scatterers: 15245 At special positions: 0 Unit cell: (97.524, 119.467, 117.841, 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 92 16.00 P 56 15.00 Mg 6 11.99 O 3273 8.00 N 2605 7.00 C 9213 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.