Starting phenix.real_space_refine on Sun Aug 9 10:34:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8e_23716/08_2026/7m8e_23716.cif" } resolution = 3.4 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= 0.056 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 Zn 2 6.06 5 P 49 5.49 5 Mg 1 5.21 5 S 135 5.16 5 C 21059 2.51 5 N 6009 2.21 5 O 6625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.13s 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: 33880 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 10396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10396 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7719 Classifications: {'peptide': 967} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 931} Chain: "1" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "2" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "3" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14581 SG CYS D 70 67.582 123.454 124.282 1.00132.86 S ATOM 14595 SG CYS D 72 70.497 125.753 124.707 1.00136.55 S ATOM 14703 SG CYS D 85 67.111 127.434 123.997 1.00139.51 S ATOM 14727 SG CYS D 88 69.263 125.813 121.546 1.00137.43 S ATOM 20415 SG CYS D 814 28.023 95.049 73.037 1.00100.48 S ATOM 20980 SG CYS D 888 31.566 96.196 74.097 1.00 96.21 S ATOM 21031 SG CYS D 895 29.747 93.284 75.690 1.00 86.90 S ATOM 21052 SG CYS D 898 31.006 92.760 72.479 1.00 87.17 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 33709 OP3 A 3 1 .*. O " Time building chain proxies: 5.46, per 1000 atoms: 0.16 Number of scatterers: 33880 At special positions: 0 Unit cell: (163.76, 165.54, 211.82, 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) Zn 2 29.99 S 135 16.00 P 49 15.00 Mg 1 11.99 O 6625 8.00 N 6009 7.00 C 21059 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.