Starting phenix.real_space_refine on Thu Aug 6 17:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.map" model { file = "/net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xqb_22288/08_2026/6xqb_22288.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= 0.002 sd= 0.038 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1603 1.98 5 H 7987 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 16323 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 12682 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 25, 'TRANS': 775} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1713 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 993 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 444 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Unexpected atoms: {' A%rna3p_pur,HO3'': 1} Classifications: {'RNAv2': 7} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna3p': 6} Chain: "F" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 259 Classifications: {'RNAv2': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "A" 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 3213 SG CYS A 301 37.207 66.986 36.975 1.00131.34 S ATOM 3290 SG CYS A 306 37.350 65.836 33.243 1.00128.23 S ATOM 3355 SG CYS A 310 40.424 66.248 34.854 1.00134.44 S ATOM 6095 SG CYS A 487 19.687 63.110 45.316 1.00126.47 S ATOM 8612 SG CYS A 645 17.972 62.844 42.341 1.00141.82 S ATOM 8622 SG CYS A 646 22.155 64.389 43.308 1.00142.48 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 16054 HO3' A E 9 .*. H " Time building chain proxies: 2.88, per 1000 atoms: 0.18 Number of scatterers: 16323 At special positions: 0 Unit cell: (84.55, 97.01, 108.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 61 16.00 P 15 15.00 Mg 1 11.99 O 1603 8.00 N 1392 7.00 C 5262 6.00 H 7987 1.00 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.