Starting phenix.real_space_refine on Fri Jul 3 09:09:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.map" model { file = "/net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pbb_17583/07_2026/8pbb_17583.cif" } resolution = 2.49 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= 0.068 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: 5 Type Number sf(0) Gaussians Fe 8 7.16 5 S 82 5.16 5 C 8522 2.51 5 N 2260 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13334 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 384} Chain breaks: 5 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3437 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 418} Chain breaks: 2 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 384} Chain breaks: 5 Chain: "D" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3437 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 418} Chain breaks: 2 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3913 SG CYS B 104 74.127 81.561 48.979 1.00 63.32 S ATOM 160 SG CYS A 75 73.206 78.168 51.875 1.00 35.82 S ATOM 3345 SG CYS B 20 70.359 76.400 46.744 1.00 25.80 S ATOM 3513 SG CYS B 45 76.826 76.293 46.828 1.00 44.32 S ATOM 6819 SG CYS C 75 33.917 20.571 51.857 1.00 35.40 S ATOM 10572 SG CYS D 104 32.989 17.200 48.953 1.00 62.56 S ATOM 10004 SG CYS D 20 36.766 22.473 46.864 1.00 26.07 S ATOM 10172 SG CYS D 45 30.164 22.484 46.872 1.00 43.60 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM13319 S1 CLF B 501 .*. S " "HETATM13327 S1 CLF D 501 .*. S " Time building chain proxies: 2.22, per 1000 atoms: 0.17 Number of scatterers: 13334 At special positions: 0 Unit cell: (107.973, 100.44, 101.277, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 8 26.01 S 82 16.00 O 2462 8.00 N 2260 7.00 C 8522 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: 2 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.