Starting phenix.real_space_refine on Sat Jul 4 03:48:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.map" model { file = "/net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crs_26957/07_2026/8crs_26957.cif" } resolution = 2.04 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= 0.032 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 Mo 2 10.26 5 Fe 32 7.16 5 S 142 5.16 5 C 10296 2.51 5 N 2710 2.21 5 O 4706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s 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: 17888 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'1N7': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {' FE': 1, '1N7': 2, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 343 Classifications: {'water': 343} Link IDs: {None: 342} Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 520 Classifications: {'water': 520} Link IDs: {None: 519} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 315 Classifications: {'water': 315} Link IDs: {None: 314} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 514 Classifications: {'water': 514} Link IDs: {None: 513} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 72.296 29.726 57.718 1.00 26.58 S ATOM 1170 SG CYS A 154 87.647 40.792 45.504 1.00 21.56 S ATOM 4549 SG CYS B 95 83.763 42.938 42.608 1.00 31.78 S ATOM 465 SG CYS A 62 81.899 39.378 47.987 1.00 19.53 S ATOM 652 SG CYS A 88 84.273 45.696 47.812 1.00 22.26 S ATOM 652 SG CYS A 88 84.273 45.696 47.812 1.00 22.26 S ATOM 5002 SG CYS B 153 88.254 45.480 44.148 1.00 33.02 S ATOM 4369 SG CYS B 70 82.615 49.630 42.687 1.00 28.57 S ATOM 4549 SG CYS B 95 83.763 42.938 42.608 1.00 31.78 S ATOM 10053 SG CYS C 275 38.130 98.999 57.789 1.00 26.52 S ATOM 9134 SG CYS C 154 22.859 87.896 45.508 1.00 21.04 S ATOM 12513 SG CYS D 95 26.734 85.706 42.618 1.00 30.17 S ATOM 8429 SG CYS C 62 28.601 89.326 47.993 1.00 19.48 S ATOM 8616 SG CYS C 88 26.245 83.072 47.781 1.00 22.88 S ATOM 8616 SG CYS C 88 26.245 83.072 47.781 1.00 22.88 S ATOM 12966 SG CYS D 153 22.230 83.223 44.155 1.00 26.81 S ATOM 12333 SG CYS D 70 27.931 79.052 42.817 1.00 24.97 S ATOM 12513 SG CYS D 95 26.734 85.706 42.618 1.00 30.17 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM16004 S1 CLF B 601 .*. S " "HETATM16139 S1 CLF D 602 .*. S " Time building chain proxies: 3.31, per 1000 atoms: 0.19 Number of scatterers: 17888 At special positions: 0 Unit cell: (111.15, 128.7, 96.2, 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) Mo 2 41.97 Fe 32 26.01 S 142 16.00 O 4706 8.00 N 2710 7.00 C 10296 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.