Starting phenix.real_space_refine on Sat Jul 4 02:38:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enm_28273/07_2026/8enm_28273.map" } resolution = 2.14 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= 0.029 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 138 5.16 5 C 10171 2.51 5 N 2703 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s 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: 17722 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3795 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain breaks: 1 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: 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: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 349 Classifications: {'water': 349} Link IDs: {None: 348} Chain: "B" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 501 Classifications: {'water': 501} Link IDs: {None: 500} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 352 Classifications: {'water': 352} Link IDs: {None: 351} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 491 Classifications: {'water': 491} Link IDs: {None: 490} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 101.479 35.100 60.219 1.00 58.39 S ATOM 1170 SG CYS A 154 102.167 54.066 48.155 1.00 48.05 S ATOM 4554 SG CYS B 95 97.965 52.385 45.312 1.00 42.86 S ATOM 465 SG CYS A 62 99.641 48.644 50.636 1.00 42.49 S ATOM 652 SG CYS A 88 96.265 54.353 50.367 1.00 52.20 S ATOM 652 SG CYS A 88 96.265 54.353 50.367 1.00 52.20 S ATOM 5007 SG CYS B 153 98.864 57.269 46.752 1.00 42.07 S ATOM 4374 SG CYS B 70 92.115 55.465 45.213 1.00 43.29 S ATOM 4554 SG CYS B 95 97.965 52.385 45.312 1.00 42.86 S ATOM 10058 SG CYS C 275 25.928 50.699 60.212 1.00 55.56 S ATOM 9139 SG CYS C 154 25.232 31.735 48.155 1.00 47.90 S ATOM 12518 SG CYS D 95 29.429 33.419 45.311 1.00 41.67 S ATOM 8434 SG CYS C 62 27.760 37.155 50.638 1.00 41.78 S ATOM 8621 SG CYS C 88 31.136 31.446 50.368 1.00 50.60 S ATOM 8621 SG CYS C 88 31.136 31.446 50.368 1.00 50.60 S ATOM 12971 SG CYS D 153 28.525 28.554 46.748 1.00 41.78 S ATOM 12338 SG CYS D 70 35.287 30.331 45.217 1.00 44.64 S ATOM 12518 SG CYS D 95 29.429 33.419 45.311 1.00 41.67 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM15966 S1 CLF B 600 .*. S " "HETATM16015 S1 CLF D 602 .*. S " Time building chain proxies: 3.60, per 1000 atoms: 0.20 Number of scatterers: 17722 At special positions: 0 Unit cell: (128.05, 86.45, 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 138 16.00 O 4676 8.00 N 2703 7.00 C 10171 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.