Starting phenix.real_space_refine on Fri Jul 3 21:57:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.map" model { file = "/net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ut6_26756/07_2026/7ut6_26756.cif" } resolution = 1.91 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= 0.078 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 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 3397 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: 16442 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 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: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 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: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 47.781 104.752 58.633 1.00 23.62 S ATOM 4552 SG CYS B 95 31.507 99.319 42.686 1.00 19.10 S ATOM 1170 SG CYS A 154 29.327 103.527 45.294 1.00 18.14 S ATOM 465 SG CYS A 62 34.754 101.543 48.190 1.00 15.85 S ATOM 652 SG CYS A 88 28.975 97.621 48.314 1.00 17.18 S ATOM 652 SG CYS A 88 28.975 97.621 48.314 1.00 17.18 S ATOM 5005 SG CYS B 153 26.040 99.849 43.955 1.00 19.41 S ATOM 4372 SG CYS B 70 28.447 93.339 43.009 1.00 16.63 S ATOM 4552 SG CYS B 95 31.507 99.319 42.686 1.00 19.10 S ATOM 10056 SG CYS C 275 34.252 27.956 63.734 1.00 24.05 S ATOM 12516 SG CYS D 95 52.299 31.045 49.128 1.00 19.28 S ATOM 9134 SG CYS C 154 54.145 27.316 52.603 1.00 17.76 S ATOM 8429 SG CYS C 62 48.362 29.629 54.543 1.00 13.97 S ATOM 8616 SG CYS C 88 54.169 33.585 54.676 1.00 13.41 S ATOM 8616 SG CYS C 88 54.169 33.585 54.676 1.00 13.41 S ATOM 12969 SG CYS D 153 57.575 30.764 51.077 1.00 19.66 S ATOM 12336 SG CYS D 70 55.352 37.030 48.883 1.00 16.19 S ATOM 12516 SG CYS D 95 52.299 31.045 49.128 1.00 19.28 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM15965 S1 CLF B 602 .*. S " "HETATM16013 S1 CLF D 602 .*. S " Time building chain proxies: 4.51, per 1000 atoms: 0.27 Number of scatterers: 16442 At special positions: 0 Unit cell: (84.76, 130.4, 101.06, 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 139 16.00 O 3397 8.00 N 2702 7.00 C 10170 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.