Starting phenix.real_space_refine on Tue Oct 27 17:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqk_40708/10_2026/8sqk_40708.map" } resolution = 3.01 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= 1.029 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 72 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 8104 2.51 5 N 2244 2.21 5 O 2833 1.98 5 H 12229 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25574 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 14710 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 929, 14689 Classifications: {'peptide': 929} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Conformer: "B" Number of residues, atoms: 929, 14689 Classifications: {'peptide': 929} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} bond proxies already assigned to first conformer: 14856 Chain: "B" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2825 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1153 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2842 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1651 Classifications: {'peptide': 113} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Unexpected atoms: {' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1123 Unexpected atoms: {' U%rna3p_pyr,HO3'': 1} Classifications: {'RNAv2': 35} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna3p': 34} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Classifications: {'RNAv2': 1} Modifications used: {'rna2p_pur': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Classifications: {'RNA': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Classifications: {'RNA': 1} Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3, 'water': 110} Link IDs: {None: 112} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4810 SG CYS A 301 31.985 89.334 110.936 1.00 31.71 S ATOM 4887 SG CYS A 306 33.308 92.664 112.215 1.00 47.50 S ATOM 4952 SG CYS A 310 33.937 89.432 113.971 1.00 30.32 S ATOM 7709 SG CYS A 487 30.472 90.544 89.816 1.00 30.25 S ATOM 10247 SG CYS A 645 30.690 93.996 90.930 1.00 44.42 S ATOM 10257 SG CYS A 646 29.230 91.204 93.185 1.00 39.37 S Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 24197 HO3' G P 35 .*. H " "ATOM 25321 HO3' U T 134 .*. H " Time building chain proxies: 6.09, per 1000 atoms: 0.24 Number of scatterers: 25574 At special positions: 0 Unit cell: (94.1775, 137.477, 166.705, 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 89 16.00 P 72 15.00 Mg 1 11.99 O 2833 8.00 N 2244 7.00 C 8104 6.00 H 12229 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: 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.