Starting phenix.real_space_refine on Sat Aug 8 03:00:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.map" model { file = "/net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sq9_40699/08_2026/8sq9_40699.cif" } resolution = 2.9 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= 0.958 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 73 5.49 5 Mg 4 5.21 5 S 87 5.16 5 C 8027 2.51 5 N 2209 2.21 5 O 2923 1.98 5 H 12087 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25412 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 14726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 14659 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Conformer: "B" Number of residues, atoms: 926, 14659 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} bond proxies already assigned to first conformer: 14778 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2773 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1152 Classifications: {'peptide': 73} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2849 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1461 Classifications: {'peptide': 98} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Unexpected atoms: {' A%rna3p_pur,HO3'': 1} Classifications: {'RNAv2': 32} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1122 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 33} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 250 Unusual residues: {' MG': 4, ' ZN': 2, 'WSB': 2} Classifications: {'undetermined': 8, 'water': 186} Link IDs: {None: 193} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "T" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4824 SG CYS A 301 31.115 87.929 108.501 1.00 78.43 S ATOM 4901 SG CYS A 306 32.066 91.480 109.803 1.00 82.22 S ATOM 4966 SG CYS A 310 32.955 88.054 111.554 1.00 68.52 S ATOM 7723 SG CYS A 487 29.931 89.626 87.986 1.00 61.74 S ATOM 10238 SG CYS A 645 30.043 92.848 88.727 1.00 69.49 S ATOM 10248 SG CYS A 646 28.660 90.357 91.035 1.00 79.21 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 41 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.50 residue: pdb=" N AARG A 726 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 726 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 23977 HO3' A P 35 .*. H " Time building chain proxies: 5.19, per 1000 atoms: 0.20 Number of scatterers: 25412 At special positions: 0 Unit cell: (91.934, 135.763, 163.557, 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 87 16.00 P 73 15.00 Mg 4 11.99 O 2923 8.00 N 2209 7.00 C 8027 6.00 H 12087 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: 1 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.