Starting phenix.real_space_refine on Fri Aug 7 16:49:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.map" model { file = "/net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8urb_42488/08_2026/8urb_42488.cif" } resolution = 3.4 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= 0.002 sd= 0.049 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 41 5.49 5 S 82 5.16 5 C 7239 2.51 5 N 1974 2.21 5 O 2316 1.98 5 H 11060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 22714 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 14521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 14521 Classifications: {'peptide': 921} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 895} Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2901 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain: "C" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1072 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2909 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 178} Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 639 Unexpected atoms: {' U%rna2p_pyr,HO3'': 1} Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 670 Classifications: {'RNAv2': 21} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 9} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4641 SG CYS A 296 33.356 94.490 113.706 1.00 58.21 S ATOM 4707 SG CYS A 301 35.192 97.441 115.219 1.00 43.72 S ATOM 4771 SG CYS A 305 35.279 94.028 116.947 1.00 43.40 S ATOM 7554 SG CYS A 482 32.799 95.250 91.808 1.00 41.59 S ATOM 10058 SG CYS A 640 33.477 98.838 92.934 1.00 58.82 S ATOM 10069 SG CYS A 641 31.431 96.466 95.177 1.00 46.50 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 22036 HO3' U I 33 .*. H " Time building chain proxies: 3.95, per 1000 atoms: 0.17 Number of scatterers: 22714 At special positions: 0 Unit cell: (92.568, 122.36, 169.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 41 15.00 O 2316 8.00 N 1974 7.00 C 7239 6.00 H 11060 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.