Starting phenix.real_space_refine on Thu Aug 6 23:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ptj_17872/08_2026/8ptj_17872.cif" } resolution = 2.86 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= 0.001 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 1 6.06 5 P 18 5.49 5 S 54 5.16 5 C 5616 2.51 5 N 1587 2.21 5 O 1757 1.98 5 H 8841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 17874 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7862 Classifications: {'peptide': 511} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 490} Chain breaks: 1 Chain: "C" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 2792 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain breaks: 2 Chain: "D" Number of atoms: 285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 192 Unexpected atoms: {' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Conformer: "B" Number of residues, atoms: 6, 192 Unexpected atoms: {' G%rna2p_pur,HO3'': 1} Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 3} bond proxies already assigned to first conformer: 105 Chain: "V" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 281 Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 45.530 46.138 18.978 1.00 67.01 S ATOM 4472 SG CYS A 282 43.431 44.368 16.160 1.00 66.74 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P A A D 12 " occ=0.60 ... (64 atoms not shown) pdb=" H2 B A D 12 " occ=0.40 residue: pdb=" P A U D 13 " occ=0.60 ... (58 atoms not shown) pdb=" H6 B U D 13 " occ=0.40 residue: pdb=" P A U D 14 " occ=0.60 ... (58 atoms not shown) pdb=" H6 B U D 14 " occ=0.40 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17583 HO3' G D 17 .*. H " Time building chain proxies: 3.00, per 1000 atoms: 0.17 Number of scatterers: 17874 At special positions: 0 Unit cell: (88.2, 87.36, 123.48, 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 1 29.99 S 54 16.00 P 18 15.00 O 1757 8.00 N 1587 7.00 C 5616 6.00 H 8841 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.