Starting phenix.real_space_refine on Thu Aug 6 16:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.cif" model { file = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2026/8psq_17860.cif" } resolution = 2.65 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= 0.003 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 1 6.06 5 P 28 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 5032 2.51 5 N 1457 2.21 5 O 1618 1.98 5 H 7898 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 16079 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5030 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 18, 'TRANS': 296} Chain: "B" Number of atoms: 7973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain: "C" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2221 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "V" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 386 Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 466 Unexpected atoms: {' C%rna3p_pyr,HO3'': 1} Classifications: {'RNAv2': 15} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} 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 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 961 SG CYS A 161 48.028 44.792 80.976 1.00 33.76 S ATOM 2850 SG CYS A 282 46.959 47.528 83.512 1.00 39.94 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 16069 HO3' C S 15 .*. H " Time building chain proxies: 2.19, per 1000 atoms: 0.14 Number of scatterers: 16079 At special positions: 0 Unit cell: (88.2, 94.08, 99.96, 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 1 29.99 S 44 16.00 P 28 15.00 Mg 1 11.99 O 1618 8.00 N 1457 7.00 C 5032 6.00 H 7898 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.