Starting phenix.real_space_refine on Sun Oct 25 00:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.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 { model { file = "/net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lyt_23601/10_2026/7lyt_23601.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= 0.298 sd= 1.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 899 atoms to isotropic. 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 94 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4475 2.51 5 N 1392 2.21 5 O 1644 1.98 5 H 6722 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s 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: 14354 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 11358 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 41, 'TRANS': 670} Chain: "B" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1259 Classifications: {'RNAv2': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1045 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 632 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' SC': 3} Unexpected atoms: {' SC,C1'': 3, ' SC,C2': 3, ' SC,C2'': 3, ' SC,C3'': 3, ' SC,C4': 3, ' SC,C4'': 3, ' SC,C5': 3, ' SC,C5'': 3, ' SC,C6': 3, ' SC,N1': 3, ' SC,N3': 3, ' SC,N4': 3, ' SC,O2': 3, ' SC,O3'': 3, ' SC,O4'': 3, ' SC,O5'': 3, ' SC,OP1': 3, ' SC,P': 3, ' SC,S2P': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10645 SG CYS A 667 19.951 34.452 36.126 1.00 74.36 S ATOM 10691 SG CYS A 670 19.371 30.891 34.874 1.00 74.35 S ATOM 10893 SG CYS A 685 20.918 33.488 32.615 1.00 72.22 S ATOM 10933 SG CYS A 688 17.233 33.644 33.534 1.00 73.11 S Number of atoms with unknown nonbonded energy type symbols: 57 "HETATM14295 C1' SC D 11 .*. C " "HETATM14296 C2 SC D 11 .*. C " "HETATM14297 C2' SC D 11 .*. C " "HETATM14298 C3' SC D 11 .*. C " "HETATM14299 C4 SC D 11 .*. C " "HETATM14300 C4' SC D 11 .*. C " "HETATM14301 C5 SC D 11 .*. C " "HETATM14302 C5' SC D 11 .*. C " "HETATM14303 C6 SC D 11 .*. C " "HETATM14304 N1 SC D 11 .*. N " ... (remaining 47 not shown) Time building chain proxies: 2.59, per 1000 atoms: 0.18 Number of scatterers: 14354 At special positions: 0 Unit cell: (88.085, 98.12, 124.88, 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 24 16.00 P 94 15.00 Mg 2 11.99 O 1644 8.00 N 1392 7.00 C 4475 6.00 H 6722 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: 57 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.