Starting phenix.real_space_refine on Sat Oct 24 18:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wvf_32852/10_2026/7wvf_32852.cif" } resolution = 3.91 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= 0.065 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 38 5.16 5 C 8738 2.51 5 N 2408 2.21 5 O 2975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 14249 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5284 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 917 Classifications: {'RNAv2': 46} Modifications used: {'rna3p_pyr': 46} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1009 Unusual residues: {' I%rna3p': 46} Unexpected atoms: {' I%rna3p,C1'': 46, ' I%rna3p,C2': 46, ' I%rna3p,C2'': 46, ' I%rna3p,C3'': 46, ' I%rna3p,C4': 46, ' I%rna3p,C4'': 46, ' I%rna3p,C5': 46, ' I%rna3p,C5'': 46, ' I%rna3p,C6': 46, ' I%rna3p,C8': 46, ' I%rna3p,N1': 46, ' I%rna3p,N3': 46, ' I%rna3p,N7': 46, ' I%rna3p,N9': 46, ' I%rna3p,O2'': 46, ' I%rna3p,O3'': 46, ' I%rna3p,O4'': 46, ' I%rna3p,O5'': 46, ' I%rna3p,O6': 46, ' I%rna3p,OP1': 45, ' I%rna3p,OP2': 45, ' I%rna3p,P': 45} Classifications: {'undetermined': 46} Modifications used: {'rna3p': 46} Link IDs: {'rna3p': 45} Chain: "C" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1755 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Number of atoms with unknown nonbonded energy type symbols: 1009 "ATOM 11486 C1' I F 1 .*. C " "ATOM 11487 C2 I F 1 .*. C " "ATOM 11488 C2' I F 1 .*. C " "ATOM 11489 C3' I F 1 .*. C " "ATOM 11490 C4 I F 1 .*. C " "ATOM 11491 C4' I F 1 .*. C " "ATOM 11492 C5 I F 1 .*. C " "ATOM 11493 C5' I F 1 .*. C " "ATOM 11494 C6 I F 1 .*. C " "ATOM 11495 C8 I F 1 .*. C " ... (remaining 999 not shown) Time building chain proxies: 3.10, per 1000 atoms: 0.22 Number of scatterers: 14249 At special positions: 0 Unit cell: (96.6985, 95.612, 203.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 90 15.00 O 2975 8.00 N 2408 7.00 C 8738 6.00 sf(0) = scattering factor at diffraction angle 0. Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 1009 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.