Starting phenix.real_space_refine on Tue Oct 27 10:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wv4_32845/10_2026/7wv4_32845.cif" } resolution = 3.35 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= -0.006 sd= 1.057 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 158 5.49 5 S 68 5.16 5 C 15040 2.51 5 N 4144 2.21 5 O 5080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s 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: 24490 Number of models: 1 Model: "" Number of chains: 6 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: "C" 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: "D" 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: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1597 Classifications: {'RNAv2': 80} Modifications used: {'rna3p_pyr': 80} Link IDs: {'rna3p': 79} 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: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1757 Unusual residues: {' I%rna3p': 80} Unexpected atoms: {' I%rna3p,C1'': 80, ' I%rna3p,C2': 80, ' I%rna3p,C2'': 80, ' I%rna3p,C3'': 80, ' I%rna3p,C4': 80, ' I%rna3p,C4'': 80, ' I%rna3p,C5': 80, ' I%rna3p,C5'': 80, ' I%rna3p,C6': 80, ' I%rna3p,C8': 80, ' I%rna3p,N1': 80, ' I%rna3p,N3': 80, ' I%rna3p,N7': 80, ' I%rna3p,N9': 80, ' I%rna3p,O2'': 80, ' I%rna3p,O3'': 80, ' I%rna3p,O4'': 80, ' I%rna3p,O5'': 80, ' I%rna3p,O6': 80, ' I%rna3p,OP1': 79, ' I%rna3p,OP2': 79, ' I%rna3p,P': 79} Classifications: {'undetermined': 80} Modifications used: {'rna3p': 80} Link IDs: {'rna3p': 79} Number of atoms with unknown nonbonded energy type symbols: 1757 "ATOM 22734 C1' I F 1 .*. C " "ATOM 22735 C2 I F 1 .*. C " "ATOM 22736 C2' I F 1 .*. C " "ATOM 22737 C3' I F 1 .*. C " "ATOM 22738 C4 I F 1 .*. C " "ATOM 22739 C4' I F 1 .*. C " "ATOM 22740 C5 I F 1 .*. C " "ATOM 22741 C5' I F 1 .*. C " "ATOM 22742 C6 I F 1 .*. C " "ATOM 22743 C8 I F 1 .*. C " ... (remaining 1747 not shown) Time building chain proxies: 5.19, per 1000 atoms: 0.21 Number of scatterers: 24490 At special positions: 0 Unit cell: (98.5545, 113.215, 257.382, 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 68 16.00 P 158 15.00 O 5080 8.00 N 4144 7.00 C 15040 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: 1757 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.