Starting phenix.real_space_refine on Fri Aug 7 01:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtl_14144/08_2026/7qtl_14144.map" } resolution = 2.48 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= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 2 5.21 5 S 126 5.16 5 C 11329 2.51 5 N 3199 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s 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: 18397 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 Chain: "B" Number of atoms: 5736 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 717, 5728 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 686} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 717, 5728 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 686} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5829 Chain: "C" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5767 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 29, 'TRANS': 696} Chain breaks: 2 Chain: "V" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 284 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "R" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "M" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2TM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU B 218 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 218 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 17281 OP3 A V 1 .*. O " Time building chain proxies: 5.02, per 1000 atoms: 0.27 Number of scatterers: 18397 At special positions: 0 Unit cell: (117.029, 126.781, 122.718, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 50 15.00 Mg 2 11.99 O 3691 8.00 N 3199 7.00 C 11329 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: 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.