Starting phenix.real_space_refine on Sun Jul 5 20:51:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps1_17842/07_2026/8ps1_17842.map" } resolution = 2.8 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= 0.017 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 10 5.49 5 S 108 5.16 5 C 18953 2.51 5 N 4980 2.21 5 O 5736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29787 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1584, 12379 Classifications: {'peptide': 1584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1522} Chain breaks: 3 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: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16010 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'J8W:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'COA': 1, 'FMN': 1, 'NAP': 1} Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1} Unresolved non-hydrogen planarities: 17 Number of atoms with unknown nonbonded energy type symbols: 48 "HETATM29692 C1B COA G2102 .*. C " "HETATM29693 C2A COA G2102 .*. C " "HETATM29694 C2B COA G2102 .*. C " "HETATM29695 C2P COA G2102 .*. C " "HETATM29696 C3B COA G2102 .*. C " "HETATM29697 C3P COA G2102 .*. C " "HETATM29698 C4A COA G2102 .*. C " "HETATM29699 C4B COA G2102 .*. C " "HETATM29700 C5A COA G2102 .*. C " "HETATM29701 C5B COA G2102 .*. C " ... (remaining 38 not shown) Time building chain proxies: 5.49, per 1000 atoms: 0.18 Number of scatterers: 29787 At special positions: 0 Unit cell: (185.68, 182.515, 178.295, 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 108 16.00 P 10 15.00 O 5736 8.00 N 4980 7.00 C 18953 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: 48 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.