Starting phenix.real_space_refine on Thu Jul 2 01:39:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.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/7n0l_24108/07_2026/7n0l_24108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2026/7n0l_24108.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= 0.000 sd= 0.004 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 6 5.49 5 S 34 5.16 5 C 3460 2.51 5 N 868 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.00s 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: 5270 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2587 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2587 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 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': 1} 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 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 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': 1} 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: 96 "HETATM 5175 C1B COA A 401 .*. C " "HETATM 5176 C2A COA A 401 .*. C " "HETATM 5177 C2B COA A 401 .*. C " "HETATM 5178 C2P COA A 401 .*. C " "HETATM 5179 C3B COA A 401 .*. C " "HETATM 5180 C3P COA A 401 .*. C " "HETATM 5181 C4A COA A 401 .*. C " "HETATM 5182 C4B COA A 401 .*. C " "HETATM 5183 C5A COA A 401 .*. C " "HETATM 5184 C5B COA A 401 .*. C " ... (remaining 86 not shown) Time building chain proxies: 1.33, per 1000 atoms: 0.25 Number of scatterers: 5270 At special positions: 0 Unit cell: (101.97, 89.61, 88.58, 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 34 16.00 P 6 15.00 O 902 8.00 N 868 7.00 C 3460 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: 96 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.