Starting phenix.real_space_refine on Sun Jul 5 23:15:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.map" model { file = "/net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uia_20784/07_2026/6uia_20784.cif" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.003 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 178 5.16 5 C 20298 2.51 5 N 5374 2.21 5 O 5864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.03s 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: 31720 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8058 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 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 "HETATM31625 C1B COA A1201 .*. C " "HETATM31626 C2A COA A1201 .*. C " "HETATM31627 C2B COA A1201 .*. C " "HETATM31628 C2P COA A1201 .*. C " "HETATM31629 C3B COA A1201 .*. C " "HETATM31630 C3P COA A1201 .*. C " "HETATM31631 C4A COA A1201 .*. C " "HETATM31632 C4B COA A1201 .*. C " "HETATM31633 C5A COA A1201 .*. C " "HETATM31634 C5B COA A1201 .*. C " ... (remaining 86 not shown) Time building chain proxies: 11.55, per 1000 atoms: 0.36 Number of scatterers: 31720 At special positions: 0 Unit cell: (187.05, 171.39, 140.07, 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 178 16.00 P 6 15.00 O 5864 8.00 N 5374 7.00 C 20298 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.