Starting phenix.real_space_refine on Fri Oct 30 02:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.map" model { file = "/net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oqc_13029/10_2026/7oqc_13029.cif" } resolution = 4.1 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= 0.006 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 621 5.49 5 S 82 5.16 5 C 19852 2.51 5 N 5980 2.21 5 O 8515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s 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: 35050 Number of models: 1 Model: "" Number of chains: 19 Chain: "F" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1758 Classifications: {'peptide': 267} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASN:plan1': 7, 'PHE:plan': 6, 'ASP:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 13, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "I" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 636 Unusual residues: {' N%rna3p': 53} Unexpected atoms: {' N%rna3p,C1'': 53, ' N%rna3p,C2'': 53, ' N%rna3p,C3'': 53, ' N%rna3p,C4'': 53, ' N%rna3p,C5'': 53, ' N%rna3p,O2'': 53, ' N%rna3p,O3'': 53, ' N%rna3p,O4'': 53, ' N%rna3p,O5'': 53, ' N%rna3p,OP1': 53, ' N%rna3p,OP2': 53, ' N%rna3p,P': 53} Classifications: {'undetermined': 53} Modifications used: {'rna3p': 53} Link IDs: {'rna3p': 52} Chain: "E" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4561 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 531} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 687 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "1" Number of atoms: 11822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 11822 Classifications: {'RNAv2': 558} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 35, 'rna3p_pur': 241, 'rna3p_pyr': 258} Link IDs: {'rna2p': 59, 'rna3p': 498} Chain breaks: 1 Chain: "G" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1954 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1570 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 186} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "b" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "d" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "e" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 600 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 585 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "g" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 556 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain breaks: 1 Chain: "h" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "i" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1201 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 12, 'HIS:plan': 3, 'GLU:plan': 13, 'ARG:plan': 8, 'PHE:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 221 Chain: "D" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 3530 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1418 Unresolved non-hydrogen angles: 1833 Unresolved non-hydrogen dihedrals: 1212 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'ARG:plan': 16, 'ASP:plan': 21, 'GLN:plan1': 19, 'PHE:plan': 26, 'ASN:plan1': 32, 'TYR:plan': 18, 'TRP:plan': 12, 'GLU:plan': 23, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 827 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1059 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 14, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 506 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASN:plan1': 7, 'TYR:plan': 7, 'HIS:plan': 4, 'GLU:plan': 10, 'PHE:plan': 7, 'GLN:plan1': 6, 'ARG:plan': 9, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 274 Number of atoms with unknown nonbonded energy type symbols: 636 "ATOM 1970 C1' N I 103 .*. C " "ATOM 1971 C2' N I 103 .*. C " "ATOM 1972 C3' N I 103 .*. C " "ATOM 1973 C4' N I 103 .*. C " "ATOM 1974 C5' N I 103 .*. C " "ATOM 1975 O2' N I 103 .*. O " "ATOM 1976 O3' N I 103 .*. O " "ATOM 1977 O4' N I 103 .*. O " "ATOM 1978 O5' N I 103 .*. O " "ATOM 1979 OP1 N I 103 .*. O " ... (remaining 626 not shown) Time building chain proxies: 6.43, per 1000 atoms: 0.18 Number of scatterers: 35050 At special positions: 0 Unit cell: (154.28, 228.52, 213.44, 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 82 16.00 P 621 15.00 O 8515 8.00 N 5980 7.00 C 19852 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: 636 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.