Starting phenix.real_space_refine on Sat Aug 8 09:43:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyh_29578/08_2026/8fyh_29578.cif" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1862 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 14 6.06 5 P 16 5.49 5 S 118 5.16 5 C 16116 2.51 5 N 4722 2.21 5 O 4652 1.98 5 H 195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 25833 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2931 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 10 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 852 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 12, 'GLU:plan': 24, 'ARG:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 362 Chain: "C" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2654 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 12, 'TRANS': 354} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2722 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 6, 'ASN:plan1': 10, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 199 Chain: "A" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3425 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 25, 'TRANS': 488} Chain breaks: 6 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 27, 'TYR:plan': 8, 'ARG:plan': 17, 'GLN:plan1': 13, 'PHE:plan': 6, 'ASN:plan1': 17, 'ASP:plan': 16, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 460 Chain: "E" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 696 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2931 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 10 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 852 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 12, 'GLU:plan': 24, 'ARG:plan': 9, 'HIS:plan': 6, 'ASN:plan1': 11, 'PHE:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 362 Chain: "I" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2654 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 12, 'TRANS': 354} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASP:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "J" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2722 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 22, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 20, 'GLN:plan1': 6, 'ASN:plan1': 10, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 199 Chain: "G" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3425 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 25, 'TRANS': 488} Chain breaks: 6 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLU:plan': 27, 'TYR:plan': 8, 'ARG:plan': 17, 'GLN:plan1': 13, 'PHE:plan': 6, 'ASN:plan1': 17, 'ASP:plan': 16, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 460 Chain: "K" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 187 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 27} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 696 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 589 Unexpected atoms: {' G%rna3p_pur,HO5'': 1} Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 14} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10238 SG CYS A 528 90.339 116.747 101.330 1.00 60.88 S ATOM 10283 SG CYS A 535 90.228 113.510 103.412 1.00 64.47 S ATOM 10306 SG CYS A 539 87.780 116.324 104.167 1.00 62.99 S ATOM 10238 SG CYS A 528 90.339 116.747 101.330 1.00 60.88 S ATOM 10319 SG CYS A 541 86.635 117.692 101.125 1.00 58.37 S ATOM 10371 SG CYS A 548 87.792 114.126 100.436 1.00 52.02 S ATOM 10406 SG CYS A 552 88.656 116.974 97.981 1.00 54.69 S ATOM 10283 SG CYS A 535 90.228 113.510 103.412 1.00 64.47 S ATOM 10371 SG CYS A 548 87.792 114.126 100.436 1.00 52.02 S ATOM 10417 SG CYS A 554 91.461 113.258 99.843 1.00 63.09 S ATOM 10440 SG CYS A 558 89.164 110.638 101.245 1.00 60.11 S ATOM 10483 SG CYS A 565 80.615 107.180 84.657 1.00 41.18 S ATOM 10500 SG CYS A 567 77.901 104.647 83.793 1.00 42.37 S ATOM 10529 SG CYS A 571 78.377 107.825 81.753 1.00 43.37 S ATOM 10568 SG CYS A 576 76.870 107.831 85.365 1.00 41.61 S ATOM 10529 SG CYS A 571 78.377 107.825 81.753 1.00 43.37 S ATOM 10635 SG CYS A 585 79.879 110.752 83.790 1.00 40.34 S ATOM 10687 SG CYS A 593 81.762 109.337 80.816 1.00 45.19 S ATOM 10752 SG CYS A 606 78.593 111.403 80.386 1.00 45.47 S ATOM 10483 SG CYS A 565 80.615 107.180 84.657 1.00 41.18 S ATOM 10581 SG CYS A 578 80.133 109.766 87.445 1.00 39.24 S ATOM 10635 SG CYS A 585 79.879 110.752 83.790 1.00 40.34 S ATOM 10666 SG CYS A 590 83.240 109.917 85.431 1.00 40.89 S ATOM 9400 SG CYS A 286 90.777 127.789 90.691 1.00 47.70 S ATOM 9422 SG CYS A 289 89.985 128.993 87.154 1.00 48.85 S ATOM 9464 SG CYS A 294 88.805 131.009 90.118 1.00 52.79 S ATOM 22853 SG CYS G 528 59.702 94.795 98.482 1.00 66.92 S ATOM 22898 SG CYS G 535 59.018 98.554 98.482 1.00 75.43 S ATOM 22921 SG CYS G 539 60.623 96.897 101.551 1.00 72.84 S ATOM 22853 SG CYS G 528 59.702 94.795 98.482 1.00 66.92 S ATOM 22934 SG CYS G 541 62.975 94.420 100.451 1.00 66.08 S ATOM 22986 SG CYS G 548 62.570 97.127 97.799 1.00 59.26 S ATOM 23021 SG CYS G 552 62.658 93.378 96.783 1.00 62.91 S ATOM 22898 SG CYS G 535 59.018 98.554 98.482 1.00 75.43 S ATOM 22986 SG CYS G 548 62.570 97.127 97.799 1.00 59.26 S ATOM 23032 SG CYS G 554 59.866 97.024 95.106 1.00 68.11 S ATOM 23055 SG CYS G 558 61.321 100.342 96.145 1.00 60.99 S ATOM 23098 SG CYS G 565 77.208 97.039 86.046 1.00 51.59 S ATOM 23115 SG CYS G 567 80.326 99.205 85.523 1.00 52.76 S ATOM 23144 SG CYS G 571 80.441 95.423 85.244 1.00 50.12 S ATOM 23183 SG CYS G 576 79.995 97.323 88.679 1.00 48.33 S ATOM 23144 SG CYS G 571 80.441 95.423 85.244 1.00 50.12 S ATOM 23250 SG CYS G 585 77.790 93.647 87.384 1.00 47.91 S ATOM 23302 SG CYS G 593 77.778 93.291 83.553 1.00 52.35 S ATOM 23367 SG CYS G 606 80.365 91.604 85.781 1.00 52.79 S ATOM 23098 SG CYS G 565 77.208 97.039 86.046 1.00 51.59 S ATOM 23196 SG CYS G 578 75.887 96.170 89.555 1.00 47.84 S ATOM 23250 SG CYS G 585 77.790 93.647 87.384 1.00 47.91 S ATOM 23281 SG CYS G 590 74.200 94.646 86.600 1.00 49.28 S ATOM 22015 SG CYS G 286 63.244 80.196 95.522 1.00 53.44 S ATOM 22037 SG CYS G 289 65.666 77.827 93.732 1.00 52.91 S ATOM 22079 SG CYS G 294 64.902 77.319 97.365 1.00 57.60 S Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="ZN ZN A 801 " occ=0.47 residue: pdb="ZN ZN A 802 " occ=0.40 residue: pdb="ZN ZN A 803 " occ=0.67 residue: pdb="ZN ZN A 804 " occ=0.49 residue: pdb="ZN ZN A 805 " occ=0.62 residue: pdb="ZN ZN A 806 " occ=0.00 residue: pdb="ZN ZN A 807 " occ=0.51 residue: pdb="ZN ZN G 801 " occ=0.47 residue: pdb="ZN ZN G 802 " occ=0.29 residue: pdb="ZN ZN G 803 " occ=0.68 residue: pdb="ZN ZN G 804 " occ=0.37 residue: pdb="ZN ZN G 805 " occ=0.57 ... (remaining 2 not shown) Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 25262 HO5' G M 1 .*. H " Time building chain proxies: 4.62, per 1000 atoms: 0.18 Number of scatterers: 25833 At special positions: 0 Unit cell: (171.214, 203.117, 146.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 14 29.99 S 118 16.00 P 16 15.00 O 4652 8.00 N 4722 7.00 C 16116 6.00 H 195 1.00 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.