Starting phenix.real_space_refine (version: dev) on Mon Dec 19 00:27:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x76_33033/12_2022/7x76_33033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x76_33033/12_2022/7x76_33033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x76_33033/12_2022/7x76_33033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x76_33033/12_2022/7x76_33033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x76_33033/12_2022/7x76_33033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x76_33033/12_2022/7x76_33033.pdb" } resolution = 3.67 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= 0.002 sd= 0.038 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "C GLU 713": "OE1" <-> "OE2" Residue "C GLU 803": "OE1" <-> "OE2" Residue "C GLU 894": "OE1" <-> "OE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1099": "OE1" <-> "OE2" Residue "C GLU 1104": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D GLU 682": "OE1" <-> "OE2" Residue "D GLU 825": "OE1" <-> "OE2" Residue "D GLU 999": "OE1" <-> "OE2" Residue "D GLU 1028": "OE1" <-> "OE2" Residue "D GLU 1031": "OE1" <-> "OE2" Residue "D GLU 1233": "OE1" <-> "OE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F GLU 423": "OE1" <-> "OE2" Residue "F GLU 441": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 64334 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3539 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3633 Classifications: {'peptide': 233} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 17325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 17325 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 19864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 19864 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1202 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4834 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1931 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1931 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1932 Unexpected atoms: {'PRO,H': 1} Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1931 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 2648 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 2658 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "S" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 891 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25372 SG CYS D 60 70.393 109.749 112.749 1.00 79.33 S ATOM 25403 SG CYS D 62 69.303 111.204 116.016 1.00 83.27 S ATOM 25636 SG CYS D 75 73.097 110.494 115.556 1.00 84.78 S ATOM 25685 SG CYS D 78 71.138 107.815 116.026 1.00 75.31 S ATOM 38592 SG CYS D 886 109.802 62.072 84.229 1.00 74.81 S ATOM 39738 SG CYS D 962 106.346 62.270 85.687 1.00 69.27 S ATOM 39828 SG CYS D 969 106.934 63.572 82.071 1.00 63.11 S ATOM 39865 SG CYS D 972 106.928 59.988 82.798 1.00 62.78 S ATOM 51690 SG CYS G 90 59.866 187.807 79.119 1.00220.71 S ATOM 51734 SG CYS G 93 57.306 187.585 76.116 1.00222.83 S ATOM 52265 SG CYS G 130 57.255 189.531 79.614 1.00224.76 S ATOM 52297 SG CYS G 133 56.010 186.046 79.203 1.00221.26 S ATOM 51533 SG CYS G 79 74.083 196.273 76.605 1.00222.47 S ATOM 53621 SG CYS H 90 91.152 179.840 93.884 1.00233.56 S ATOM 53665 SG CYS H 93 93.787 177.901 95.156 1.00234.11 S ATOM 54196 SG CYS H 130 93.147 182.059 94.032 1.00233.87 S ATOM 54228 SG CYS H 133 95.168 180.525 94.428 1.00234.03 S ATOM 53464 SG CYS H 79 75.970 175.168 99.408 1.00220.86 S ATOM 55553 SG CYS M 90 64.529 173.460 35.972 1.00227.13 S ATOM 55597 SG CYS M 93 61.023 174.066 37.513 1.00225.05 S ATOM 56128 SG CYS M 130 61.482 172.138 34.234 1.00223.14 S ATOM 56160 SG CYS M 133 62.058 175.933 34.466 1.00215.70 S ATOM 55396 SG CYS M 79 66.872 159.521 42.742 1.00219.24 S ATOM 57484 SG CYS N 90 94.440 156.053 36.528 1.00216.64 S ATOM 57528 SG CYS N 93 98.279 155.819 36.590 1.00215.13 S ATOM 58059 SG CYS N 130 96.144 154.343 33.748 1.00210.96 S ATOM 58091 SG CYS N 133 96.265 152.716 37.192 1.00203.88 S ATOM 57327 SG CYS N 79 92.135 167.278 25.864 1.00223.17 S Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 54267 H PRO M 6 .*. H " Time building chain proxies: 27.43, per 1000 atoms: 0.43 Number of scatterers: 64334 At special positions: 0 Unit cell: (132.3, 227.85, 200.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 14 29.99 S 114 16.00 P 168 15.00 Mg 1 11.99 O 6660 8.00 N 5895 7.00 C 20046 6.00 H 31436 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.