Starting phenix.real_space_refine (version: dev) on Mon Dec 19 13:18:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/12_2022/7boi_12244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/12_2022/7boi_12244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/12_2022/7boi_12244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/12_2022/7boi_12244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/12_2022/7boi_12244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7boi_12244/12_2022/7boi_12244.pdb" } resolution = 2.98 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= -0.000 sd= 0.005 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 "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 35970 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 23172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 23057 Unknown residues: {'4OC': 1, 'G7M': 1, 'MA6': 2, 'UR3': 1} Classifications: {'RNA': 1073} Modifications used: {'rna2p_pur': 79, 'rna2p_pyr': 52, 'rna3p': 3, 'rna3p_pur': 542, 'rna3p_pyr': 397} Link IDs: {'rna2p': 130, 'rna3p': 938} Chain breaks: 6 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 551 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "W" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2456 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Unusual residues: {' MG': 70} Classifications: {'undetermined': 70} Link IDs: {None: 69} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'GNP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35454 SG CYS W 297 103.267 175.784 111.924 1.00138.41 S ATOM 35500 SG CYS W 302 100.646 176.420 109.591 1.00139.90 S ATOM 35559 SG CYS W 310 104.236 175.553 107.507 1.00143.63 S Number of atoms with unknown nonbonded energy type symbols: 115 "HETATM11295 P G7M A 527 .*. P " "HETATM11296 OP1 G7M A 527 .*. O " "HETATM11297 OP2 G7M A 527 .*. O " "HETATM11298 O5' G7M A 527 .*. O " "HETATM11299 C5' G7M A 527 .*. C " "HETATM11300 C4' G7M A 527 .*. C " "HETATM11301 O4' G7M A 527 .*. O " "HETATM11302 C3' G7M A 527 .*. C " "HETATM11303 O3' G7M A 527 .*. O " "HETATM11304 C2' G7M A 527 .*. C " ... (remaining 105 not shown) Time building chain proxies: 21.61, per 1000 atoms: 0.60 Number of scatterers: 35970 At special positions: 0 Unit cell: (137.795, 218.085, 147.56, 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 1 29.99 S 51 16.00 P 1081 15.00 Mg 72 11.99 O 9803 8.00 N 6688 7.00 C 18274 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: 115 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.