Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:46:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e70_27932/12_2022/8e70_27932_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e70_27932/12_2022/8e70_27932.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e70_27932/12_2022/8e70_27932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e70_27932/12_2022/8e70_27932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e70_27932/12_2022/8e70_27932_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e70_27932/12_2022/8e70_27932_neut_updated.pdb" } 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 ------------------------------------------------------------------------------- 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= 0.001 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 "e ARG 30": "NH1" <-> "NH2" Residue "e PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "e TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 211": "OE1" <-> "OE2" Residue "e GLU 214": "OE1" <-> "OE2" Residue "e GLU 218": "OE1" <-> "OE2" Residue "e GLU 226": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 334": "OE1" <-> "OE2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "f ARG 30": "NH1" <-> "NH2" Residue "f PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 128": "NH1" <-> "NH2" Residue "f TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 211": "OE1" <-> "OE2" Residue "f GLU 214": "OE1" <-> "OE2" Residue "f GLU 218": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 333": "OE1" <-> "OE2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 128": "NH1" <-> "NH2" Residue "c TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 214": "OE1" <-> "OE2" Residue "c GLU 218": "OE1" <-> "OE2" Residue "c GLU 226": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 333": "OE1" <-> "OE2" Residue "c GLU 334": "OE1" <-> "OE2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 128": "NH1" <-> "NH2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 214": "OE1" <-> "OE2" Residue "b GLU 218": "OE1" <-> "OE2" Residue "b GLU 226": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 333": "OE1" <-> "OE2" Residue "b GLU 334": "OE1" <-> "OE2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 214": "OE1" <-> "OE2" Residue "a GLU 218": "OE1" <-> "OE2" Residue "a GLU 226": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 333": "OE1" <-> "OE2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "d TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 214": "OE1" <-> "OE2" Residue "d GLU 218": "OE1" <-> "OE2" Residue "d GLU 226": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 21097 Number of models: 1 Model: "" Number of chains: 13 Chain: "8" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1225 Unexpected atoms: {' DC,HN41': 2, ' DC,HN42': 2} Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Number of atoms with unknown nonbonded energy type symbols: 4 "ATOM 1163 HN41 DC 8 58 .*. H " "ATOM 1164 HN42 DC 8 58 .*. H " "ATOM 1186 HN41 DC 8 59 .*. H " "ATOM 1187 HN42 DC 8 59 .*. H " Time building chain proxies: 11.87, per 1000 atoms: 0.56 Number of scatterers: 21097 At special positions: 0 Unit cell: (121.866, 135.763, 149.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 102 16.00 P 73 15.00 Mg 6 11.99 F 18 9.00 O 4131 8.00 N 3696 7.00 C 13002 6.00 Be 6 4.00 H 63 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: 4 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.