Starting phenix.real_space_refine (version: dev) on Mon Dec 19 01:10:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vad_21137/12_2022/6vad_21137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vad_21137/12_2022/6vad_21137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vad_21137/12_2022/6vad_21137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vad_21137/12_2022/6vad_21137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vad_21137/12_2022/6vad_21137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vad_21137/12_2022/6vad_21137.pdb" } resolution = 3.3 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= 0.003 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 37223 atoms to isotropic. 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 26": "OE1" <-> "OE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ASP 391": "OD1" <-> "OD2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 770": "OD1" <-> "OD2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 863": "OD1" <-> "OD2" Residue "A ASP 876": "OD1" <-> "OD2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 962": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 974": "OE1" <-> "OE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A PHE 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1052": "OD1" <-> "OD2" Residue "A PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A TYR 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ASP 490": "OD1" <-> "OD2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 633": "OD1" <-> "OD2" Residue "B GLU 642": "OE1" <-> "OE2" Residue "B ASP 662": "OD1" <-> "OD2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 675": "OD1" <-> "OD2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 807": "OE1" <-> "OE2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "B TYR 829": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 929": "OD1" <-> "OD2" Residue "B PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 964": "OE1" <-> "OE2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1011": "OE1" <-> "OE2" Residue "B PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1040": "OE1" <-> "OE2" Residue "B PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1171": "OD1" <-> "OD2" Residue "B ASP 1180": "OD1" <-> "OD2" Residue "B GLU 1194": "OE1" <-> "OE2" Residue "B GLU 1202": "OE1" <-> "OE2" Residue "B GLU 1250": "OE1" <-> "OE2" Residue "B PHE 1275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1314": "OD1" <-> "OD2" Residue "B PHE 1315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1329": "OE1" <-> "OE2" Residue "B PHE 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1350": "OD1" <-> "OD2" Residue "B GLU 1365": "OE1" <-> "OE2" 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: 37613 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 18879 Unexpected atoms: {'PRO,H': 3} Classifications: {'peptide': 1168} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 1129} Chain breaks: 9 Chain: "B" Number of atoms: 18734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1153, 18734 Classifications: {'peptide': 1153} Link IDs: {'PTRANS': 40, 'TRANS': 1112} Chain breaks: 14 Number of atoms with unknown nonbonded energy type symbols: 3 "ATOM 3910 H PRO A 260 .*. H " "ATOM 6194 H PRO A 408 .*. H " "ATOM 16786 H PRO A1126 .*. H " Time building chain proxies: 13.78, per 1000 atoms: 0.37 Number of scatterers: 37613 At special positions: 0 Unit cell: (177.67, 131.89, 115.54, 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 106 16.00 O 3432 8.00 N 3076 7.00 C 11903 6.00 H 19096 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: 3 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.