Starting phenix.real_space_refine on Sat Aug 10 12:24:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/08_2024/7rb2_24392.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/08_2024/7rb2_24392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/08_2024/7rb2_24392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/08_2024/7rb2_24392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/08_2024/7rb2_24392.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/08_2024/7rb2_24392.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 1.000 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 16352 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10537 2.51 5 N 2659 2.21 5 O 3124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 264": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F ASP 39": "OD1" <-> "OD2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 304": "OE1" <-> "OE2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 335": "OD1" <-> "OD2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16386 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2783 Chain: "B" Number of atoms: 2737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2783 Chain: "C" Number of atoms: 2721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2716 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 347, 2716 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2767 Chain: "D" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "E" Number of atoms: 2733 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2779 Chain: "F" Number of atoms: 2733 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2779 Time building chain proxies: 16.07, per 1000 atoms: 0.98 Number of scatterers: 16386 At special positions: 0 Unit cell: (111.354, 110.523, 124.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3124 8.00 N 2659 7.00 C 10537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 5.7 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 39 sheets defined 27.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.554A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.920A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.726A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.507A pdb=" N LEU B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.848A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.691A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.761A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.567A pdb=" N LEU C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.702A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 230 removed outlier: 3.961A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.668A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 removed outlier: 3.572A pdb=" N LEU D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.670A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'D' and resid 227 through 230 removed outlier: 3.736A pdb=" N TYR D 230 " --> pdb=" O LEU D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.727A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 1 through 13 removed outlier: 3.922A pdb=" N VAL E 5 " --> pdb=" O SER E 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 removed outlier: 3.592A pdb=" N LEU E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.908A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.509A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 removed outlier: 3.593A pdb=" N LEU F 72 " --> pdb=" O GLU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 removed outlier: 3.849A pdb=" N LEU F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.688A pdb=" N VAL F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.698A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.578A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.124A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 142 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.002A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.766A pdb=" N GLU A 264 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 281 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 266 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.733A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 26 removed outlier: 6.555A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.042A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.508A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB2, first strand: chain 'B' and resid 264 through 266 removed outlier: 3.749A pdb=" N GLU B 264 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 281 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.358A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.539A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.217A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.419A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AB8, first strand: chain 'C' and resid 264 through 266 removed outlier: 3.916A pdb=" N GLU C 264 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 281 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.359A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.531A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.198A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC4, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.488A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AC6, first strand: chain 'D' and resid 264 through 266 removed outlier: 3.838A pdb=" N GLU D 264 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 281 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 315 through 322 removed outlier: 6.582A pdb=" N TRP D 332 " --> pdb=" O GLU D 339 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 removed outlier: 6.570A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.151A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.525A pdb=" N ALA E 92 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.346A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AD4, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AD5, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.184A pdb=" N GLU E 264 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR E 281 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.427A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 25 through 26 removed outlier: 6.560A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.121A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.555A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'F' and resid 264 through 266 removed outlier: 3.927A pdb=" N GLU F 264 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR F 281 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.356A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3423 1.33 - 1.45: 3727 1.45 - 1.57: 9482 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 16734 Sorted by residual: bond pdb=" N THR D 340 " pdb=" CA THR D 340 " ideal model delta sigma weight residual 1.455 1.494 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N THR F 340 " pdb=" CA THR F 340 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.27e-02 6.20e+03 8.78e+00 bond pdb=" C PRO D 343 " pdb=" O PRO D 343 " ideal model delta sigma weight residual 1.233 1.205 0.029 1.06e-02 8.90e+03 7.30e+00 bond pdb=" N THR C 340 " pdb=" CA THR C 340 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.25e-02 6.40e+03 6.88e+00 bond pdb=" C PRO B 343 " pdb=" O PRO B 343 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.08e-02 8.57e+03 6.31e+00 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.38: 393 106.38 - 113.29: 9345 113.29 - 120.20: 5764 120.20 - 127.11: 7086 127.11 - 134.02: 142 Bond angle restraints: 22730 Sorted by residual: angle pdb=" N GLU E 223 " pdb=" CA GLU E 223 " pdb=" CB GLU E 223 " ideal model delta sigma weight residual 110.30 117.22 -6.92 1.54e+00 4.22e-01 2.02e+01 angle pdb=" C TYR C 342 " pdb=" CA TYR C 342 " pdb=" CB TYR C 342 " ideal model delta sigma weight residual 109.42 116.23 -6.81 1.57e+00 4.06e-01 1.88e+01 angle pdb=" N GLU F 223 " pdb=" CA GLU F 223 " pdb=" CB GLU F 223 " ideal model delta sigma weight residual 110.20 116.58 -6.38 1.49e+00 4.50e-01 1.83e+01 angle pdb=" C PRO F 343 " pdb=" CA PRO F 343 " pdb=" CB PRO F 343 " ideal model delta sigma weight residual 111.46 106.28 5.18 1.21e+00 6.83e-01 1.83e+01 angle pdb=" C PRO D 343 " pdb=" CA PRO D 343 " pdb=" CB PRO D 343 " ideal model delta sigma weight residual 111.11 106.18 4.93 1.17e+00 7.31e-01 1.78e+01 ... (remaining 22725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9088 17.97 - 35.94: 734 35.94 - 53.91: 120 53.91 - 71.88: 41 71.88 - 89.85: 17 Dihedral angle restraints: 10000 sinusoidal: 3934 harmonic: 6066 Sorted by residual: dihedral pdb=" CA LEU F 297 " pdb=" C LEU F 297 " pdb=" N LEU F 298 " pdb=" CA LEU F 298 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR A 340 " pdb=" C THR A 340 " pdb=" N PHE A 341 " pdb=" CA PHE A 341 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TYR E 230 " pdb=" C TYR E 230 " pdb=" N ALA E 231 " pdb=" CA ALA E 231 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 9997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1735 0.047 - 0.095: 703 0.095 - 0.142: 169 0.142 - 0.190: 10 0.190 - 0.237: 5 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CG LEU D 227 " pdb=" CB LEU D 227 " pdb=" CD1 LEU D 227 " pdb=" CD2 LEU D 227 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PHE F 341 " pdb=" N PHE F 341 " pdb=" C PHE F 341 " pdb=" CB PHE F 341 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR C 342 " pdb=" N TYR C 342 " pdb=" C TYR C 342 " pdb=" CB TYR C 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2619 not shown) Planarity restraints: 2924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C THR A 340 " -0.073 2.00e-02 2.50e+03 pdb=" O THR A 340 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 341 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 194 " -0.019 2.00e-02 2.50e+03 2.03e-02 7.25e+00 pdb=" CG PHE F 194 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE F 194 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE F 194 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 194 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 194 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 194 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 328 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C SER C 328 " 0.037 2.00e-02 2.50e+03 pdb=" O SER C 328 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 329 " -0.012 2.00e-02 2.50e+03 ... (remaining 2921 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 15210 3.20 - 3.77: 24677 3.77 - 4.33: 35792 4.33 - 4.90: 60090 Nonbonded interactions: 136001 Sorted by model distance: nonbonded pdb=" OD2 ASP E 212 " pdb=" OH TYR E 225 " model vdw 2.075 3.040 nonbonded pdb=" OH TYR F 193 " pdb=" OE2 GLU F 304 " model vdw 2.081 3.040 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.082 3.040 nonbonded pdb=" OD2 ASP D 212 " pdb=" OH TYR D 225 " model vdw 2.105 3.040 nonbonded pdb=" OD2 ASP A 212 " pdb=" OH TYR A 225 " model vdw 2.109 3.040 ... (remaining 135996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 225 or (resid 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 263 or (resid 264 an \ d (name N or name CA or name C or name O or name CB )) or resid 265 through 333 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 345)) selection = (chain 'B' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 225 or (resid 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 263 or (resid 264 an \ d (name N or name CA or name C or name O or name CB )) or resid 265 through 333 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 345)) selection = (chain 'C' and (resid -1 through 35 or resid 37 through 201 or (resid 202 and (n \ ame N or name CA or name C or name O or name CB )) or resid 203 or (resid 204 an \ d (name N or name CA or name C or name O or name CB )) or resid 205 through 225 \ or (resid 226 and (name N or name CA or name C or name O or name CB )) or resid \ 227 through 263 or (resid 264 and (name N or name CA or name C or name O or name \ CB )) or resid 265 through 345)) selection = (chain 'D' and (resid -1 through 35 or resid 37 through 190 or (resid 191 and (n \ ame N or name CA or name C or name O or name CB )) or resid 192 through 203 or ( \ resid 204 and (name N or name CA or name C or name O or name CB )) or resid 205 \ through 222 or (resid 223 and (name N or name CA or name C or name O or name CB \ )) or resid 224 through 263 or (resid 264 and (name N or name CA or name C or na \ me O or name CB )) or resid 265 through 333 or (resid 334 and (name N or name CA \ or name C or name O or name CB )) or resid 335 through 345)) selection = (chain 'E' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 222 or (resid 223 and (name N or name CA or name C or na \ me O or name CB )) or resid 224 through 225 or (resid 226 and (name N or name CA \ or name C or name O or name CB )) or resid 227 through 263 or (resid 264 and (n \ ame N or name CA or name C or name O or name CB )) or resid 265 through 333 or ( \ resid 334 and (name N or name CA or name C or name O or name CB )) or resid 335 \ through 345)) selection = (chain 'F' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 225 or (resid 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 333 or (resid 334 an \ d (name N or name CA or name C or name O or name CB )) or resid 335 through 345) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.22 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 55.390 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 16734 Z= 0.505 Angle : 0.743 7.639 22730 Z= 0.434 Chirality : 0.051 0.237 2622 Planarity : 0.004 0.042 2924 Dihedral : 14.446 89.852 6088 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.33 % Allowed : 0.65 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 2076 helix: -0.83 (0.22), residues: 516 sheet: -1.02 (0.30), residues: 366 loop : -0.42 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 58 HIS 0.005 0.001 HIS A 242 PHE 0.046 0.003 PHE F 194 TYR 0.021 0.002 TYR E 179 ARG 0.013 0.001 ARG F 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 247 time to evaluate : 1.881 Fit side-chains REVERT: A 199 ASN cc_start: 0.7720 (t0) cc_final: 0.7514 (t0) REVERT: A 301 ASP cc_start: 0.7884 (m-30) cc_final: 0.7592 (m-30) REVERT: B 342 TYR cc_start: 0.6896 (p90) cc_final: 0.6193 (m-10) REVERT: C 199 ASN cc_start: 0.7765 (t0) cc_final: 0.7345 (t0) REVERT: C 301 ASP cc_start: 0.7923 (m-30) cc_final: 0.7616 (m-30) REVERT: D 172 VAL cc_start: 0.8885 (p) cc_final: 0.8485 (m) REVERT: D 330 MET cc_start: 0.6994 (tpt) cc_final: 0.6341 (tpt) REVERT: D 342 TYR cc_start: 0.6735 (p90) cc_final: 0.6014 (m-10) REVERT: E 199 ASN cc_start: 0.8293 (t0) cc_final: 0.8004 (t0) REVERT: E 264 GLU cc_start: 0.6732 (pt0) cc_final: 0.6510 (pt0) REVERT: E 266 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7832 (mm-30) REVERT: F 21 GLU cc_start: 0.8070 (mp0) cc_final: 0.7722 (mp0) REVERT: F 183 ASP cc_start: 0.8337 (m-30) cc_final: 0.8115 (m-30) REVERT: F 235 ILE cc_start: 0.8819 (pt) cc_final: 0.8593 (pt) REVERT: F 301 ASP cc_start: 0.7738 (m-30) cc_final: 0.7454 (m-30) REVERT: F 340 THR cc_start: 0.4671 (OUTLIER) cc_final: 0.4290 (p) outliers start: 6 outliers final: 3 residues processed: 252 average time/residue: 0.2765 time to fit residues: 104.7582 Evaluate side-chains 214 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.0050 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: