Starting phenix.real_space_refine on Sun Apr 14 21:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/04_2024/7rb2_24392.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/04_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_24392/04_2024/7rb2_24392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/04_2024/7rb2_24392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/04_2024/7rb2_24392.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb2_24392/04_2024/7rb2_24392.pdb" } 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-5288/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: 15.57, per 1000 atoms: 0.95 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: 7.18 Conformation dependent library (CDL) restraints added in 6.1 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: 1.71 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: 5.24 Time building geometry restraints manager: 7.68 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 2.440 nonbonded pdb=" OH TYR F 193 " pdb=" OE2 GLU F 304 " model vdw 2.081 2.440 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.082 2.440 nonbonded pdb=" OD2 ASP D 212 " pdb=" OH TYR D 225 " model vdw 2.105 2.440 nonbonded pdb=" OD2 ASP A 212 " pdb=" OH TYR A 225 " model vdw 2.109 2.440 ... (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 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 56.540 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.110 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.040 ------------------------------------------------------------------------------- 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 : 2.013 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: 0.2947 time to fit residues: 111.4965 Evaluate side-chains 214 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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: 1.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 136 ASN B 28 ASN B 249 HIS C 4 ASN D 309 GLN E 28 ASN F 11 ASN F 244 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16734 Z= 0.196 Angle : 0.543 6.170 22730 Z= 0.297 Chirality : 0.045 0.244 2622 Planarity : 0.004 0.027 2924 Dihedral : 5.130 49.448 2214 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.49 % Allowed : 6.22 % Favored : 93.29 % 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: -0.40 (0.19), residues: 2076 helix: 0.07 (0.23), residues: 516 sheet: -0.48 (0.30), residues: 360 loop : -0.25 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS D 337 PHE 0.027 0.002 PHE F 194 TYR 0.015 0.002 TYR B 179 ARG 0.006 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 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 270 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 261 time to evaluate : 2.016 Fit side-chains REVERT: A 301 ASP cc_start: 0.7872 (m-30) cc_final: 0.7629 (m-30) REVERT: B 342 TYR cc_start: 0.6817 (p90) cc_final: 0.6044 (m-10) REVERT: C 199 ASN cc_start: 0.7760 (t0) cc_final: 0.7402 (t0) REVERT: C 236 VAL cc_start: 0.8887 (t) cc_final: 0.8616 (t) REVERT: C 301 ASP cc_start: 0.7919 (m-30) cc_final: 0.7641 (m-30) REVERT: D 330 MET cc_start: 0.6695 (tpt) cc_final: 0.6396 (tpt) REVERT: D 342 TYR cc_start: 0.6643 (p90) cc_final: 0.5889 (m-10) REVERT: E 199 ASN cc_start: 0.8289 (t0) cc_final: 0.7962 (t0) REVERT: E 235 ILE cc_start: 0.8872 (pt) cc_final: 0.8544 (mt) REVERT: E 342 TYR cc_start: 0.6752 (p90) cc_final: 0.5560 (m-10) REVERT: F 28 ASN cc_start: 0.7667 (m110) cc_final: 0.7357 (m110) REVERT: F 235 ILE cc_start: 0.8895 (pt) cc_final: 0.8662 (pt) REVERT: F 301 ASP cc_start: 0.7675 (m-30) cc_final: 0.7472 (m-30) outliers start: 9 outliers final: 4 residues processed: 267 average time/residue: 0.2979 time to fit residues: 117.1198 Evaluate side-chains 218 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN D 28 ASN E 28 ASN F 175 GLN F 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16734 Z= 0.195 Angle : 0.506 6.121 22730 Z= 0.276 Chirality : 0.045 0.175 2622 Planarity : 0.003 0.034 2924 Dihedral : 4.727 48.382 2210 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.82 % Allowed : 8.40 % Favored : 90.78 % 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: -0.14 (0.19), residues: 2076 helix: 0.41 (0.24), residues: 516 sheet: -0.04 (0.31), residues: 360 loop : -0.26 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 PHE 0.022 0.002 PHE F 194 TYR 0.014 0.001 TYR A 179 ARG 0.005 0.001 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 3 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 264 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8775 (tt) cc_final: 0.8517 (pt) REVERT: A 301 ASP cc_start: 0.7847 (m-30) cc_final: 0.7595 (m-30) REVERT: B 342 TYR cc_start: 0.6974 (p90) cc_final: 0.5995 (m-10) REVERT: C 199 ASN cc_start: 0.7780 (t0) cc_final: 0.7470 (t0) REVERT: C 236 VAL cc_start: 0.8841 (t) cc_final: 0.8613 (t) REVERT: C 301 ASP cc_start: 0.7898 (m-30) cc_final: 0.7609 (m-30) REVERT: C 342 TYR cc_start: 0.6701 (p90) cc_final: 0.5321 (m-10) REVERT: D 227 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5743 (mp) REVERT: D 330 MET cc_start: 0.6708 (tpt) cc_final: 0.6442 (tpt) REVERT: D 342 TYR cc_start: 0.6818 (p90) cc_final: 0.5829 (m-10) REVERT: E 199 ASN cc_start: 0.8289 (t0) cc_final: 0.7946 (t0) REVERT: E 235 ILE cc_start: 0.8866 (pt) cc_final: 0.8458 (mt) REVERT: F 28 ASN cc_start: 0.7604 (m110) cc_final: 0.7340 (m110) REVERT: F 199 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7609 (p0) REVERT: F 235 ILE cc_start: 0.8912 (pt) cc_final: 0.8659 (pt) REVERT: F 301 ASP cc_start: 0.7635 (m-30) cc_final: 0.7422 (m-30) outliers start: 15 outliers final: 7 residues processed: 256 average time/residue: 0.2973 time to fit residues: 113.9683 Evaluate side-chains 241 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 232 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 234 HIS B 28 ASN C 28 ASN D 28 ASN E 28 ASN F 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16734 Z= 0.209 Angle : 0.497 6.327 22730 Z= 0.271 Chirality : 0.044 0.155 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.664 48.910 2210 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.76 % Allowed : 10.09 % Favored : 89.14 % 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: -0.05 (0.19), residues: 2076 helix: 0.44 (0.24), residues: 522 sheet: 0.15 (0.31), residues: 360 loop : -0.23 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 332 HIS 0.005 0.001 HIS D 337 PHE 0.025 0.002 PHE F 194 TYR 0.013 0.001 TYR A 179 ARG 0.005 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 4 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 261 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 1.989 Fit side-chains REVERT: A 79 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8524 (pt) REVERT: A 301 ASP cc_start: 0.7862 (m-30) cc_final: 0.7617 (m-30) REVERT: B 342 TYR cc_start: 0.7052 (p90) cc_final: 0.6003 (m-10) REVERT: C 199 ASN cc_start: 0.7701 (t0) cc_final: 0.7434 (t0) REVERT: C 236 VAL cc_start: 0.8811 (t) cc_final: 0.8607 (t) REVERT: C 301 ASP cc_start: 0.7908 (m-30) cc_final: 0.7616 (m-30) REVERT: C 342 TYR cc_start: 0.6753 (p90) cc_final: 0.5181 (m-10) REVERT: D 227 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5735 (mp) REVERT: D 330 MET cc_start: 0.6656 (tpt) cc_final: 0.6423 (tpt) REVERT: D 342 TYR cc_start: 0.6758 (p90) cc_final: 0.5773 (m-10) REVERT: E 199 ASN cc_start: 0.8279 (t0) cc_final: 0.7934 (t0) REVERT: E 292 CYS cc_start: 0.7067 (t) cc_final: 0.6811 (t) REVERT: F 28 ASN cc_start: 0.7591 (m110) cc_final: 0.7345 (m110) REVERT: F 235 ILE cc_start: 0.8915 (pt) cc_final: 0.8655 (pt) outliers start: 14 outliers final: 8 residues processed: 253 average time/residue: 0.2953 time to fit residues: 110.9393 Evaluate side-chains 234 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 28 ASN B 28 ASN C 28 ASN D 163 ASN E 28 ASN F 4 ASN F 152 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16734 Z= 0.120 Angle : 0.454 6.523 22730 Z= 0.248 Chirality : 0.043 0.138 2622 Planarity : 0.003 0.038 2924 Dihedral : 4.303 49.615 2210 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.65 % Allowed : 11.46 % Favored : 87.89 % 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: 0.10 (0.19), residues: 2076 helix: 0.65 (0.24), residues: 516 sheet: 0.35 (0.30), residues: 360 loop : -0.20 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 PHE 0.018 0.001 PHE F 194 TYR 0.016 0.001 TYR C 342 ARG 0.004 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 5 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 291 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 279 time to evaluate : 2.022 Fit side-chains REVERT: A 79 ILE cc_start: 0.8716 (tt) cc_final: 0.8515 (pt) REVERT: A 301 ASP cc_start: 0.7833 (m-30) cc_final: 0.7594 (m-30) REVERT: B 193 TYR cc_start: 0.7702 (m-80) cc_final: 0.6805 (m-80) REVERT: B 342 TYR cc_start: 0.7004 (p90) cc_final: 0.5924 (m-10) REVERT: C 199 ASN cc_start: 0.7703 (t0) cc_final: 0.7465 (t0) REVERT: C 301 ASP cc_start: 0.7888 (m-30) cc_final: 0.7599 (m-30) REVERT: D 227 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5622 (mp) REVERT: D 330 MET cc_start: 0.6606 (tpt) cc_final: 0.6362 (tpt) REVERT: D 342 TYR cc_start: 0.6855 (p90) cc_final: 0.5746 (m-10) REVERT: E 199 ASN cc_start: 0.8265 (t0) cc_final: 0.7915 (t0) REVERT: E 201 GLN cc_start: 0.8677 (mp10) cc_final: 0.8389 (mp10) REVERT: E 264 GLU cc_start: 0.6471 (pt0) cc_final: 0.6199 (pt0) REVERT: E 266 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 292 CYS cc_start: 0.6898 (t) cc_final: 0.6608 (t) REVERT: F 28 ASN cc_start: 0.7498 (m110) cc_final: 0.7271 (m110) REVERT: F 79 ILE cc_start: 0.8876 (tt) cc_final: 0.8604 (pt) REVERT: F 199 ASN cc_start: 0.7776 (p0) cc_final: 0.7463 (p0) REVERT: F 235 ILE cc_start: 0.8915 (pt) cc_final: 0.8649 (pt) outliers start: 12 outliers final: 8 residues processed: 285 average time/residue: 0.2936 time to fit residues: 124.7110 Evaluate side-chains 250 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 241 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 103 optimal weight: 1.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN D 136 ASN E 28 ASN F 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16734 Z= 0.130 Angle : 0.456 6.664 22730 Z= 0.249 Chirality : 0.043 0.213 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.228 49.980 2210 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.38 % Allowed : 12.71 % Favored : 86.91 % 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: 0.21 (0.19), residues: 2076 helix: 0.71 (0.24), residues: 516 sheet: 0.66 (0.31), residues: 348 loop : -0.21 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 PHE 0.018 0.001 PHE B 194 TYR 0.011 0.001 TYR B 179 ARG 0.005 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 6 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 256 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 249 time to evaluate : 1.958 Fit side-chains REVERT: A 79 ILE cc_start: 0.8720 (tt) cc_final: 0.8510 (pt) REVERT: A 301 ASP cc_start: 0.7841 (m-30) cc_final: 0.7621 (m-30) REVERT: B 193 TYR cc_start: 0.7693 (m-80) cc_final: 0.6712 (m-80) REVERT: B 342 TYR cc_start: 0.6926 (p90) cc_final: 0.5882 (m-10) REVERT: C 199 ASN cc_start: 0.7729 (t0) cc_final: 0.7473 (t0) REVERT: C 301 ASP cc_start: 0.7867 (m-30) cc_final: 0.7590 (m-30) REVERT: D 227 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5623 (mp) REVERT: D 330 MET cc_start: 0.6637 (tpt) cc_final: 0.6406 (tpt) REVERT: D 342 TYR cc_start: 0.6893 (p90) cc_final: 0.5751 (m-10) REVERT: E 138 ARG cc_start: 0.7474 (mmm160) cc_final: 0.7271 (mmm160) REVERT: E 199 ASN cc_start: 0.8252 (t0) cc_final: 0.7883 (t0) REVERT: E 201 GLN cc_start: 0.8674 (mp10) cc_final: 0.8404 (mp10) REVERT: E 264 GLU cc_start: 0.6447 (pt0) cc_final: 0.6156 (pt0) REVERT: E 266 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7551 (mm-30) REVERT: E 292 CYS cc_start: 0.6894 (t) cc_final: 0.6606 (t) REVERT: F 28 ASN cc_start: 0.7520 (m110) cc_final: 0.7295 (m110) REVERT: F 79 ILE cc_start: 0.8861 (tt) cc_final: 0.8594 (pt) REVERT: F 199 ASN cc_start: 0.7911 (p0) cc_final: 0.7589 (p0) REVERT: F 235 ILE cc_start: 0.8920 (pt) cc_final: 0.8656 (pt) REVERT: F 332 TRP cc_start: 0.6382 (m-10) cc_final: 0.6143 (m-10) outliers start: 7 outliers final: 5 residues processed: 254 average time/residue: 0.3062 time to fit residues: 114.8647 Evaluate side-chains 242 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN D 28 ASN E 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16734 Z= 0.137 Angle : 0.451 6.813 22730 Z= 0.247 Chirality : 0.044 0.193 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.165 50.536 2210 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.49 % Allowed : 13.09 % Favored : 86.42 % 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: 0.23 (0.19), residues: 2076 helix: 0.64 (0.24), residues: 522 sheet: 0.54 (0.30), residues: 360 loop : -0.11 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 PHE 0.019 0.001 PHE B 194 TYR 0.011 0.001 TYR F 342 ARG 0.005 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 7 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 260 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 1.880 Fit side-chains REVERT: A 79 ILE cc_start: 0.8714 (tt) cc_final: 0.8495 (pt) REVERT: A 301 ASP cc_start: 0.7818 (m-30) cc_final: 0.7597 (m-30) REVERT: B 79 ILE cc_start: 0.8786 (tt) cc_final: 0.8511 (pt) REVERT: B 193 TYR cc_start: 0.7659 (m-80) cc_final: 0.6609 (m-80) REVERT: B 342 TYR cc_start: 0.6900 (p90) cc_final: 0.5783 (m-10) REVERT: C 199 ASN cc_start: 0.7752 (t0) cc_final: 0.7477 (t0) REVERT: C 301 ASP cc_start: 0.7852 (m-30) cc_final: 0.7576 (m-30) REVERT: D 155 VAL cc_start: 0.8897 (t) cc_final: 0.8658 (p) REVERT: D 227 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5634 (mp) REVERT: D 330 MET cc_start: 0.6618 (tpt) cc_final: 0.6403 (tpt) REVERT: D 342 TYR cc_start: 0.6887 (p90) cc_final: 0.5751 (m-10) REVERT: E 193 TYR cc_start: 0.7614 (m-80) cc_final: 0.6324 (m-80) REVERT: E 199 ASN cc_start: 0.8230 (t0) cc_final: 0.7864 (t0) REVERT: E 201 GLN cc_start: 0.8678 (mp10) cc_final: 0.8426 (mp10) REVERT: E 264 GLU cc_start: 0.6464 (pt0) cc_final: 0.6147 (pt0) REVERT: E 266 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7561 (mm-30) REVERT: E 292 CYS cc_start: 0.6851 (t) cc_final: 0.6556 (t) REVERT: F 28 ASN cc_start: 0.7492 (m110) cc_final: 0.7258 (m110) REVERT: F 79 ILE cc_start: 0.8846 (tt) cc_final: 0.8594 (pt) REVERT: F 235 ILE cc_start: 0.8930 (pt) cc_final: 0.8663 (pt) outliers start: 9 outliers final: 7 residues processed: 257 average time/residue: 0.3023 time to fit residues: 114.7039 Evaluate side-chains 243 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN D 28 ASN E 28 ASN E 136 ASN F 28 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16734 Z= 0.210 Angle : 0.484 6.881 22730 Z= 0.264 Chirality : 0.044 0.189 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.361 50.901 2210 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.71 % Allowed : 13.09 % Favored : 86.20 % 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: 0.20 (0.19), residues: 2076 helix: 0.54 (0.24), residues: 528 sheet: 0.57 (0.30), residues: 360 loop : -0.10 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 PHE 0.029 0.002 PHE B 194 TYR 0.013 0.002 TYR F 193 ARG 0.005 0.001 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 8 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 248 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 2.125 Fit side-chains REVERT: A 172 VAL cc_start: 0.8905 (p) cc_final: 0.8598 (m) REVERT: A 301 ASP cc_start: 0.7855 (m-30) cc_final: 0.7610 (m-30) REVERT: B 193 TYR cc_start: 0.7676 (m-80) cc_final: 0.6563 (m-80) REVERT: B 342 TYR cc_start: 0.6858 (p90) cc_final: 0.5809 (m-10) REVERT: C 172 VAL cc_start: 0.8933 (p) cc_final: 0.8609 (m) REVERT: C 199 ASN cc_start: 0.7756 (t0) cc_final: 0.7467 (t0) REVERT: C 301 ASP cc_start: 0.7901 (m-30) cc_final: 0.7612 (m-30) REVERT: D 21 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: D 227 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5654 (mp) REVERT: D 330 MET cc_start: 0.6657 (tpt) cc_final: 0.6429 (tpt) REVERT: D 342 TYR cc_start: 0.6909 (p90) cc_final: 0.5694 (m-10) REVERT: E 199 ASN cc_start: 0.8248 (t0) cc_final: 0.7861 (t0) REVERT: E 201 GLN cc_start: 0.8681 (mp10) cc_final: 0.8385 (mp10) REVERT: E 266 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7425 (mm-30) REVERT: E 292 CYS cc_start: 0.6909 (t) cc_final: 0.6645 (t) REVERT: F 28 ASN cc_start: 0.7481 (m-40) cc_final: 0.7262 (m110) REVERT: F 79 ILE cc_start: 0.8864 (tt) cc_final: 0.8615 (pt) REVERT: F 235 ILE cc_start: 0.8932 (pt) cc_final: 0.8668 (pt) outliers start: 13 outliers final: 10 residues processed: 246 average time/residue: 0.2957 time to fit residues: 108.3017 Evaluate side-chains 241 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 28 ASN B 28 ASN C 28 ASN E 28 ASN F 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16734 Z= 0.222 Angle : 0.490 6.957 22730 Z= 0.267 Chirality : 0.045 0.183 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.439 50.610 2210 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.71 % Allowed : 13.53 % Favored : 85.76 % 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: 0.18 (0.19), residues: 2076 helix: 0.51 (0.24), residues: 528 sheet: 0.58 (0.31), residues: 360 loop : -0.12 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 PHE 0.031 0.002 PHE B 194 TYR 0.012 0.001 TYR E 179 ARG 0.006 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 9 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 244 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 2.049 Fit side-chains REVERT: A 172 VAL cc_start: 0.8908 (p) cc_final: 0.8610 (m) REVERT: A 301 ASP cc_start: 0.7748 (m-30) cc_final: 0.7503 (m-30) REVERT: B 193 TYR cc_start: 0.7675 (m-80) cc_final: 0.6501 (m-80) REVERT: B 342 TYR cc_start: 0.6894 (p90) cc_final: 0.5817 (m-10) REVERT: C 172 VAL cc_start: 0.8928 (p) cc_final: 0.8613 (m) REVERT: C 199 ASN cc_start: 0.7777 (t0) cc_final: 0.7464 (t0) REVERT: C 301 ASP cc_start: 0.7920 (m-30) cc_final: 0.7623 (m-30) REVERT: D 21 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: D 227 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5626 (mt) REVERT: D 330 MET cc_start: 0.6653 (tpt) cc_final: 0.6426 (tpt) REVERT: D 342 TYR cc_start: 0.6900 (p90) cc_final: 0.5699 (m-10) REVERT: E 193 TYR cc_start: 0.7541 (m-80) cc_final: 0.6281 (m-80) REVERT: E 199 ASN cc_start: 0.8248 (t0) cc_final: 0.7853 (t0) REVERT: E 201 GLN cc_start: 0.8681 (mp10) cc_final: 0.8379 (mp10) REVERT: E 264 GLU cc_start: 0.6694 (pt0) cc_final: 0.6415 (pt0) REVERT: E 266 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7598 (mm-30) REVERT: E 292 CYS cc_start: 0.6940 (t) cc_final: 0.6678 (t) REVERT: F 79 ILE cc_start: 0.8858 (tt) cc_final: 0.8600 (pt) REVERT: F 235 ILE cc_start: 0.8925 (pt) cc_final: 0.8662 (pt) outliers start: 13 outliers final: 10 residues processed: 242 average time/residue: 0.2900 time to fit residues: 105.2986 Evaluate side-chains 238 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 5.9990 chunk 118 optimal weight: 0.0020 chunk 91 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 128 optimal weight: 0.0040 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 4 ASN B 28 ASN C 28 ASN E 28 ASN E 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16734 Z= 0.118 Angle : 0.446 7.128 22730 Z= 0.243 Chirality : 0.043 0.184 2622 Planarity : 0.003 0.028 2924 Dihedral : 4.141 50.773 2210 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.49 % Allowed : 13.86 % Favored : 85.65 % 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: 0.30 (0.19), residues: 2076 helix: 0.71 (0.24), residues: 516 sheet: 1.21 (0.32), residues: 306 loop : -0.24 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 332 HIS 0.005 0.001 HIS D 337 PHE 0.018 0.001 PHE B 194 TYR 0.009 0.001 TYR A 179 ARG 0.004 0.000 ARG B 257 ********************** REFINEMENT MACRO_CYCLE 10 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 262 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 1.992 Fit side-chains REVERT: A 301 ASP cc_start: 0.7699 (m-30) cc_final: 0.7472 (m-30) REVERT: B 79 ILE cc_start: 0.8778 (tt) cc_final: 0.8506 (pt) REVERT: B 193 TYR cc_start: 0.7603 (m-80) cc_final: 0.6342 (m-80) REVERT: B 236 VAL cc_start: 0.8706 (t) cc_final: 0.8490 (t) REVERT: B 342 TYR cc_start: 0.6879 (p90) cc_final: 0.5735 (m-10) REVERT: C 199 ASN cc_start: 0.7755 (t0) cc_final: 0.7449 (t0) REVERT: C 301 ASP cc_start: 0.7863 (m-30) cc_final: 0.7573 (m-30) REVERT: D 21 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: D 227 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5659 (mp) REVERT: D 330 MET cc_start: 0.6618 (tpt) cc_final: 0.6362 (tpt) REVERT: D 342 TYR cc_start: 0.6848 (p90) cc_final: 0.5647 (m-10) REVERT: E 193 TYR cc_start: 0.7421 (m-80) cc_final: 0.6069 (m-80) REVERT: E 199 ASN cc_start: 0.8217 (t0) cc_final: 0.7800 (t0) REVERT: E 201 GLN cc_start: 0.8682 (mp10) cc_final: 0.8425 (mp10) REVERT: E 266 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7441 (mm-30) REVERT: E 292 CYS cc_start: 0.6819 (t) cc_final: 0.6515 (t) REVERT: F 28 ASN cc_start: 0.7632 (m110) cc_final: 0.7347 (m110) REVERT: F 79 ILE cc_start: 0.8836 (tt) cc_final: 0.8592 (pt) REVERT: F 235 ILE cc_start: 0.8912 (pt) cc_final: 0.8645 (pt) outliers start: 9 outliers final: 7 residues processed: 260 average time/residue: 0.3016 time to fit residues: 117.3683 Evaluate side-chains 241 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 232 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 0.0020 chunk 67 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN E 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120533 restraints weight = 40376.499| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.75 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16734 Z= 0.125 Angle : 0.448 7.073 22730 Z= 0.244 Chirality : 0.043 0.174 2622 Planarity : 0.003 0.028 2924 Dihedral : 4.069 51.143 2210 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.65 % Allowed : 13.97 % Favored : 85.38 % 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: 0.35 (0.19), residues: 2076 helix: 0.77 (0.24), residues: 516 sheet: 1.23 (0.32), residues: 306 loop : -0.21 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 332 HIS 0.005 0.001 HIS D 337 PHE 0.019 0.001 PHE F 194 TYR 0.013 0.001 TYR F 278 ARG 0.004 0.000 ARG F 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3382.73 seconds wall clock time: 62 minutes 48.07 seconds (3768.07 seconds total)