Starting phenix.real_space_refine on Fri Mar 22 07:57:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7me0_23786/03_2024/7me0_23786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7me0_23786/03_2024/7me0_23786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7me0_23786/03_2024/7me0_23786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7me0_23786/03_2024/7me0_23786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7me0_23786/03_2024/7me0_23786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7me0_23786/03_2024/7me0_23786.pdb" } resolution = 2.48 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 PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 300": "OD1" <-> "OD2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 124": "OD1" <-> "OD2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 220": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" 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 266": "OE1" <-> "OE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 300": "OD1" <-> "OD2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 128": "OD1" <-> "OD2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 260": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 304": "OE1" <-> "OE2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "F ASP 335": "OD1" <-> "OD2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15.43, per 1000 atoms: 0.94 Number of scatterers: 16386 At special positions: 0 Unit cell: (113.016, 108.861, 123.819, 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: 5.34 Conformation dependent library (CDL) restraints added in 5.7 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 27.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.664A 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 1 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.692A 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 1 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.590A 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 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 137 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 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 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 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.827A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.602A 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: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.951A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 266 removed outlier: 4.792A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 322 removed outlier: 7.163A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 26 removed outlier: 6.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.179A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.179A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.970A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.820A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.212A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.601A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.186A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.186A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AC3, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.936A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.804A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.114A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 24 through 26 removed outlier: 6.591A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.162A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.162A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AD2, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.940A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.791A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 315 through 322 removed outlier: 7.244A pdb=" N SER D 328 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET D 330 " --> pdb=" O PHE D 341 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE D 341 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP D 332 " --> pdb=" O GLU D 339 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 removed outlier: 6.622A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.183A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.183A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE1, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.051A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 266 removed outlier: 3.638A pdb=" N GLU E 264 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.162A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.595A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.181A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.181A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE9, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.933A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.835A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.188A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1668 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: 6.34 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5307 1.34 - 1.46: 3096 1.46 - 1.57: 8229 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 16734 Sorted by residual: bond pdb=" C PHE A 341 " pdb=" N TYR A 342 " ideal model delta sigma weight residual 1.329 1.304 0.025 1.35e-02 5.49e+03 3.39e+00 bond pdb=" C PHE D 341 " pdb=" N TYR D 342 " ideal model delta sigma weight residual 1.329 1.305 0.024 1.35e-02 5.49e+03 3.16e+00 bond pdb=" C PHE C 341 " pdb=" N TYR C 342 " ideal model delta sigma weight residual 1.329 1.314 0.015 1.35e-02 5.49e+03 1.26e+00 bond pdb=" C THR C 120 " pdb=" N VAL C 121 " ideal model delta sigma weight residual 1.330 1.310 0.021 1.97e-02 2.58e+03 1.09e+00 bond pdb=" C THR A 120 " pdb=" N VAL A 121 " ideal model delta sigma weight residual 1.330 1.310 0.020 1.97e-02 2.58e+03 1.07e+00 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.16: 336 106.16 - 113.12: 9292 113.12 - 120.08: 5674 120.08 - 127.05: 7273 127.05 - 134.01: 155 Bond angle restraints: 22730 Sorted by residual: angle pdb=" C VAL A 22 " pdb=" CA VAL A 22 " pdb=" CB VAL A 22 " ideal model delta sigma weight residual 109.33 113.54 -4.21 9.80e-01 1.04e+00 1.84e+01 angle pdb=" CA VAL A 22 " pdb=" C VAL A 22 " pdb=" N PRO A 23 " ideal model delta sigma weight residual 116.57 119.42 -2.85 9.80e-01 1.04e+00 8.44e+00 angle pdb=" N VAL B 314 " pdb=" CA VAL B 314 " pdb=" C VAL B 314 " ideal model delta sigma weight residual 111.45 108.77 2.68 9.30e-01 1.16e+00 8.29e+00 angle pdb=" C ASN F 28 " pdb=" CA ASN F 28 " pdb=" CB ASN F 28 " ideal model delta sigma weight residual 112.11 108.69 3.42 1.46e+00 4.69e-01 5.48e+00 angle pdb=" N VAL A 22 " pdb=" CA VAL A 22 " pdb=" C VAL A 22 " ideal model delta sigma weight residual 109.19 107.36 1.83 8.20e-01 1.49e+00 5.00e+00 ... (remaining 22725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9220 17.90 - 35.79: 535 35.79 - 53.69: 168 53.69 - 71.58: 62 71.58 - 89.48: 15 Dihedral angle restraints: 10000 sinusoidal: 3934 harmonic: 6066 Sorted by residual: dihedral pdb=" CA THR B 192 " pdb=" C THR B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR E 192 " pdb=" C THR E 192 " pdb=" N TYR E 193 " pdb=" CA TYR E 193 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA THR D 192 " pdb=" C THR D 192 " pdb=" N TYR D 193 " pdb=" CA TYR D 193 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1268 0.029 - 0.059: 826 0.059 - 0.088: 311 0.088 - 0.118: 181 0.118 - 0.147: 36 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CB VAL E 22 " pdb=" CA VAL E 22 " pdb=" CG1 VAL E 22 " pdb=" CG2 VAL E 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE D 79 " pdb=" N ILE D 79 " pdb=" C ILE D 79 " pdb=" CB ILE D 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CB VAL A 22 " pdb=" CA VAL A 22 " pdb=" CG1 VAL A 22 " pdb=" CG2 VAL A 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 2619 not shown) Planarity restraints: 2924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 262 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 224 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C ARG A 224 " -0.020 2.00e-02 2.50e+03 pdb=" O ARG A 224 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 225 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 156 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO C 157 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.016 5.00e-02 4.00e+02 ... (remaining 2921 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 341 2.69 - 3.24: 15815 3.24 - 3.79: 27298 3.79 - 4.35: 37097 4.35 - 4.90: 59896 Nonbonded interactions: 140447 Sorted by model distance: nonbonded pdb=" OD2 ASP A 212 " pdb=" OH TYR A 225 " model vdw 2.135 2.440 nonbonded pdb=" OD2 ASP C 212 " pdb=" OH TYR C 225 " model vdw 2.141 2.440 nonbonded pdb=" OD2 ASP D 212 " pdb=" OH TYR D 225 " model vdw 2.159 2.440 nonbonded pdb=" OD2 ASP E 212 " pdb=" OH TYR E 225 " model vdw 2.160 2.440 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.163 2.440 ... (remaining 140442 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 4.450 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 54.870 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 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 : 0.006 0.041 16734 Z= 0.415 Angle : 0.551 4.922 22730 Z= 0.318 Chirality : 0.048 0.147 2622 Planarity : 0.003 0.031 2924 Dihedral : 14.315 89.476 6088 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.96 % Allowed : 6.82 % Favored : 88.22 % 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: -0.22 (0.17), residues: 2076 helix: 0.20 (0.22), residues: 516 sheet: 0.97 (0.30), residues: 312 loop : -0.56 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 58 HIS 0.006 0.002 HIS F 95 PHE 0.013 0.002 PHE D 268 TYR 0.013 0.002 TYR D 225 ARG 0.004 0.001 ARG F 257 *********************** 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 281 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 190 time to evaluate : 1.849 Fit side-chains REVERT: A 199 ASN cc_start: 0.8371 (t0) cc_final: 0.8113 (t0) REVERT: A 332 TRP cc_start: 0.7875 (m100) cc_final: 0.7184 (m-10) REVERT: B 113 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 199 ASN cc_start: 0.8695 (t0) cc_final: 0.8121 (t0) REVERT: B 201 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8160 (mm110) REVERT: C 232 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: C 332 TRP cc_start: 0.8040 (m100) cc_final: 0.7759 (m100) REVERT: D 332 TRP cc_start: 0.8044 (m100) cc_final: 0.7803 (m100) REVERT: E 313 VAL cc_start: 0.8448 (t) cc_final: 0.7856 (m) REVERT: F 199 ASN cc_start: 0.8486 (t0) cc_final: 0.8092 (t0) REVERT: F 201 GLN cc_start: 0.8193 (mp10) cc_final: 0.7753 (mp10) REVERT: F 332 TRP cc_start: 0.8164 (m100) cc_final: 0.7919 (m100) outliers start: 91 outliers final: 58 residues processed: 263 average time/residue: 1.1702 time to fit residues: 344.8243 Evaluate side-chains 226 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 166 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16734 Z= 0.206 Angle : 0.513 10.336 22730 Z= 0.278 Chirality : 0.046 0.137 2622 Planarity : 0.003 0.026 2924 Dihedral : 8.764 81.085 2307 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.98 % Allowed : 9.71 % Favored : 86.31 % 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 (0.17), residues: 2076 helix: 0.31 (0.22), residues: 534 sheet: 1.14 (0.28), residues: 360 loop : -0.41 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 332 HIS 0.005 0.001 HIS C 337 PHE 0.010 0.001 PHE A 221 TYR 0.011 0.001 TYR B 225 ARG 0.006 0.000 ARG A 138 *********************** 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 256 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 183 time to evaluate : 1.839 Fit side-chains REVERT: A 44 GLU cc_start: 0.7978 (tt0) cc_final: 0.7768 (tt0) REVERT: A 199 ASN cc_start: 0.8401 (t0) cc_final: 0.8044 (t0) REVERT: A 332 TRP cc_start: 0.7964 (m100) cc_final: 0.7611 (m-10) REVERT: B 199 ASN cc_start: 0.8596 (t0) cc_final: 0.8185 (t0) REVERT: B 201 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8252 (mp10) REVERT: C 44 GLU cc_start: 0.7973 (tt0) cc_final: 0.7757 (tt0) REVERT: C 202 GLU cc_start: 0.8034 (pm20) cc_final: 0.7820 (pm20) REVERT: C 232 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8873 (m-80) REVERT: C 313 VAL cc_start: 0.8481 (t) cc_final: 0.7968 (m) REVERT: D 332 TRP cc_start: 0.8192 (m100) cc_final: 0.7962 (m100) REVERT: E 313 VAL cc_start: 0.8542 (t) cc_final: 0.7994 (m) REVERT: F 199 ASN cc_start: 0.8450 (t0) cc_final: 0.8034 (t0) REVERT: F 201 GLN cc_start: 0.8220 (mp10) cc_final: 0.7773 (mp10) outliers start: 73 outliers final: 53 residues processed: 238 average time/residue: 1.2089 time to fit residues: 320.9436 Evaluate side-chains 221 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16734 Z= 0.254 Angle : 0.514 9.742 22730 Z= 0.280 Chirality : 0.047 0.146 2622 Planarity : 0.003 0.030 2924 Dihedral : 8.535 80.453 2286 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.93 % Allowed : 11.29 % Favored : 84.78 % 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: 0.10 (0.17), residues: 2076 helix: 0.39 (0.22), residues: 534 sheet: 1.17 (0.28), residues: 360 loop : -0.40 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 332 HIS 0.006 0.001 HIS F 337 PHE 0.010 0.001 PHE F 268 TYR 0.010 0.001 TYR D 225 ARG 0.004 0.000 ARG C 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 245 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 173 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8326 (t0) cc_final: 0.7975 (t0) REVERT: B 199 ASN cc_start: 0.8559 (t0) cc_final: 0.8089 (t0) REVERT: B 201 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8181 (mp10) REVERT: C 199 ASN cc_start: 0.8176 (t0) cc_final: 0.7847 (t0) REVERT: C 232 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: C 313 VAL cc_start: 0.8537 (t) cc_final: 0.8110 (m) REVERT: D 332 TRP cc_start: 0.8166 (m100) cc_final: 0.7919 (m100) REVERT: E 313 VAL cc_start: 0.8578 (t) cc_final: 0.8061 (m) REVERT: F 199 ASN cc_start: 0.8441 (t0) cc_final: 0.8011 (t0) REVERT: F 201 GLN cc_start: 0.8240 (mp10) cc_final: 0.7767 (mp10) outliers start: 72 outliers final: 59 residues processed: 225 average time/residue: 1.2098 time to fit residues: 304.0777 Evaluate side-chains 226 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 166 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 0.0000 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 0.1980 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 GLN E 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16734 Z= 0.134 Angle : 0.468 10.634 22730 Z= 0.252 Chirality : 0.044 0.144 2622 Planarity : 0.003 0.031 2924 Dihedral : 7.993 77.396 2281 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.38 % Allowed : 12.27 % Favored : 84.34 % 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 (0.18), residues: 2076 helix: 0.62 (0.23), residues: 534 sheet: 1.31 (0.28), residues: 360 loop : -0.31 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 332 HIS 0.005 0.001 HIS F 337 PHE 0.009 0.001 PHE A 221 TYR 0.008 0.001 TYR B 225 ARG 0.006 0.000 ARG A 138 *********************** 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 249 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 187 time to evaluate : 1.905 Fit side-chains REVERT: A 199 ASN cc_start: 0.8220 (t0) cc_final: 0.7834 (t0) REVERT: A 332 TRP cc_start: 0.7889 (m100) cc_final: 0.7562 (m-10) REVERT: B 199 ASN cc_start: 0.8471 (t0) cc_final: 0.7908 (t0) REVERT: B 232 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 313 VAL cc_start: 0.8427 (t) cc_final: 0.8008 (m) REVERT: D 44 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: D 332 TRP cc_start: 0.8163 (m100) cc_final: 0.7943 (m-10) REVERT: E 313 VAL cc_start: 0.8568 (t) cc_final: 0.8120 (m) REVERT: F 199 ASN cc_start: 0.8374 (t0) cc_final: 0.7922 (t0) REVERT: F 201 GLN cc_start: 0.8232 (mp10) cc_final: 0.7739 (mp10) outliers start: 62 outliers final: 39 residues processed: 237 average time/residue: 1.2150 time to fit residues: 321.4809 Evaluate side-chains 216 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL 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: 5.9990 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1482 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= 0.149 Angle : 0.472 10.235 22730 Z= 0.253 Chirality : 0.045 0.143 2622 Planarity : 0.003 0.034 2924 Dihedral : 7.659 76.632 2264 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.44 % Allowed : 12.66 % Favored : 83.91 % 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: 0.36 (0.18), residues: 2076 helix: 0.67 (0.23), residues: 534 sheet: 1.35 (0.28), residues: 360 loop : -0.26 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 332 HIS 0.005 0.001 HIS F 337 PHE 0.008 0.001 PHE A 7 TYR 0.008 0.001 TYR E 278 ARG 0.005 0.000 ARG C 138 *********************** 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 241 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 178 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8127 (t0) cc_final: 0.7809 (t0) REVERT: B 199 ASN cc_start: 0.8380 (t0) cc_final: 0.8171 (t0) REVERT: B 232 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8206 (t80) REVERT: C 199 ASN cc_start: 0.8124 (t0) cc_final: 0.7595 (OUTLIER) REVERT: C 313 VAL cc_start: 0.8385 (t) cc_final: 0.7969 (m) REVERT: D 44 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: D 204 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8450 (mptm) REVERT: D 332 TRP cc_start: 0.8170 (m100) cc_final: 0.7932 (m100) REVERT: E 313 VAL cc_start: 0.8575 (t) cc_final: 0.8162 (m) REVERT: F 199 ASN cc_start: 0.8355 (t0) cc_final: 0.7846 (t0) REVERT: F 201 GLN cc_start: 0.8200 (mp10) cc_final: 0.7684 (mp10) outliers start: 63 outliers final: 43 residues processed: 224 average time/residue: 1.2342 time to fit residues: 308.4539 Evaluate side-chains 219 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16734 Z= 0.242 Angle : 0.513 10.498 22730 Z= 0.276 Chirality : 0.046 0.144 2622 Planarity : 0.003 0.040 2924 Dihedral : 7.602 79.797 2256 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 12.98 % Favored : 83.69 % 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: 0.26 (0.17), residues: 2076 helix: 0.56 (0.23), residues: 534 sheet: 1.22 (0.28), residues: 360 loop : -0.30 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 332 HIS 0.005 0.001 HIS F 337 PHE 0.010 0.001 PHE E 268 TYR 0.011 0.001 TYR D 225 ARG 0.005 0.000 ARG C 138 *********************** 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 234 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 173 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8236 (t0) cc_final: 0.7943 (t0) REVERT: B 232 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8157 (t80) REVERT: C 232 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: C 313 VAL cc_start: 0.8399 (t) cc_final: 0.7973 (m) REVERT: D 204 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8449 (mptm) REVERT: D 332 TRP cc_start: 0.8144 (m100) cc_final: 0.7910 (m100) REVERT: E 313 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8173 (m) REVERT: F 199 ASN cc_start: 0.8417 (t0) cc_final: 0.7968 (t0) REVERT: F 201 GLN cc_start: 0.8230 (mp10) cc_final: 0.7731 (mp10) outliers start: 61 outliers final: 46 residues processed: 216 average time/residue: 1.2727 time to fit residues: 305.4031 Evaluate side-chains 220 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1427 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= 0.187 Angle : 0.500 11.745 22730 Z= 0.266 Chirality : 0.045 0.142 2622 Planarity : 0.003 0.042 2924 Dihedral : 7.456 79.124 2256 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.11 % Allowed : 13.64 % Favored : 83.25 % 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 (0.17), residues: 2076 helix: 0.61 (0.23), residues: 534 sheet: 1.24 (0.28), residues: 360 loop : -0.28 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 332 HIS 0.006 0.001 HIS F 337 PHE 0.009 0.001 PHE E 268 TYR 0.010 0.001 TYR D 225 ARG 0.007 0.000 ARG C 138 *********************** 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 228 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 171 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8156 (t0) cc_final: 0.7820 (t0) REVERT: B 232 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8127 (t80) REVERT: C 313 VAL cc_start: 0.8327 (t) cc_final: 0.7930 (m) REVERT: D 204 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8453 (mptm) REVERT: D 332 TRP cc_start: 0.8151 (m100) cc_final: 0.7922 (m100) REVERT: E 313 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8201 (m) REVERT: F 199 ASN cc_start: 0.8395 (t0) cc_final: 0.7919 (t0) REVERT: F 201 GLN cc_start: 0.8242 (mp10) cc_final: 0.7722 (mp10) outliers start: 57 outliers final: 47 residues processed: 211 average time/residue: 1.2887 time to fit residues: 303.2583 Evaluate side-chains 223 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16734 Z= 0.353 Angle : 0.559 10.959 22730 Z= 0.301 Chirality : 0.048 0.174 2622 Planarity : 0.004 0.048 2924 Dihedral : 7.860 82.086 2256 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.38 % Allowed : 13.69 % Favored : 82.92 % 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: 0.08 (0.17), residues: 2076 helix: 0.35 (0.22), residues: 540 sheet: 1.07 (0.28), residues: 360 loop : -0.36 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 332 HIS 0.006 0.001 HIS F 337 PHE 0.012 0.002 PHE D 268 TYR 0.013 0.002 TYR D 225 ARG 0.004 0.001 ARG A 138 *********************** 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 231 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 169 time to evaluate : 1.944 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8236 (t0) cc_final: 0.7942 (t0) REVERT: C 232 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8761 (m-80) REVERT: C 313 VAL cc_start: 0.8383 (t) cc_final: 0.7954 (m) REVERT: D 204 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8412 (mptm) REVERT: D 332 TRP cc_start: 0.8106 (m100) cc_final: 0.7862 (m100) REVERT: E 313 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8172 (m) REVERT: F 199 ASN cc_start: 0.8463 (t0) cc_final: 0.8054 (t0) REVERT: F 201 GLN cc_start: 0.8289 (mp10) cc_final: 0.7798 (mp10) outliers start: 62 outliers final: 48 residues processed: 216 average time/residue: 1.2412 time to fit residues: 298.3922 Evaluate side-chains 218 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0980 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16734 Z= 0.146 Angle : 0.492 10.787 22730 Z= 0.263 Chirality : 0.045 0.141 2622 Planarity : 0.003 0.040 2924 Dihedral : 7.361 79.129 2254 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.45 % Allowed : 14.84 % Favored : 82.71 % 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: 0.27 (0.18), residues: 2076 helix: 0.63 (0.23), residues: 534 sheet: 1.34 (0.27), residues: 342 loop : -0.34 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 332 HIS 0.006 0.001 HIS F 337 PHE 0.009 0.001 PHE A 221 TYR 0.010 0.001 TYR D 225 ARG 0.005 0.000 ARG A 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 216 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8148 (t0) cc_final: 0.7831 (t0) REVERT: B 232 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8165 (t80) REVERT: B 332 TRP cc_start: 0.7887 (m100) cc_final: 0.7664 (m100) REVERT: C 232 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: D 44 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: D 204 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (mptm) REVERT: D 332 TRP cc_start: 0.8157 (m100) cc_final: 0.7932 (m100) REVERT: E 313 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8255 (m) REVERT: E 332 TRP cc_start: 0.7917 (m100) cc_final: 0.7639 (m100) REVERT: F 199 ASN cc_start: 0.8383 (t0) cc_final: 0.7887 (t0) REVERT: F 201 GLN cc_start: 0.8234 (mp10) cc_final: 0.7668 (mp10) outliers start: 45 outliers final: 35 residues processed: 203 average time/residue: 1.2612 time to fit residues: 285.1426 Evaluate side-chains 209 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16734 Z= 0.228 Angle : 0.533 11.577 22730 Z= 0.282 Chirality : 0.046 0.152 2622 Planarity : 0.003 0.045 2924 Dihedral : 7.487 79.937 2252 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.62 % Allowed : 14.78 % Favored : 82.60 % 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: 0.22 (0.17), residues: 2076 helix: 0.58 (0.23), residues: 534 sheet: 1.32 (0.27), residues: 342 loop : -0.37 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP F 332 HIS 0.005 0.001 HIS F 337 PHE 0.010 0.001 PHE E 268 TYR 0.011 0.001 TYR F 237 ARG 0.004 0.000 ARG E 135 ********************** 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 219 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8196 (t0) cc_final: 0.7859 (t0) REVERT: B 232 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8210 (t80) REVERT: C 232 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: D 204 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8444 (mptm) REVERT: D 332 TRP cc_start: 0.8132 (m100) cc_final: 0.7905 (m100) REVERT: E 313 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8240 (m) REVERT: E 332 TRP cc_start: 0.7916 (m100) cc_final: 0.7677 (m100) REVERT: F 199 ASN cc_start: 0.8424 (t0) cc_final: 0.7967 (t0) REVERT: F 201 GLN cc_start: 0.8231 (mp10) cc_final: 0.7713 (mp10) outliers start: 48 outliers final: 40 residues processed: 204 average time/residue: 1.2389 time to fit residues: 281.8117 Evaluate side-chains 213 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.080924 restraints weight = 43064.478| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.31 r_work: 0.2866 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16734 Z= 0.234 Angle : 0.538 12.471 22730 Z= 0.285 Chirality : 0.046 0.151 2622 Planarity : 0.003 0.047 2924 Dihedral : 7.532 80.692 2252 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.67 % Allowed : 14.78 % Favored : 82.54 % 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 (0.17), residues: 2076 helix: 0.55 (0.23), residues: 534 sheet: 1.28 (0.27), residues: 342 loop : -0.37 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 332 HIS 0.006 0.001 HIS F 337 PHE 0.011 0.001 PHE E 268 TYR 0.011 0.001 TYR D 225 ARG 0.004 0.000 ARG B 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5848.14 seconds wall clock time: 104 minutes 14.95 seconds (6254.95 seconds total)