Starting phenix.real_space_refine on Sat Jun 14 14:23:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bb1_15953/06_2025/8bb1_15953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bb1_15953/06_2025/8bb1_15953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bb1_15953/06_2025/8bb1_15953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bb1_15953/06_2025/8bb1_15953.map" model { file = "/net/cci-nas-00/data/ceres_data/8bb1_15953/06_2025/8bb1_15953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bb1_15953/06_2025/8bb1_15953.cif" } resolution = 2.8 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 88 5.16 5 Cl 4 4.86 5 C 10180 2.51 5 N 2784 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16168 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.04, per 1000 atoms: 0.74 Number of scatterers: 16168 At special positions: 0 Unit cell: (123.487, 150.188, 96.7875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 88 16.00 O 3112 8.00 N 2784 7.00 C 10180 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 - 3.00 Amino acid : True - 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: 4.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 38.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 14 through 34 removed outlier: 3.657A pdb=" N ASP A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.560A pdb=" N THR A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.601A pdb=" N ILE A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.590A pdb=" N MET A 236 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 269 through 288 removed outlier: 4.798A pdb=" N ALA A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 3.555A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 removed outlier: 4.089A pdb=" N ILE A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.737A pdb=" N ALA A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 356 " --> pdb=" O GLU A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 356' Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.707A pdb=" N LYS A 369 " --> pdb=" O PRO A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'B' and resid 14 through 34 removed outlier: 3.659A pdb=" N ASP B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 135 through 154 removed outlier: 3.558A pdb=" N THR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.601A pdb=" N ILE B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.576A pdb=" N MET B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 269 through 288 removed outlier: 4.794A pdb=" N ALA B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 removed outlier: 3.556A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 removed outlier: 4.093A pdb=" N ILE B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.740A pdb=" N ALA B 355 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.708A pdb=" N LYS B 369 " --> pdb=" O PRO B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 14 through 34 removed outlier: 3.659A pdb=" N ASP C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 135 through 154 removed outlier: 3.561A pdb=" N THR C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.594A pdb=" N ILE C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.575A pdb=" N MET C 236 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 255' Processing helix chain 'C' and resid 269 through 288 removed outlier: 4.795A pdb=" N ALA C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 3.552A pdb=" N LEU C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 removed outlier: 4.092A pdb=" N ILE C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.733A pdb=" N ALA C 355 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 356' Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.729A pdb=" N LYS C 369 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.658A pdb=" N ASP D 20 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 135 through 154 removed outlier: 3.561A pdb=" N THR D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 206 through 211 removed outlier: 3.601A pdb=" N ILE D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.564A pdb=" N MET D 236 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA D 255 " --> pdb=" O GLY D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 269 through 288 removed outlier: 4.794A pdb=" N ALA D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 removed outlier: 3.557A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 removed outlier: 4.090A pdb=" N ILE D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.733A pdb=" N ALA D 355 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 356 " --> pdb=" O GLU D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 352 through 356' Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.710A pdb=" N LYS D 369 " --> pdb=" O PRO D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'E' and resid 23 through 41 removed outlier: 3.546A pdb=" N ALA E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 77 through 92 Processing helix chain 'F' and resid 23 through 41 removed outlier: 3.546A pdb=" N ALA F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 77 through 92 Processing helix chain 'G' and resid 23 through 41 removed outlier: 3.545A pdb=" N ALA G 41 " --> pdb=" O THR G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 77 through 92 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.545A pdb=" N ALA H 41 " --> pdb=" O THR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 77 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 5.445A pdb=" N ASP A 163 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN A 171 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE A 180 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP A 173 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 178 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N LYS A 221 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 181 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A 223 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 183 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 98 removed outlier: 6.278A pdb=" N VAL A 50 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 94 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 52 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY A 96 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY A 54 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLN A 98 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 56 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 127 removed outlier: 3.639A pdb=" N SER A 309 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 10 removed outlier: 5.441A pdb=" N ASP B 163 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B 171 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE B 180 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP B 173 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 178 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N LYS B 221 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 181 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE B 223 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 183 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 98 removed outlier: 6.275A pdb=" N VAL B 50 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 94 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 52 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY B 96 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY B 54 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLN B 98 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE B 56 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.636A pdb=" N SER B 309 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.439A pdb=" N ASP C 163 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN C 171 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE C 180 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP C 173 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL C 178 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N LYS C 221 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP C 181 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N PHE C 223 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 183 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 98 removed outlier: 6.252A pdb=" N VAL C 50 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ALA C 94 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL C 52 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 96 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY C 54 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLN C 98 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 56 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 127 removed outlier: 3.635A pdb=" N SER C 309 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.437A pdb=" N ASP D 163 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN D 171 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE D 180 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASP D 173 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N LYS D 221 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP D 181 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE D 223 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 183 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 98 removed outlier: 6.265A pdb=" N VAL D 50 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA D 94 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL D 52 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY D 96 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY D 54 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN D 98 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 56 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 127 removed outlier: 3.636A pdb=" N SER D 309 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 47 through 54 removed outlier: 6.702A pdb=" N GLU E 49 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ARG E 74 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR E 51 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG E 72 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 126 through 129 Processing sheet with id=AB6, first strand: chain 'F' and resid 47 through 54 removed outlier: 6.700A pdb=" N GLU F 49 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ARG F 74 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR F 51 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG F 72 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 126 through 129 Processing sheet with id=AB8, first strand: chain 'G' and resid 47 through 54 removed outlier: 6.700A pdb=" N GLU G 49 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG G 74 " --> pdb=" O GLU G 49 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR G 51 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG G 72 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 126 through 129 Processing sheet with id=AC1, first strand: chain 'H' and resid 47 through 54 removed outlier: 6.699A pdb=" N GLU H 49 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG H 74 " --> pdb=" O GLU H 49 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR H 51 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG H 72 " --> pdb=" O THR H 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 126 through 129 732 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5412 1.34 - 1.46: 3440 1.46 - 1.58: 7468 1.58 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 16456 Sorted by residual: bond pdb=" CA GLY B 233 " pdb=" C GLY B 233 " ideal model delta sigma weight residual 1.511 1.498 0.013 1.97e-02 2.58e+03 4.09e-01 bond pdb=" CG1 ILE C 296 " pdb=" CD1 ILE C 296 " ideal model delta sigma weight residual 1.513 1.493 0.020 3.90e-02 6.57e+02 2.66e-01 bond pdb=" CG1 ILE A 296 " pdb=" CD1 ILE A 296 " ideal model delta sigma weight residual 1.513 1.493 0.020 3.90e-02 6.57e+02 2.66e-01 bond pdb=" CG1 ILE B 296 " pdb=" CD1 ILE B 296 " ideal model delta sigma weight residual 1.513 1.493 0.020 3.90e-02 6.57e+02 2.61e-01 bond pdb=" CG1 ILE D 296 " pdb=" CD1 ILE D 296 " ideal model delta sigma weight residual 1.513 1.493 0.020 3.90e-02 6.57e+02 2.55e-01 ... (remaining 16451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 21633 0.97 - 1.93: 516 1.93 - 2.90: 96 2.90 - 3.86: 35 3.86 - 4.83: 12 Bond angle restraints: 22292 Sorted by residual: angle pdb=" CA LEU B 121 " pdb=" CB LEU B 121 " pdb=" CG LEU B 121 " ideal model delta sigma weight residual 116.30 121.13 -4.83 3.50e+00 8.16e-02 1.90e+00 angle pdb=" CA LEU D 121 " pdb=" CB LEU D 121 " pdb=" CG LEU D 121 " ideal model delta sigma weight residual 116.30 121.12 -4.82 3.50e+00 8.16e-02 1.90e+00 angle pdb=" CA LEU A 121 " pdb=" CB LEU A 121 " pdb=" CG LEU A 121 " ideal model delta sigma weight residual 116.30 121.11 -4.81 3.50e+00 8.16e-02 1.89e+00 angle pdb=" CA LEU C 121 " pdb=" CB LEU C 121 " pdb=" CG LEU C 121 " ideal model delta sigma weight residual 116.30 121.08 -4.78 3.50e+00 8.16e-02 1.86e+00 angle pdb=" C ARG B 161 " pdb=" CA ARG B 161 " pdb=" CB ARG B 161 " ideal model delta sigma weight residual 109.32 111.62 -2.30 1.71e+00 3.42e-01 1.82e+00 ... (remaining 22287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 9411 16.74 - 33.47: 389 33.47 - 50.21: 44 50.21 - 66.94: 16 66.94 - 83.68: 12 Dihedral angle restraints: 9872 sinusoidal: 3864 harmonic: 6008 Sorted by residual: dihedral pdb=" CA ARG C 161 " pdb=" C ARG C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta harmonic sigma weight residual 180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA ARG A 161 " pdb=" C ARG A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual -180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.95e+00 dihedral pdb=" CA ARG D 161 " pdb=" C ARG D 161 " pdb=" N PRO D 162 " pdb=" CA PRO D 162 " ideal model delta harmonic sigma weight residual -180.00 -164.26 -15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 9869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1407 0.026 - 0.052: 636 0.052 - 0.077: 245 0.077 - 0.103: 129 0.103 - 0.129: 83 Chirality restraints: 2500 Sorted by residual: chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO B 162 " pdb=" N PRO B 162 " pdb=" C PRO B 162 " pdb=" CB PRO B 162 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO D 162 " pdb=" N PRO D 162 " pdb=" C PRO D 162 " pdb=" CB PRO D 162 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2497 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 72 " -0.122 9.50e-02 1.11e+02 5.50e-02 2.41e+00 pdb=" NE ARG F 72 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG F 72 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG F 72 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 72 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 72 " -0.121 9.50e-02 1.11e+02 5.47e-02 2.38e+00 pdb=" NE ARG H 72 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG H 72 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 72 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 72 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 72 " 0.122 9.50e-02 1.11e+02 5.51e-02 2.37e+00 pdb=" NE ARG G 72 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG G 72 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 72 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 72 " 0.000 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2487 2.76 - 3.30: 14978 3.30 - 3.83: 26705 3.83 - 4.37: 33423 4.37 - 4.90: 57567 Nonbonded interactions: 135160 Sorted by model distance: nonbonded pdb=" OD2 ASP C 266 " pdb=" OG SER C 268 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP A 266 " pdb=" OG SER A 268 " model vdw 2.227 3.040 nonbonded pdb=" OD2 ASP D 266 " pdb=" OG SER D 268 " model vdw 2.227 3.040 nonbonded pdb=" OD2 ASP B 266 " pdb=" OG SER B 268 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR D 130 " pdb=" O MET D 134 " model vdw 2.252 3.040 ... (remaining 135155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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=1.00 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: 6.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 41.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 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 : 0.003 0.024 16456 Z= 0.131 Angle : 0.416 4.829 22292 Z= 0.218 Chirality : 0.041 0.129 2500 Planarity : 0.005 0.055 2904 Dihedral : 10.046 83.678 6016 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.71 % Allowed : 3.41 % Favored : 95.88 % 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: 0.54 (0.18), residues: 2068 helix: 1.25 (0.21), residues: 612 sheet: 0.54 (0.23), residues: 536 loop : -0.29 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 149 HIS 0.003 0.001 HIS D 189 PHE 0.012 0.001 PHE E 127 TYR 0.008 0.001 TYR F 118 ARG 0.013 0.001 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.22401 ( 732) hydrogen bonds : angle 7.59998 ( 2016) covalent geometry : bond 0.00305 (16456) covalent geometry : angle 0.41565 (22292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 256 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9418 (ptm) cc_final: 0.9094 (ptm) REVERT: A 82 MET cc_start: 0.8881 (mtt) cc_final: 0.8627 (mtm) REVERT: A 181 ASP cc_start: 0.8942 (t70) cc_final: 0.8661 (t0) REVERT: A 299 SER cc_start: 0.9476 (m) cc_final: 0.9238 (p) REVERT: A 311 MET cc_start: 0.9297 (ttp) cc_final: 0.9077 (ttt) REVERT: B 49 MET cc_start: 0.9411 (ptm) cc_final: 0.9104 (ptm) REVERT: B 82 MET cc_start: 0.8909 (mtt) cc_final: 0.8660 (mtm) REVERT: B 181 ASP cc_start: 0.8930 (t70) cc_final: 0.8654 (t0) REVERT: B 299 SER cc_start: 0.9474 (m) cc_final: 0.9227 (p) REVERT: B 311 MET cc_start: 0.9307 (ttp) cc_final: 0.9085 (ttt) REVERT: C 49 MET cc_start: 0.9409 (ptm) cc_final: 0.9106 (ptm) REVERT: C 82 MET cc_start: 0.8881 (mtt) cc_final: 0.8627 (mtm) REVERT: C 181 ASP cc_start: 0.8932 (t70) cc_final: 0.8651 (t0) REVERT: C 299 SER cc_start: 0.9478 (m) cc_final: 0.9250 (p) REVERT: C 311 MET cc_start: 0.9300 (ttp) cc_final: 0.9068 (ttt) REVERT: D 49 MET cc_start: 0.9416 (ptm) cc_final: 0.9117 (ptm) REVERT: D 82 MET cc_start: 0.8882 (mtt) cc_final: 0.8626 (mtm) REVERT: D 181 ASP cc_start: 0.8957 (t70) cc_final: 0.8682 (t0) REVERT: D 299 SER cc_start: 0.9478 (m) cc_final: 0.9234 (p) REVERT: D 311 MET cc_start: 0.9311 (ttp) cc_final: 0.9068 (ttt) REVERT: E 1 MET cc_start: 0.9261 (ttm) cc_final: 0.8789 (ttt) REVERT: E 24 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8383 (t0) REVERT: E 29 SER cc_start: 0.9670 (t) cc_final: 0.9344 (p) REVERT: E 49 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8353 (mt-10) REVERT: E 51 THR cc_start: 0.9220 (p) cc_final: 0.8984 (m) REVERT: E 89 CYS cc_start: 0.7965 (m) cc_final: 0.7587 (m) REVERT: E 129 GLU cc_start: 0.8799 (tt0) cc_final: 0.8398 (tt0) REVERT: F 1 MET cc_start: 0.9266 (ttm) cc_final: 0.8796 (ttt) REVERT: F 24 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8382 (t0) REVERT: F 29 SER cc_start: 0.9670 (t) cc_final: 0.9344 (p) REVERT: F 49 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8356 (mt-10) REVERT: F 51 THR cc_start: 0.9224 (p) cc_final: 0.8989 (m) REVERT: F 89 CYS cc_start: 0.7969 (m) cc_final: 0.7593 (m) REVERT: F 129 GLU cc_start: 0.8801 (tt0) cc_final: 0.8399 (tt0) REVERT: G 1 MET cc_start: 0.9251 (ttm) cc_final: 0.8770 (ttt) REVERT: G 24 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8375 (t0) REVERT: G 29 SER cc_start: 0.9669 (t) cc_final: 0.9340 (p) REVERT: G 49 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8354 (mt-10) REVERT: G 51 THR cc_start: 0.9219 (p) cc_final: 0.8984 (m) REVERT: G 89 CYS cc_start: 0.7967 (m) cc_final: 0.7587 (m) REVERT: G 129 GLU cc_start: 0.8785 (tt0) cc_final: 0.8388 (tt0) REVERT: H 1 MET cc_start: 0.9248 (ttm) cc_final: 0.8787 (ttt) REVERT: H 24 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8376 (t0) REVERT: H 29 SER cc_start: 0.9670 (t) cc_final: 0.9344 (p) REVERT: H 49 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8347 (mt-10) REVERT: H 51 THR cc_start: 0.9218 (p) cc_final: 0.8982 (m) REVERT: H 89 CYS cc_start: 0.7956 (m) cc_final: 0.7574 (m) REVERT: H 129 GLU cc_start: 0.8803 (tt0) cc_final: 0.8401 (tt0) outliers start: 12 outliers final: 4 residues processed: 264 average time/residue: 1.4916 time to fit residues: 429.8327 Evaluate side-chains 208 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain H residue 24 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0970 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 21 GLN B 14 HIS B 21 GLN C 14 HIS C 21 GLN D 14 HIS D 21 GLN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.053849 restraints weight = 36786.666| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.18 r_work: 0.2679 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16456 Z= 0.152 Angle : 0.514 6.064 22292 Z= 0.280 Chirality : 0.043 0.137 2500 Planarity : 0.004 0.031 2904 Dihedral : 4.308 28.244 2272 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.35 % Allowed : 8.47 % Favored : 90.18 % 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: 0.88 (0.18), residues: 2068 helix: 1.94 (0.21), residues: 604 sheet: 0.69 (0.23), residues: 520 loop : -0.34 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 149 HIS 0.003 0.001 HIS A 189 PHE 0.012 0.001 PHE E 127 TYR 0.013 0.001 TYR C 280 ARG 0.008 0.001 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 732) hydrogen bonds : angle 5.50089 ( 2016) covalent geometry : bond 0.00338 (16456) covalent geometry : angle 0.51423 (22292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9370 (ptm) cc_final: 0.9080 (ptm) REVERT: A 181 ASP cc_start: 0.9020 (t70) cc_final: 0.8746 (t0) REVERT: A 299 SER cc_start: 0.9472 (m) cc_final: 0.9181 (p) REVERT: B 49 MET cc_start: 0.9365 (ptm) cc_final: 0.9080 (ptm) REVERT: B 181 ASP cc_start: 0.9016 (t70) cc_final: 0.8740 (t0) REVERT: B 299 SER cc_start: 0.9471 (m) cc_final: 0.9189 (p) REVERT: C 49 MET cc_start: 0.9371 (ptm) cc_final: 0.9082 (ptm) REVERT: C 181 ASP cc_start: 0.9006 (t70) cc_final: 0.8730 (t0) REVERT: C 299 SER cc_start: 0.9488 (m) cc_final: 0.9189 (p) REVERT: D 49 MET cc_start: 0.9377 (ptm) cc_final: 0.9091 (ptm) REVERT: D 181 ASP cc_start: 0.9028 (t70) cc_final: 0.8760 (t0) REVERT: D 299 SER cc_start: 0.9471 (m) cc_final: 0.9190 (p) REVERT: E 1 MET cc_start: 0.9224 (ttm) cc_final: 0.8722 (ttt) REVERT: E 28 MET cc_start: 0.9206 (tpp) cc_final: 0.8623 (tpp) REVERT: E 29 SER cc_start: 0.9679 (t) cc_final: 0.9331 (p) REVERT: E 49 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8386 (mt-10) REVERT: E 51 THR cc_start: 0.9288 (p) cc_final: 0.8900 (t) REVERT: E 68 GLU cc_start: 0.8090 (pm20) cc_final: 0.7882 (pm20) REVERT: E 69 LYS cc_start: 0.8756 (mtpm) cc_final: 0.8417 (mtpm) REVERT: E 76 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8629 (tmmt) REVERT: E 77 ASP cc_start: 0.8240 (t70) cc_final: 0.7599 (p0) REVERT: E 89 CYS cc_start: 0.7810 (m) cc_final: 0.7574 (m) REVERT: E 129 GLU cc_start: 0.8921 (tt0) cc_final: 0.8690 (tt0) REVERT: F 1 MET cc_start: 0.9229 (ttm) cc_final: 0.8726 (ttt) REVERT: F 28 MET cc_start: 0.9209 (tpp) cc_final: 0.8626 (tpp) REVERT: F 29 SER cc_start: 0.9679 (t) cc_final: 0.9331 (p) REVERT: F 49 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8391 (mt-10) REVERT: F 51 THR cc_start: 0.9288 (p) cc_final: 0.8898 (t) REVERT: F 68 GLU cc_start: 0.8087 (pm20) cc_final: 0.7865 (pm20) REVERT: F 69 LYS cc_start: 0.8757 (mtpm) cc_final: 0.8419 (mtpm) REVERT: F 76 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8622 (tmmt) REVERT: F 77 ASP cc_start: 0.8236 (t70) cc_final: 0.7606 (p0) REVERT: F 89 CYS cc_start: 0.7805 (m) cc_final: 0.7574 (m) REVERT: F 129 GLU cc_start: 0.8898 (tt0) cc_final: 0.8664 (tt0) REVERT: G 1 MET cc_start: 0.9220 (ttm) cc_final: 0.8724 (ttt) REVERT: G 28 MET cc_start: 0.9210 (tpp) cc_final: 0.8628 (tpp) REVERT: G 29 SER cc_start: 0.9678 (t) cc_final: 0.9328 (p) REVERT: G 49 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8417 (mt-10) REVERT: G 51 THR cc_start: 0.9290 (p) cc_final: 0.8902 (t) REVERT: G 68 GLU cc_start: 0.8089 (pm20) cc_final: 0.7865 (pm20) REVERT: G 69 LYS cc_start: 0.8751 (mtpm) cc_final: 0.8413 (mtpm) REVERT: G 76 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8621 (tmmt) REVERT: G 77 ASP cc_start: 0.8241 (t70) cc_final: 0.7614 (p0) REVERT: G 89 CYS cc_start: 0.7794 (m) cc_final: 0.7562 (m) REVERT: G 129 GLU cc_start: 0.8894 (tt0) cc_final: 0.8660 (tt0) REVERT: H 1 MET cc_start: 0.9216 (ttm) cc_final: 0.8707 (ttt) REVERT: H 28 MET cc_start: 0.9209 (tpp) cc_final: 0.8625 (tpp) REVERT: H 29 SER cc_start: 0.9680 (t) cc_final: 0.9330 (p) REVERT: H 49 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8376 (mt-10) REVERT: H 51 THR cc_start: 0.9289 (p) cc_final: 0.8904 (t) REVERT: H 68 GLU cc_start: 0.8108 (pm20) cc_final: 0.7896 (pm20) REVERT: H 69 LYS cc_start: 0.8752 (mtpm) cc_final: 0.8412 (mtpm) REVERT: H 76 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8628 (tmmt) REVERT: H 77 ASP cc_start: 0.8240 (t70) cc_final: 0.7599 (p0) REVERT: H 89 CYS cc_start: 0.7789 (m) cc_final: 0.7557 (m) REVERT: H 129 GLU cc_start: 0.8898 (tt0) cc_final: 0.8663 (tt0) outliers start: 23 outliers final: 8 residues processed: 224 average time/residue: 1.7051 time to fit residues: 412.6884 Evaluate side-chains 206 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053601 restraints weight = 36775.806| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.10 r_work: 0.2681 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16456 Z= 0.163 Angle : 0.516 6.222 22292 Z= 0.275 Chirality : 0.043 0.136 2500 Planarity : 0.004 0.035 2904 Dihedral : 4.245 28.364 2264 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 10.24 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2068 helix: 2.02 (0.22), residues: 604 sheet: 0.52 (0.22), residues: 520 loop : -0.29 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 149 HIS 0.006 0.001 HIS A 189 PHE 0.010 0.001 PHE E 127 TYR 0.014 0.002 TYR H 45 ARG 0.007 0.001 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 732) hydrogen bonds : angle 5.16995 ( 2016) covalent geometry : bond 0.00369 (16456) covalent geometry : angle 0.51553 (22292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9373 (ptm) cc_final: 0.8976 (ptm) REVERT: A 181 ASP cc_start: 0.9046 (t70) cc_final: 0.8758 (t0) REVERT: A 203 MET cc_start: 0.9203 (tpp) cc_final: 0.8971 (tpt) REVERT: A 299 SER cc_start: 0.9462 (m) cc_final: 0.9171 (p) REVERT: B 49 MET cc_start: 0.9373 (ptm) cc_final: 0.8987 (ptm) REVERT: B 181 ASP cc_start: 0.9040 (t70) cc_final: 0.8753 (t0) REVERT: B 299 SER cc_start: 0.9461 (m) cc_final: 0.9174 (p) REVERT: C 49 MET cc_start: 0.9376 (ptm) cc_final: 0.8989 (ptm) REVERT: C 181 ASP cc_start: 0.9038 (t70) cc_final: 0.8752 (t0) REVERT: C 299 SER cc_start: 0.9479 (m) cc_final: 0.9191 (p) REVERT: D 49 MET cc_start: 0.9380 (ptm) cc_final: 0.8995 (ptm) REVERT: D 181 ASP cc_start: 0.9045 (t70) cc_final: 0.8520 (t0) REVERT: D 203 MET cc_start: 0.9208 (tpp) cc_final: 0.8952 (tpt) REVERT: D 299 SER cc_start: 0.9471 (m) cc_final: 0.9189 (p) REVERT: E 1 MET cc_start: 0.9182 (ttm) cc_final: 0.8744 (ttt) REVERT: E 19 ARG cc_start: 0.9022 (mtp85) cc_final: 0.8770 (mtt-85) REVERT: E 28 MET cc_start: 0.9227 (tpp) cc_final: 0.8746 (tmm) REVERT: E 29 SER cc_start: 0.9695 (t) cc_final: 0.9303 (p) REVERT: E 49 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8509 (mt-10) REVERT: E 51 THR cc_start: 0.9150 (p) cc_final: 0.8836 (t) REVERT: E 68 GLU cc_start: 0.8109 (pm20) cc_final: 0.7857 (pm20) REVERT: E 69 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: E 76 LYS cc_start: 0.9059 (tmmt) cc_final: 0.8676 (tmmt) REVERT: E 77 ASP cc_start: 0.8176 (t70) cc_final: 0.7422 (p0) REVERT: E 89 CYS cc_start: 0.7790 (m) cc_final: 0.7534 (m) REVERT: E 94 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7851 (mm110) REVERT: E 95 ASP cc_start: 0.8237 (p0) cc_final: 0.7986 (p0) REVERT: E 129 GLU cc_start: 0.8891 (tt0) cc_final: 0.8582 (tt0) REVERT: F 1 MET cc_start: 0.9199 (ttm) cc_final: 0.8761 (ttt) REVERT: F 19 ARG cc_start: 0.9028 (mtp85) cc_final: 0.8775 (mtt-85) REVERT: F 28 MET cc_start: 0.9229 (tpp) cc_final: 0.8747 (tmm) REVERT: F 29 SER cc_start: 0.9695 (t) cc_final: 0.9306 (p) REVERT: F 49 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8542 (mt-10) REVERT: F 51 THR cc_start: 0.9159 (p) cc_final: 0.8842 (t) REVERT: F 68 GLU cc_start: 0.8036 (pm20) cc_final: 0.7803 (pm20) REVERT: F 69 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8277 (mtpp) REVERT: F 76 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8677 (tmmt) REVERT: F 77 ASP cc_start: 0.8175 (t70) cc_final: 0.7419 (p0) REVERT: F 89 CYS cc_start: 0.7782 (m) cc_final: 0.7542 (m) REVERT: F 94 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7853 (mm110) REVERT: F 95 ASP cc_start: 0.8248 (p0) cc_final: 0.8002 (p0) REVERT: F 129 GLU cc_start: 0.8786 (tt0) cc_final: 0.8455 (tt0) REVERT: G 1 MET cc_start: 0.9194 (ttm) cc_final: 0.8763 (ttt) REVERT: G 19 ARG cc_start: 0.9021 (mtp85) cc_final: 0.8764 (mtt-85) REVERT: G 28 MET cc_start: 0.9225 (tpp) cc_final: 0.8744 (tmm) REVERT: G 29 SER cc_start: 0.9693 (t) cc_final: 0.9301 (p) REVERT: G 49 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8541 (mt-10) REVERT: G 51 THR cc_start: 0.9158 (p) cc_final: 0.8841 (t) REVERT: G 68 GLU cc_start: 0.8049 (pm20) cc_final: 0.7811 (pm20) REVERT: G 69 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8277 (mtpp) REVERT: G 76 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8687 (tmmt) REVERT: G 77 ASP cc_start: 0.8188 (t70) cc_final: 0.7435 (p0) REVERT: G 89 CYS cc_start: 0.7772 (m) cc_final: 0.7528 (m) REVERT: G 94 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7848 (mm110) REVERT: G 95 ASP cc_start: 0.8284 (p0) cc_final: 0.8014 (p0) REVERT: G 129 GLU cc_start: 0.8782 (tt0) cc_final: 0.8447 (tt0) REVERT: H 1 MET cc_start: 0.9194 (ttm) cc_final: 0.8773 (ttt) REVERT: H 19 ARG cc_start: 0.9030 (mtp85) cc_final: 0.8775 (mtt-85) REVERT: H 28 MET cc_start: 0.9233 (tpp) cc_final: 0.8749 (tmm) REVERT: H 29 SER cc_start: 0.9696 (t) cc_final: 0.9302 (p) REVERT: H 49 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8536 (mt-10) REVERT: H 51 THR cc_start: 0.9156 (p) cc_final: 0.8840 (t) REVERT: H 68 GLU cc_start: 0.8034 (pm20) cc_final: 0.7794 (pm20) REVERT: H 69 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8270 (mtpp) REVERT: H 76 LYS cc_start: 0.9058 (tmmt) cc_final: 0.8677 (tmmt) REVERT: H 77 ASP cc_start: 0.8180 (t70) cc_final: 0.7428 (p0) REVERT: H 89 CYS cc_start: 0.7769 (m) cc_final: 0.7510 (m) REVERT: H 94 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7840 (mm110) REVERT: H 95 ASP cc_start: 0.8289 (p0) cc_final: 0.8017 (p0) REVERT: H 129 GLU cc_start: 0.8785 (tt0) cc_final: 0.8451 (tt0) outliers start: 19 outliers final: 12 residues processed: 227 average time/residue: 1.7381 time to fit residues: 427.3934 Evaluate side-chains 216 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.054747 restraints weight = 37591.103| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.19 r_work: 0.2696 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16456 Z= 0.175 Angle : 0.515 6.165 22292 Z= 0.274 Chirality : 0.043 0.135 2500 Planarity : 0.004 0.037 2904 Dihedral : 4.266 29.613 2264 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.65 % Allowed : 10.29 % Favored : 88.06 % 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: 0.88 (0.18), residues: 2068 helix: 2.14 (0.22), residues: 600 sheet: 0.49 (0.22), residues: 520 loop : -0.34 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 92 HIS 0.004 0.001 HIS D 189 PHE 0.010 0.001 PHE E 127 TYR 0.024 0.002 TYR H 118 ARG 0.008 0.001 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 732) hydrogen bonds : angle 4.96807 ( 2016) covalent geometry : bond 0.00399 (16456) covalent geometry : angle 0.51500 (22292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9372 (ptm) cc_final: 0.8943 (ptm) REVERT: A 181 ASP cc_start: 0.9088 (t70) cc_final: 0.8792 (t0) REVERT: A 203 MET cc_start: 0.9166 (tpp) cc_final: 0.8881 (tpt) REVERT: A 299 SER cc_start: 0.9461 (m) cc_final: 0.9142 (p) REVERT: B 49 MET cc_start: 0.9372 (ptm) cc_final: 0.8949 (ptm) REVERT: B 181 ASP cc_start: 0.9079 (t70) cc_final: 0.8782 (t0) REVERT: B 299 SER cc_start: 0.9467 (m) cc_final: 0.9148 (p) REVERT: C 49 MET cc_start: 0.9381 (ptm) cc_final: 0.8958 (ptm) REVERT: C 181 ASP cc_start: 0.9090 (t70) cc_final: 0.8792 (t0) REVERT: C 299 SER cc_start: 0.9473 (m) cc_final: 0.9152 (p) REVERT: D 49 MET cc_start: 0.9383 (ptm) cc_final: 0.8960 (ptm) REVERT: D 181 ASP cc_start: 0.9087 (t70) cc_final: 0.8599 (t0) REVERT: D 203 MET cc_start: 0.9167 (tpp) cc_final: 0.8877 (tpt) REVERT: D 299 SER cc_start: 0.9470 (m) cc_final: 0.9155 (p) REVERT: E 1 MET cc_start: 0.9196 (ttm) cc_final: 0.8755 (ttt) REVERT: E 19 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8707 (mtt-85) REVERT: E 28 MET cc_start: 0.9170 (tpp) cc_final: 0.8571 (tpp) REVERT: E 29 SER cc_start: 0.9680 (t) cc_final: 0.9329 (p) REVERT: E 49 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8560 (mt-10) REVERT: E 51 THR cc_start: 0.9131 (p) cc_final: 0.8731 (t) REVERT: E 68 GLU cc_start: 0.7964 (pm20) cc_final: 0.7701 (pm20) REVERT: E 69 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8238 (mtpp) REVERT: E 76 LYS cc_start: 0.9033 (tmmt) cc_final: 0.8605 (tmmt) REVERT: E 77 ASP cc_start: 0.8083 (t70) cc_final: 0.7307 (p0) REVERT: E 89 CYS cc_start: 0.7650 (m) cc_final: 0.7450 (m) REVERT: E 94 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7804 (mm110) REVERT: E 95 ASP cc_start: 0.8429 (p0) cc_final: 0.8129 (p0) REVERT: E 122 ARG cc_start: 0.8197 (tmm160) cc_final: 0.7777 (tmm160) REVERT: E 129 GLU cc_start: 0.8792 (tt0) cc_final: 0.8514 (tt0) REVERT: F 1 MET cc_start: 0.9201 (ttm) cc_final: 0.8758 (ttt) REVERT: F 19 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8706 (mtt-85) REVERT: F 28 MET cc_start: 0.9168 (tpp) cc_final: 0.8568 (tpp) REVERT: F 29 SER cc_start: 0.9689 (t) cc_final: 0.9350 (p) REVERT: F 49 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8528 (mt-10) REVERT: F 51 THR cc_start: 0.9137 (p) cc_final: 0.8735 (t) REVERT: F 68 GLU cc_start: 0.7948 (pm20) cc_final: 0.7684 (pm20) REVERT: F 69 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8234 (mtpp) REVERT: F 76 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8618 (tmmt) REVERT: F 77 ASP cc_start: 0.8100 (t70) cc_final: 0.7325 (p0) REVERT: F 94 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7807 (mm110) REVERT: F 95 ASP cc_start: 0.8422 (p0) cc_final: 0.8120 (p0) REVERT: F 122 ARG cc_start: 0.8198 (tmm160) cc_final: 0.7782 (tmm160) REVERT: F 129 GLU cc_start: 0.8800 (tt0) cc_final: 0.8517 (tt0) REVERT: G 1 MET cc_start: 0.9174 (ttm) cc_final: 0.8737 (ttt) REVERT: G 19 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8707 (mtt-85) REVERT: G 28 MET cc_start: 0.9164 (tpp) cc_final: 0.8564 (tpp) REVERT: G 29 SER cc_start: 0.9679 (t) cc_final: 0.9328 (p) REVERT: G 49 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8529 (mt-10) REVERT: G 51 THR cc_start: 0.9139 (p) cc_final: 0.8741 (t) REVERT: G 68 GLU cc_start: 0.7969 (pm20) cc_final: 0.7706 (pm20) REVERT: G 69 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: G 76 LYS cc_start: 0.9033 (tmmt) cc_final: 0.8617 (tmmt) REVERT: G 77 ASP cc_start: 0.8092 (t70) cc_final: 0.7312 (p0) REVERT: G 89 CYS cc_start: 0.7634 (m) cc_final: 0.7431 (m) REVERT: G 94 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7867 (mm110) REVERT: G 95 ASP cc_start: 0.8421 (p0) cc_final: 0.8115 (p0) REVERT: G 122 ARG cc_start: 0.8192 (tmm160) cc_final: 0.7793 (tmm160) REVERT: G 129 GLU cc_start: 0.8798 (tt0) cc_final: 0.8513 (tt0) REVERT: H 1 MET cc_start: 0.9197 (ttm) cc_final: 0.8740 (ttt) REVERT: H 19 ARG cc_start: 0.8956 (mtp85) cc_final: 0.8709 (mtt-85) REVERT: H 28 MET cc_start: 0.9175 (tpp) cc_final: 0.8575 (tpp) REVERT: H 29 SER cc_start: 0.9691 (t) cc_final: 0.9350 (p) REVERT: H 49 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8571 (mt-10) REVERT: H 51 THR cc_start: 0.9131 (p) cc_final: 0.8736 (t) REVERT: H 68 GLU cc_start: 0.7946 (pm20) cc_final: 0.7684 (pm20) REVERT: H 69 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8239 (mtpp) REVERT: H 76 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8610 (tmmt) REVERT: H 77 ASP cc_start: 0.8089 (t70) cc_final: 0.7319 (p0) REVERT: H 89 CYS cc_start: 0.7622 (m) cc_final: 0.7419 (m) REVERT: H 94 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7858 (mm110) REVERT: H 95 ASP cc_start: 0.8414 (p0) cc_final: 0.8087 (p0) REVERT: H 122 ARG cc_start: 0.8195 (tmm160) cc_final: 0.7779 (tmm160) REVERT: H 129 GLU cc_start: 0.8801 (tt0) cc_final: 0.8515 (tt0) outliers start: 28 outliers final: 16 residues processed: 224 average time/residue: 1.6370 time to fit residues: 397.6299 Evaluate side-chains 224 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 101 optimal weight: 0.8980 chunk 120 optimal weight: 0.0370 chunk 153 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 GLN D 297 GLN E 152 GLN F 90 ASN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.075773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054603 restraints weight = 37385.622| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.13 r_work: 0.2708 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16456 Z= 0.160 Angle : 0.507 6.606 22292 Z= 0.270 Chirality : 0.043 0.135 2500 Planarity : 0.004 0.038 2904 Dihedral : 4.220 29.873 2264 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.47 % Allowed : 10.76 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2068 helix: 2.16 (0.22), residues: 600 sheet: 0.46 (0.22), residues: 520 loop : -0.33 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 149 HIS 0.003 0.001 HIS D 189 PHE 0.009 0.001 PHE G 127 TYR 0.014 0.002 TYR H 45 ARG 0.009 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 732) hydrogen bonds : angle 4.82097 ( 2016) covalent geometry : bond 0.00364 (16456) covalent geometry : angle 0.50712 (22292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9353 (ptm) cc_final: 0.8911 (ptm) REVERT: A 181 ASP cc_start: 0.9077 (t70) cc_final: 0.8582 (t0) REVERT: A 299 SER cc_start: 0.9454 (m) cc_final: 0.9146 (p) REVERT: B 49 MET cc_start: 0.9368 (ptm) cc_final: 0.8934 (ptm) REVERT: B 181 ASP cc_start: 0.9073 (t70) cc_final: 0.8554 (t0) REVERT: B 299 SER cc_start: 0.9459 (m) cc_final: 0.9155 (p) REVERT: C 49 MET cc_start: 0.9365 (ptm) cc_final: 0.8924 (ptm) REVERT: C 181 ASP cc_start: 0.9085 (t70) cc_final: 0.8588 (t0) REVERT: C 299 SER cc_start: 0.9456 (m) cc_final: 0.9159 (p) REVERT: D 49 MET cc_start: 0.9363 (ptm) cc_final: 0.8925 (ptm) REVERT: D 181 ASP cc_start: 0.9093 (t70) cc_final: 0.8570 (t0) REVERT: D 299 SER cc_start: 0.9455 (m) cc_final: 0.9163 (p) REVERT: E 1 MET cc_start: 0.9190 (ttm) cc_final: 0.8751 (ttt) REVERT: E 29 SER cc_start: 0.9682 (t) cc_final: 0.9325 (p) REVERT: E 49 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8540 (mt-10) REVERT: E 68 GLU cc_start: 0.8023 (pm20) cc_final: 0.7760 (pm20) REVERT: E 69 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8384 (mmmm) REVERT: E 76 LYS cc_start: 0.9057 (tmmt) cc_final: 0.8640 (tmmt) REVERT: E 77 ASP cc_start: 0.8085 (t70) cc_final: 0.7292 (p0) REVERT: E 89 CYS cc_start: 0.7695 (m) cc_final: 0.7491 (m) REVERT: E 94 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7820 (mm110) REVERT: E 95 ASP cc_start: 0.8479 (p0) cc_final: 0.8149 (p0) REVERT: E 122 ARG cc_start: 0.8199 (tmm160) cc_final: 0.7765 (tmm160) REVERT: E 129 GLU cc_start: 0.8794 (tt0) cc_final: 0.8495 (tt0) REVERT: F 1 MET cc_start: 0.9196 (ttm) cc_final: 0.8757 (ttt) REVERT: F 28 MET cc_start: 0.9193 (tpp) cc_final: 0.8590 (tpp) REVERT: F 29 SER cc_start: 0.9678 (t) cc_final: 0.9331 (p) REVERT: F 49 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8502 (mt-10) REVERT: F 51 THR cc_start: 0.9092 (p) cc_final: 0.8675 (t) REVERT: F 68 GLU cc_start: 0.8013 (pm20) cc_final: 0.7733 (pm20) REVERT: F 69 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8292 (mmmm) REVERT: F 76 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8633 (tmmt) REVERT: F 77 ASP cc_start: 0.8095 (t70) cc_final: 0.7311 (p0) REVERT: F 94 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7816 (mm110) REVERT: F 95 ASP cc_start: 0.8494 (p0) cc_final: 0.8129 (p0) REVERT: F 122 ARG cc_start: 0.8205 (tmm160) cc_final: 0.7765 (tmm160) REVERT: F 129 GLU cc_start: 0.8797 (tt0) cc_final: 0.8486 (tt0) REVERT: G 1 MET cc_start: 0.9189 (ttm) cc_final: 0.8747 (ttt) REVERT: G 28 MET cc_start: 0.9187 (tpp) cc_final: 0.8573 (tpp) REVERT: G 29 SER cc_start: 0.9679 (t) cc_final: 0.9329 (p) REVERT: G 49 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8498 (mt-10) REVERT: G 51 THR cc_start: 0.9109 (p) cc_final: 0.8699 (t) REVERT: G 68 GLU cc_start: 0.8020 (pm20) cc_final: 0.7746 (pm20) REVERT: G 69 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8299 (mmmm) REVERT: G 76 LYS cc_start: 0.9057 (tmmt) cc_final: 0.8635 (tmmt) REVERT: G 77 ASP cc_start: 0.8079 (t70) cc_final: 0.7282 (p0) REVERT: G 89 CYS cc_start: 0.7723 (m) cc_final: 0.7508 (m) REVERT: G 94 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7879 (mm110) REVERT: G 95 ASP cc_start: 0.8432 (p0) cc_final: 0.8079 (p0) REVERT: G 122 ARG cc_start: 0.8203 (tmm160) cc_final: 0.7764 (tmm160) REVERT: G 129 GLU cc_start: 0.8794 (tt0) cc_final: 0.8482 (tt0) REVERT: H 1 MET cc_start: 0.9196 (ttm) cc_final: 0.8764 (ttt) REVERT: H 28 MET cc_start: 0.9192 (tpp) cc_final: 0.8579 (tpp) REVERT: H 29 SER cc_start: 0.9680 (t) cc_final: 0.9330 (p) REVERT: H 49 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8542 (mt-10) REVERT: H 68 GLU cc_start: 0.8017 (pm20) cc_final: 0.7737 (pm20) REVERT: H 69 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8313 (mmmm) REVERT: H 76 LYS cc_start: 0.9057 (tmmt) cc_final: 0.8640 (tmmt) REVERT: H 77 ASP cc_start: 0.8082 (t70) cc_final: 0.7294 (p0) REVERT: H 89 CYS cc_start: 0.7694 (m) cc_final: 0.7484 (m) REVERT: H 94 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7869 (mm110) REVERT: H 95 ASP cc_start: 0.8430 (p0) cc_final: 0.8083 (p0) REVERT: H 122 ARG cc_start: 0.8203 (tmm160) cc_final: 0.7762 (tmm160) REVERT: H 129 GLU cc_start: 0.8797 (tt0) cc_final: 0.8485 (tt0) outliers start: 25 outliers final: 18 residues processed: 225 average time/residue: 1.6017 time to fit residues: 391.9696 Evaluate side-chains 218 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 132 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 chunk 194 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 188 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 168 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.076377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055326 restraints weight = 37098.124| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.09 r_work: 0.2731 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16456 Z= 0.131 Angle : 0.513 6.691 22292 Z= 0.271 Chirality : 0.043 0.138 2500 Planarity : 0.004 0.038 2904 Dihedral : 4.128 28.420 2264 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.12 % Allowed : 11.76 % Favored : 87.12 % 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: 0.88 (0.19), residues: 2068 helix: 2.22 (0.22), residues: 600 sheet: 0.20 (0.22), residues: 544 loop : -0.21 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 92 HIS 0.002 0.001 HIS D 189 PHE 0.008 0.001 PHE H 127 TYR 0.026 0.002 TYR H 118 ARG 0.009 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 732) hydrogen bonds : angle 4.74101 ( 2016) covalent geometry : bond 0.00296 (16456) covalent geometry : angle 0.51324 (22292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9338 (ptm) cc_final: 0.8909 (ptm) REVERT: A 181 ASP cc_start: 0.9066 (t70) cc_final: 0.8578 (t0) REVERT: A 299 SER cc_start: 0.9451 (m) cc_final: 0.9149 (p) REVERT: B 49 MET cc_start: 0.9369 (ptm) cc_final: 0.8977 (ptm) REVERT: B 181 ASP cc_start: 0.9072 (t70) cc_final: 0.8584 (t0) REVERT: B 299 SER cc_start: 0.9453 (m) cc_final: 0.9150 (p) REVERT: C 49 MET cc_start: 0.9350 (ptm) cc_final: 0.8927 (ptm) REVERT: C 181 ASP cc_start: 0.9083 (t70) cc_final: 0.8593 (t0) REVERT: C 299 SER cc_start: 0.9435 (m) cc_final: 0.9144 (p) REVERT: D 49 MET cc_start: 0.9368 (ptm) cc_final: 0.8970 (ptm) REVERT: D 181 ASP cc_start: 0.9065 (t70) cc_final: 0.8789 (t0) REVERT: D 299 SER cc_start: 0.9447 (m) cc_final: 0.9166 (p) REVERT: E 1 MET cc_start: 0.9187 (ttm) cc_final: 0.8753 (ttt) REVERT: E 28 MET cc_start: 0.9237 (tpp) cc_final: 0.8647 (tpt) REVERT: E 29 SER cc_start: 0.9685 (t) cc_final: 0.9347 (p) REVERT: E 49 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 68 GLU cc_start: 0.7982 (pm20) cc_final: 0.7691 (pm20) REVERT: E 69 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8290 (mmmm) REVERT: E 76 LYS cc_start: 0.9059 (tmmt) cc_final: 0.8636 (tmmt) REVERT: E 77 ASP cc_start: 0.8066 (t70) cc_final: 0.7267 (p0) REVERT: E 89 CYS cc_start: 0.7671 (m) cc_final: 0.7466 (m) REVERT: E 122 ARG cc_start: 0.8188 (tmm160) cc_final: 0.7730 (tmm160) REVERT: E 129 GLU cc_start: 0.8892 (tt0) cc_final: 0.8579 (tt0) REVERT: F 1 MET cc_start: 0.9188 (ttm) cc_final: 0.8751 (ttt) REVERT: F 29 SER cc_start: 0.9682 (t) cc_final: 0.9312 (p) REVERT: F 49 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8574 (mt-10) REVERT: F 68 GLU cc_start: 0.7973 (pm20) cc_final: 0.7702 (pm20) REVERT: F 75 CYS cc_start: 0.8969 (m) cc_final: 0.8474 (p) REVERT: F 76 LYS cc_start: 0.9053 (tmmt) cc_final: 0.8638 (tmmt) REVERT: F 77 ASP cc_start: 0.8087 (t70) cc_final: 0.7253 (p0) REVERT: F 94 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7665 (mm110) REVERT: F 95 ASP cc_start: 0.8565 (p0) cc_final: 0.8196 (p0) REVERT: F 122 ARG cc_start: 0.8191 (tmm160) cc_final: 0.7723 (tmm160) REVERT: F 129 GLU cc_start: 0.8808 (tt0) cc_final: 0.8495 (tt0) REVERT: G 1 MET cc_start: 0.9190 (ttm) cc_final: 0.8763 (ttt) REVERT: G 29 SER cc_start: 0.9683 (t) cc_final: 0.9307 (p) REVERT: G 49 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8536 (mt-10) REVERT: G 68 GLU cc_start: 0.7976 (pm20) cc_final: 0.7703 (pm20) REVERT: G 75 CYS cc_start: 0.8960 (m) cc_final: 0.8465 (p) REVERT: G 76 LYS cc_start: 0.9055 (tmmt) cc_final: 0.8629 (tmmt) REVERT: G 77 ASP cc_start: 0.8084 (t70) cc_final: 0.7253 (p0) REVERT: G 89 CYS cc_start: 0.7657 (m) cc_final: 0.7445 (m) REVERT: G 122 ARG cc_start: 0.8189 (tmm160) cc_final: 0.7724 (tmm160) REVERT: G 129 GLU cc_start: 0.8802 (tt0) cc_final: 0.8489 (tt0) REVERT: H 1 MET cc_start: 0.9184 (ttm) cc_final: 0.8759 (ttt) REVERT: H 29 SER cc_start: 0.9683 (t) cc_final: 0.9308 (p) REVERT: H 49 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8584 (mt-10) REVERT: H 68 GLU cc_start: 0.7963 (pm20) cc_final: 0.7691 (pm20) REVERT: H 76 LYS cc_start: 0.9055 (tmmt) cc_final: 0.8631 (tmmt) REVERT: H 77 ASP cc_start: 0.8061 (t70) cc_final: 0.7265 (p0) REVERT: H 89 CYS cc_start: 0.7635 (m) cc_final: 0.7428 (m) REVERT: H 122 ARG cc_start: 0.8187 (tmm160) cc_final: 0.7721 (tmm160) REVERT: H 129 GLU cc_start: 0.8804 (tt0) cc_final: 0.8490 (tt0) outliers start: 19 outliers final: 14 residues processed: 216 average time/residue: 1.5798 time to fit residues: 371.8247 Evaluate side-chains 215 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 94 optimal weight: 0.0050 chunk 182 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 200 optimal weight: 0.0070 chunk 81 optimal weight: 0.5980 chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 0.0000 chunk 138 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.1416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 297 GLN B 297 GLN D 154 ASN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058454 restraints weight = 37257.581| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.05 r_work: 0.2791 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16456 Z= 0.095 Angle : 0.507 7.824 22292 Z= 0.265 Chirality : 0.042 0.145 2500 Planarity : 0.004 0.037 2904 Dihedral : 3.831 22.865 2264 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.88 % Allowed : 12.76 % Favored : 86.35 % 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: 0.96 (0.19), residues: 2068 helix: 2.38 (0.22), residues: 600 sheet: 0.20 (0.22), residues: 544 loop : -0.20 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 159 HIS 0.002 0.000 HIS B 79 PHE 0.009 0.001 PHE B 5 TYR 0.026 0.002 TYR F 118 ARG 0.009 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 732) hydrogen bonds : angle 4.59465 ( 2016) covalent geometry : bond 0.00207 (16456) covalent geometry : angle 0.50740 (22292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9243 (ptm) cc_final: 0.8904 (ptm) REVERT: A 181 ASP cc_start: 0.8994 (t70) cc_final: 0.8546 (t0) REVERT: A 203 MET cc_start: 0.9252 (tpp) cc_final: 0.9029 (tpt) REVERT: B 49 MET cc_start: 0.9265 (ptm) cc_final: 0.8988 (ptm) REVERT: B 181 ASP cc_start: 0.8992 (t70) cc_final: 0.8551 (t0) REVERT: C 49 MET cc_start: 0.9273 (ptm) cc_final: 0.8945 (ptm) REVERT: C 181 ASP cc_start: 0.8970 (t70) cc_final: 0.8545 (t0) REVERT: D 49 MET cc_start: 0.9275 (ptm) cc_final: 0.8949 (ptm) REVERT: D 181 ASP cc_start: 0.8973 (t70) cc_final: 0.8529 (t0) REVERT: D 203 MET cc_start: 0.9249 (tpp) cc_final: 0.9022 (tpt) REVERT: E 1 MET cc_start: 0.9180 (ttm) cc_final: 0.8797 (ttt) REVERT: E 29 SER cc_start: 0.9688 (t) cc_final: 0.9310 (p) REVERT: E 47 SER cc_start: 0.8494 (m) cc_final: 0.8036 (p) REVERT: E 49 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8506 (mt-10) REVERT: E 68 GLU cc_start: 0.7979 (pm20) cc_final: 0.7276 (pm20) REVERT: E 75 CYS cc_start: 0.9019 (m) cc_final: 0.8766 (p) REVERT: E 76 LYS cc_start: 0.9099 (tmmt) cc_final: 0.8687 (tmmt) REVERT: E 77 ASP cc_start: 0.8059 (t70) cc_final: 0.7303 (p0) REVERT: E 89 CYS cc_start: 0.7527 (m) cc_final: 0.7319 (m) REVERT: E 94 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7837 (mm110) REVERT: E 95 ASP cc_start: 0.8735 (p0) cc_final: 0.8296 (p0) REVERT: E 122 ARG cc_start: 0.8224 (tmm160) cc_final: 0.7829 (tmm160) REVERT: E 129 GLU cc_start: 0.8904 (tt0) cc_final: 0.8670 (tt0) REVERT: F 1 MET cc_start: 0.9173 (ttm) cc_final: 0.8789 (ttt) REVERT: F 28 MET cc_start: 0.9124 (tpp) cc_final: 0.8596 (tpt) REVERT: F 29 SER cc_start: 0.9675 (t) cc_final: 0.9293 (p) REVERT: F 47 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8107 (p) REVERT: F 49 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8413 (mt-10) REVERT: F 68 GLU cc_start: 0.7883 (pm20) cc_final: 0.7214 (pm20) REVERT: F 69 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8220 (mmmm) REVERT: F 74 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8391 (tmm-80) REVERT: F 75 CYS cc_start: 0.8986 (m) cc_final: 0.8648 (p) REVERT: F 76 LYS cc_start: 0.9083 (tmmt) cc_final: 0.8662 (tmmt) REVERT: F 77 ASP cc_start: 0.8057 (t70) cc_final: 0.7301 (p0) REVERT: F 122 ARG cc_start: 0.8224 (tmm160) cc_final: 0.7819 (tmm160) REVERT: F 129 GLU cc_start: 0.8908 (tt0) cc_final: 0.8637 (tt0) REVERT: G 1 MET cc_start: 0.9169 (ttm) cc_final: 0.8788 (ttt) REVERT: G 28 MET cc_start: 0.9130 (tpp) cc_final: 0.8600 (tpt) REVERT: G 29 SER cc_start: 0.9673 (t) cc_final: 0.9289 (p) REVERT: G 47 SER cc_start: 0.8476 (m) cc_final: 0.7997 (p) REVERT: G 49 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8426 (mt-10) REVERT: G 68 GLU cc_start: 0.7892 (pm20) cc_final: 0.7240 (pm20) REVERT: G 69 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8207 (mmmm) REVERT: G 74 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8399 (tmm-80) REVERT: G 75 CYS cc_start: 0.8979 (m) cc_final: 0.8636 (p) REVERT: G 76 LYS cc_start: 0.9087 (tmmt) cc_final: 0.8658 (tmmt) REVERT: G 77 ASP cc_start: 0.8068 (t70) cc_final: 0.7338 (p0) REVERT: G 89 CYS cc_start: 0.7569 (m) cc_final: 0.7359 (m) REVERT: G 122 ARG cc_start: 0.8220 (tmm160) cc_final: 0.7820 (tmm160) REVERT: G 129 GLU cc_start: 0.8908 (tt0) cc_final: 0.8644 (tt0) REVERT: H 1 MET cc_start: 0.9172 (ttm) cc_final: 0.8802 (ttt) REVERT: H 28 MET cc_start: 0.9136 (tpp) cc_final: 0.8605 (tpt) REVERT: H 29 SER cc_start: 0.9675 (t) cc_final: 0.9292 (p) REVERT: H 45 TYR cc_start: 0.8930 (m-80) cc_final: 0.8729 (m-10) REVERT: H 47 SER cc_start: 0.8573 (m) cc_final: 0.8143 (p) REVERT: H 49 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8537 (mt-10) REVERT: H 68 GLU cc_start: 0.7887 (pm20) cc_final: 0.7240 (pm20) REVERT: H 69 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8198 (mmmm) REVERT: H 75 CYS cc_start: 0.8948 (m) cc_final: 0.8549 (p) REVERT: H 76 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8678 (tmmt) REVERT: H 77 ASP cc_start: 0.8037 (t70) cc_final: 0.7287 (p0) REVERT: H 89 CYS cc_start: 0.7580 (m) cc_final: 0.7358 (m) REVERT: H 122 ARG cc_start: 0.8221 (tmm160) cc_final: 0.7819 (tmm160) REVERT: H 129 GLU cc_start: 0.8914 (tt0) cc_final: 0.8650 (tt0) outliers start: 15 outliers final: 11 residues processed: 225 average time/residue: 1.6785 time to fit residues: 412.3396 Evaluate side-chains 211 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 178 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 120 optimal weight: 0.0870 chunk 124 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN E 152 GLN F 152 GLN G 94 GLN G 152 GLN H 94 GLN H 152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055710 restraints weight = 36805.435| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.08 r_work: 0.2726 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16456 Z= 0.155 Angle : 0.544 8.133 22292 Z= 0.284 Chirality : 0.043 0.152 2500 Planarity : 0.004 0.041 2904 Dihedral : 3.978 24.767 2264 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.88 % Allowed : 13.00 % Favored : 86.12 % 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: 0.91 (0.19), residues: 2068 helix: 2.35 (0.22), residues: 600 sheet: 0.20 (0.22), residues: 544 loop : -0.25 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 92 HIS 0.003 0.001 HIS C 79 PHE 0.008 0.001 PHE A 123 TYR 0.027 0.002 TYR E 118 ARG 0.009 0.001 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 732) hydrogen bonds : angle 4.59094 ( 2016) covalent geometry : bond 0.00358 (16456) covalent geometry : angle 0.54418 (22292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9366 (ptm) cc_final: 0.8989 (ptm) REVERT: A 181 ASP cc_start: 0.9056 (t70) cc_final: 0.8575 (t0) REVERT: B 49 MET cc_start: 0.9375 (ptm) cc_final: 0.9004 (ptm) REVERT: B 181 ASP cc_start: 0.9060 (t70) cc_final: 0.8587 (t0) REVERT: C 49 MET cc_start: 0.9375 (ptm) cc_final: 0.9005 (ptm) REVERT: C 181 ASP cc_start: 0.9057 (t70) cc_final: 0.8576 (t0) REVERT: D 49 MET cc_start: 0.9380 (ptm) cc_final: 0.9004 (ptm) REVERT: D 181 ASP cc_start: 0.9057 (t70) cc_final: 0.8599 (t0) REVERT: E 1 MET cc_start: 0.9127 (ttm) cc_final: 0.8705 (ttt) REVERT: E 19 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8410 (mtt-85) REVERT: E 28 MET cc_start: 0.9125 (tpp) cc_final: 0.8538 (tpt) REVERT: E 29 SER cc_start: 0.9675 (t) cc_final: 0.9315 (p) REVERT: E 49 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8579 (mt-10) REVERT: E 68 GLU cc_start: 0.7804 (pm20) cc_final: 0.7154 (pm20) REVERT: E 75 CYS cc_start: 0.8961 (m) cc_final: 0.8418 (p) REVERT: E 76 LYS cc_start: 0.9045 (tmmt) cc_final: 0.8614 (tmmt) REVERT: E 77 ASP cc_start: 0.8026 (t70) cc_final: 0.7223 (p0) REVERT: E 122 ARG cc_start: 0.8157 (tmm160) cc_final: 0.7761 (tmm160) REVERT: E 129 GLU cc_start: 0.8877 (tt0) cc_final: 0.8562 (tt0) REVERT: F 1 MET cc_start: 0.9139 (ttm) cc_final: 0.8714 (ttt) REVERT: F 28 MET cc_start: 0.9127 (tpp) cc_final: 0.8602 (tpt) REVERT: F 29 SER cc_start: 0.9670 (t) cc_final: 0.9302 (p) REVERT: F 47 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7709 (p) REVERT: F 49 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8566 (mt-10) REVERT: F 68 GLU cc_start: 0.7783 (pm20) cc_final: 0.7149 (pm20) REVERT: F 74 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8360 (tmm-80) REVERT: F 75 CYS cc_start: 0.8999 (m) cc_final: 0.8527 (p) REVERT: F 76 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8586 (tmmt) REVERT: F 77 ASP cc_start: 0.8031 (t70) cc_final: 0.7223 (p0) REVERT: F 94 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7873 (mm110) REVERT: F 122 ARG cc_start: 0.8167 (tmm160) cc_final: 0.7766 (tmm160) REVERT: F 129 GLU cc_start: 0.8786 (tt0) cc_final: 0.8489 (tt0) REVERT: G 1 MET cc_start: 0.9138 (ttm) cc_final: 0.8716 (ttt) REVERT: G 19 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8412 (mtt-85) REVERT: G 28 MET cc_start: 0.9134 (tpp) cc_final: 0.8608 (tpt) REVERT: G 29 SER cc_start: 0.9671 (t) cc_final: 0.9298 (p) REVERT: G 47 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7758 (p) REVERT: G 49 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8561 (mt-10) REVERT: G 68 GLU cc_start: 0.7692 (pm20) cc_final: 0.7119 (pm20) REVERT: G 74 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8367 (tmm-80) REVERT: G 75 CYS cc_start: 0.8989 (m) cc_final: 0.8518 (p) REVERT: G 76 LYS cc_start: 0.9042 (tmmt) cc_final: 0.8606 (tmmt) REVERT: G 77 ASP cc_start: 0.8022 (t70) cc_final: 0.7208 (p0) REVERT: G 89 CYS cc_start: 0.7574 (m) cc_final: 0.7368 (m) REVERT: G 122 ARG cc_start: 0.8179 (tmm160) cc_final: 0.7766 (tmm160) REVERT: G 129 GLU cc_start: 0.8787 (tt0) cc_final: 0.8467 (tt0) REVERT: H 1 MET cc_start: 0.9128 (ttm) cc_final: 0.8717 (ttt) REVERT: H 19 ARG cc_start: 0.8973 (mtp85) cc_final: 0.8419 (mtt-85) REVERT: H 28 MET cc_start: 0.9131 (tpp) cc_final: 0.8603 (tpt) REVERT: H 29 SER cc_start: 0.9672 (t) cc_final: 0.9300 (p) REVERT: H 49 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8619 (mt-10) REVERT: H 68 GLU cc_start: 0.7681 (pm20) cc_final: 0.7109 (pm20) REVERT: H 75 CYS cc_start: 0.8964 (m) cc_final: 0.8410 (p) REVERT: H 76 LYS cc_start: 0.9040 (tmmt) cc_final: 0.8606 (tmmt) REVERT: H 77 ASP cc_start: 0.8026 (t70) cc_final: 0.7222 (p0) REVERT: H 122 ARG cc_start: 0.8154 (tmm160) cc_final: 0.7759 (tmm160) REVERT: H 129 GLU cc_start: 0.8785 (tt0) cc_final: 0.8465 (tt0) outliers start: 15 outliers final: 12 residues processed: 214 average time/residue: 1.6022 time to fit residues: 372.8133 Evaluate side-chains 214 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 172 optimal weight: 0.0980 chunk 115 optimal weight: 0.0370 chunk 164 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN C 154 ASN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.078699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058270 restraints weight = 37334.649| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.03 r_work: 0.2774 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16456 Z= 0.102 Angle : 0.534 9.221 22292 Z= 0.277 Chirality : 0.042 0.157 2500 Planarity : 0.004 0.039 2904 Dihedral : 3.818 21.612 2264 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.00 % Allowed : 13.12 % Favored : 85.88 % 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: 0.98 (0.19), residues: 2068 helix: 2.44 (0.22), residues: 600 sheet: 0.20 (0.22), residues: 544 loop : -0.22 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 149 HIS 0.002 0.000 HIS C 79 PHE 0.008 0.001 PHE A 123 TYR 0.028 0.001 TYR G 118 ARG 0.009 0.001 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 732) hydrogen bonds : angle 4.51997 ( 2016) covalent geometry : bond 0.00232 (16456) covalent geometry : angle 0.53443 (22292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9265 (ptm) cc_final: 0.8961 (ptm) REVERT: A 181 ASP cc_start: 0.8961 (t70) cc_final: 0.8530 (t0) REVERT: B 49 MET cc_start: 0.9284 (ptm) cc_final: 0.8975 (ptm) REVERT: B 181 ASP cc_start: 0.8965 (t70) cc_final: 0.8513 (t0) REVERT: C 49 MET cc_start: 0.9289 (ptm) cc_final: 0.9001 (ptm) REVERT: C 181 ASP cc_start: 0.8988 (t70) cc_final: 0.8553 (t0) REVERT: D 49 MET cc_start: 0.9286 (ptm) cc_final: 0.8976 (ptm) REVERT: D 181 ASP cc_start: 0.8984 (t70) cc_final: 0.8547 (t0) REVERT: E 1 MET cc_start: 0.9168 (ttm) cc_final: 0.8770 (ttt) REVERT: E 19 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8486 (mtt-85) REVERT: E 28 MET cc_start: 0.9112 (tpp) cc_final: 0.8566 (tpt) REVERT: E 29 SER cc_start: 0.9675 (t) cc_final: 0.9310 (p) REVERT: E 47 SER cc_start: 0.8379 (m) cc_final: 0.7974 (p) REVERT: E 49 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8595 (mt-10) REVERT: E 68 GLU cc_start: 0.7512 (pm20) cc_final: 0.7056 (pm20) REVERT: E 69 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8091 (mmmm) REVERT: E 75 CYS cc_start: 0.8980 (m) cc_final: 0.8578 (p) REVERT: E 76 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8628 (tmmt) REVERT: E 77 ASP cc_start: 0.8059 (t70) cc_final: 0.7283 (p0) REVERT: E 95 ASP cc_start: 0.8781 (p0) cc_final: 0.8357 (p0) REVERT: E 122 ARG cc_start: 0.8234 (tmm160) cc_final: 0.7840 (tmm160) REVERT: E 129 GLU cc_start: 0.8852 (tt0) cc_final: 0.8584 (tt0) REVERT: F 1 MET cc_start: 0.9172 (ttm) cc_final: 0.8767 (ttt) REVERT: F 19 ARG cc_start: 0.8972 (mtp85) cc_final: 0.8527 (mtt-85) REVERT: F 28 MET cc_start: 0.9123 (tpp) cc_final: 0.8589 (tpt) REVERT: F 29 SER cc_start: 0.9674 (t) cc_final: 0.9319 (p) REVERT: F 47 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8004 (p) REVERT: F 49 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8537 (mt-10) REVERT: F 68 GLU cc_start: 0.7644 (pm20) cc_final: 0.7426 (pp20) REVERT: F 69 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7647 (mmmm) REVERT: F 74 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8421 (tmm-80) REVERT: F 75 CYS cc_start: 0.8986 (m) cc_final: 0.8628 (p) REVERT: F 76 LYS cc_start: 0.9057 (tmmt) cc_final: 0.8617 (tmmt) REVERT: F 77 ASP cc_start: 0.8078 (t70) cc_final: 0.7307 (p0) REVERT: F 94 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7754 (mm110) REVERT: F 95 ASP cc_start: 0.8570 (p0) cc_final: 0.8226 (p0) REVERT: F 122 ARG cc_start: 0.8238 (tmm160) cc_final: 0.7842 (tmm160) REVERT: F 129 GLU cc_start: 0.8791 (tt0) cc_final: 0.8527 (tt0) REVERT: G 1 MET cc_start: 0.9173 (ttm) cc_final: 0.8774 (ttt) REVERT: G 19 ARG cc_start: 0.8947 (mtp85) cc_final: 0.8503 (mtt-85) REVERT: G 28 MET cc_start: 0.9137 (tpp) cc_final: 0.8590 (tpt) REVERT: G 29 SER cc_start: 0.9673 (t) cc_final: 0.9293 (p) REVERT: G 47 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8010 (p) REVERT: G 49 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8497 (mt-10) REVERT: G 68 GLU cc_start: 0.7641 (pm20) cc_final: 0.7194 (pm20) REVERT: G 69 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8089 (mmmm) REVERT: G 74 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8423 (tmm-80) REVERT: G 75 CYS cc_start: 0.8978 (m) cc_final: 0.8617 (p) REVERT: G 76 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8625 (tmmt) REVERT: G 77 ASP cc_start: 0.8036 (t70) cc_final: 0.7251 (p0) REVERT: G 89 CYS cc_start: 0.7533 (m) cc_final: 0.7320 (m) REVERT: G 122 ARG cc_start: 0.8234 (tmm160) cc_final: 0.7842 (tmm160) REVERT: G 129 GLU cc_start: 0.8766 (tt0) cc_final: 0.8494 (tt0) REVERT: H 1 MET cc_start: 0.9170 (ttm) cc_final: 0.8782 (ttt) REVERT: H 19 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8496 (mtt-85) REVERT: H 28 MET cc_start: 0.9132 (tpp) cc_final: 0.8592 (tpt) REVERT: H 29 SER cc_start: 0.9673 (t) cc_final: 0.9295 (p) REVERT: H 47 SER cc_start: 0.8502 (m) cc_final: 0.8067 (p) REVERT: H 49 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8553 (mt-10) REVERT: H 68 GLU cc_start: 0.7625 (pm20) cc_final: 0.7176 (pm20) REVERT: H 69 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8062 (mmmm) REVERT: H 75 CYS cc_start: 0.8981 (m) cc_final: 0.8565 (p) REVERT: H 76 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8618 (tmmt) REVERT: H 77 ASP cc_start: 0.8044 (t70) cc_final: 0.7267 (p0) REVERT: H 95 ASP cc_start: 0.8796 (p0) cc_final: 0.8366 (p0) REVERT: H 122 ARG cc_start: 0.8228 (tmm160) cc_final: 0.7836 (tmm160) REVERT: H 129 GLU cc_start: 0.8794 (tt0) cc_final: 0.8531 (tt0) outliers start: 17 outliers final: 13 residues processed: 224 average time/residue: 1.5538 time to fit residues: 379.5169 Evaluate side-chains 225 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 107 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 0.0060 chunk 128 optimal weight: 2.9990 chunk 152 optimal weight: 0.0980 chunk 102 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 47 optimal weight: 0.0370 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 GLN D 297 GLN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.078788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058211 restraints weight = 37485.930| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.03 r_work: 0.2767 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16456 Z= 0.106 Angle : 0.541 9.234 22292 Z= 0.280 Chirality : 0.042 0.156 2500 Planarity : 0.004 0.040 2904 Dihedral : 3.759 19.898 2264 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2068 helix: 2.49 (0.22), residues: 600 sheet: 0.20 (0.22), residues: 556 loop : -0.12 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 92 HIS 0.002 0.000 HIS C 79 PHE 0.007 0.001 PHE B 123 TYR 0.027 0.001 TYR H 118 ARG 0.009 0.001 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 732) hydrogen bonds : angle 4.47971 ( 2016) covalent geometry : bond 0.00242 (16456) covalent geometry : angle 0.54123 (22292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9267 (ptm) cc_final: 0.8962 (ptm) REVERT: A 181 ASP cc_start: 0.8948 (t70) cc_final: 0.8514 (t0) REVERT: B 49 MET cc_start: 0.9283 (ptm) cc_final: 0.8974 (ptm) REVERT: B 181 ASP cc_start: 0.8962 (t70) cc_final: 0.8538 (t0) REVERT: C 49 MET cc_start: 0.9299 (ptm) cc_final: 0.9003 (ptm) REVERT: C 181 ASP cc_start: 0.8939 (t70) cc_final: 0.8505 (t0) REVERT: D 49 MET cc_start: 0.9289 (ptm) cc_final: 0.8987 (ptm) REVERT: D 181 ASP cc_start: 0.8936 (t70) cc_final: 0.8510 (t0) REVERT: E 1 MET cc_start: 0.9161 (ttm) cc_final: 0.8765 (ttt) REVERT: E 19 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8585 (mtt-85) REVERT: E 28 MET cc_start: 0.9107 (tpp) cc_final: 0.8637 (tpt) REVERT: E 29 SER cc_start: 0.9678 (t) cc_final: 0.9307 (p) REVERT: E 47 SER cc_start: 0.8313 (m) cc_final: 0.7906 (p) REVERT: E 49 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8600 (mt-10) REVERT: E 69 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8081 (tppp) REVERT: E 75 CYS cc_start: 0.8983 (m) cc_final: 0.8596 (p) REVERT: E 76 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8659 (tmmt) REVERT: E 77 ASP cc_start: 0.8090 (t70) cc_final: 0.7330 (p0) REVERT: E 95 ASP cc_start: 0.8707 (p0) cc_final: 0.8336 (p0) REVERT: E 122 ARG cc_start: 0.8229 (tmm160) cc_final: 0.7839 (tmm160) REVERT: E 129 GLU cc_start: 0.8855 (tt0) cc_final: 0.8586 (tt0) REVERT: F 1 MET cc_start: 0.9172 (ttm) cc_final: 0.8775 (ttt) REVERT: F 28 MET cc_start: 0.9087 (tpp) cc_final: 0.8598 (tpt) REVERT: F 29 SER cc_start: 0.9676 (t) cc_final: 0.9310 (p) REVERT: F 47 SER cc_start: 0.8402 (m) cc_final: 0.7970 (p) REVERT: F 69 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8049 (tppp) REVERT: F 74 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8410 (tmm-80) REVERT: F 75 CYS cc_start: 0.8989 (m) cc_final: 0.8654 (p) REVERT: F 76 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8637 (tmmt) REVERT: F 77 ASP cc_start: 0.8086 (t70) cc_final: 0.7316 (p0) REVERT: F 94 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7774 (mm110) REVERT: F 95 ASP cc_start: 0.8557 (p0) cc_final: 0.8175 (p0) REVERT: F 122 ARG cc_start: 0.8234 (tmm160) cc_final: 0.7844 (tmm160) REVERT: F 129 GLU cc_start: 0.8882 (tt0) cc_final: 0.8627 (tt0) REVERT: G 1 MET cc_start: 0.9163 (ttm) cc_final: 0.8768 (ttt) REVERT: G 19 ARG cc_start: 0.8963 (mtp85) cc_final: 0.8569 (mtt-85) REVERT: G 28 MET cc_start: 0.9095 (tpp) cc_final: 0.8518 (tpt) REVERT: G 29 SER cc_start: 0.9674 (t) cc_final: 0.9297 (p) REVERT: G 47 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.7971 (p) REVERT: G 69 LYS cc_start: 0.8560 (mmmm) cc_final: 0.7746 (mmmm) REVERT: G 74 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8407 (tmm-80) REVERT: G 75 CYS cc_start: 0.8977 (m) cc_final: 0.8640 (p) REVERT: G 76 LYS cc_start: 0.9037 (tmmt) cc_final: 0.8643 (tmmt) REVERT: G 77 ASP cc_start: 0.8069 (t70) cc_final: 0.7293 (p0) REVERT: G 89 CYS cc_start: 0.7438 (m) cc_final: 0.7229 (m) REVERT: G 122 ARG cc_start: 0.8228 (tmm160) cc_final: 0.7841 (tmm160) REVERT: G 129 GLU cc_start: 0.8773 (tt0) cc_final: 0.8506 (tt0) REVERT: H 1 MET cc_start: 0.9153 (ttm) cc_final: 0.8770 (ttt) REVERT: H 28 MET cc_start: 0.9096 (tpp) cc_final: 0.8603 (tpt) REVERT: H 29 SER cc_start: 0.9674 (t) cc_final: 0.9296 (p) REVERT: H 47 SER cc_start: 0.8424 (m) cc_final: 0.8036 (p) REVERT: H 49 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8595 (mt-10) REVERT: H 69 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8195 (tppp) REVERT: H 75 CYS cc_start: 0.8983 (m) cc_final: 0.8592 (p) REVERT: H 76 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8656 (tmmt) REVERT: H 77 ASP cc_start: 0.8076 (t70) cc_final: 0.7311 (p0) REVERT: H 122 ARG cc_start: 0.8221 (tmm160) cc_final: 0.7833 (tmm160) REVERT: H 129 GLU cc_start: 0.8863 (tt0) cc_final: 0.8596 (tt0) outliers start: 17 outliers final: 14 residues processed: 222 average time/residue: 1.5299 time to fit residues: 369.7146 Evaluate side-chains 225 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055838 restraints weight = 36796.936| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.05 r_work: 0.2731 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16456 Z= 0.155 Angle : 0.572 9.161 22292 Z= 0.298 Chirality : 0.043 0.148 2500 Planarity : 0.005 0.043 2904 Dihedral : 3.971 23.213 2264 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.00 % Allowed : 13.29 % Favored : 85.71 % 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: 0.97 (0.19), residues: 2068 helix: 2.40 (0.22), residues: 600 sheet: 0.28 (0.22), residues: 544 loop : -0.26 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 92 HIS 0.002 0.000 HIS A 189 PHE 0.010 0.001 PHE B 123 TYR 0.012 0.001 TYR D 280 ARG 0.009 0.001 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 732) hydrogen bonds : angle 4.53849 ( 2016) covalent geometry : bond 0.00362 (16456) covalent geometry : angle 0.57195 (22292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10725.67 seconds wall clock time: 184 minutes 32.88 seconds (11072.88 seconds total)