Starting phenix.real_space_refine on Sun Aug 24 02:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bb1_15953/08_2025/8bb1_15953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bb1_15953/08_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_15953/08_2025/8bb1_15953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bb1_15953/08_2025/8bb1_15953.map" model { file = "/net/cci-nas-00/data/ceres_data/8bb1_15953/08_2025/8bb1_15953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bb1_15953/08_2025/8bb1_15953.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS: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: {'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS: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: {'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS: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: {'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'HIS: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: 3.67, per 1000 atoms: 0.23 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: 0.99 Conformation dependent library (CDL) restraints added in 533.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 2.63 Time building geometry restraints manager: 1.36 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 7.170 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.000 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG F 72 TYR 0.008 0.001 TYR F 118 PHE 0.012 0.001 PHE E 127 TRP 0.016 0.001 TRP F 149 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00305 (16456) covalent geometry : angle 0.41565 (22292) hydrogen bonds : bond 0.22401 ( 732) hydrogen bonds : angle 7.59998 ( 2016) *********************** 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 : 0.499 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: 0.9418 (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 28 MET cc_start: 0.9145 (mmm) cc_final: 0.8721 (tpp) REVERT: E 29 SER cc_start: 0.9670 (t) cc_final: 0.9372 (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 28 MET cc_start: 0.9151 (mmm) cc_final: 0.8730 (tpp) REVERT: F 29 SER cc_start: 0.9670 (t) cc_final: 0.9371 (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 28 MET cc_start: 0.9143 (mmm) cc_final: 0.8723 (tpp) REVERT: G 29 SER cc_start: 0.9669 (t) cc_final: 0.9368 (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 28 MET cc_start: 0.9149 (mmm) cc_final: 0.8725 (tpp) REVERT: H 29 SER cc_start: 0.9670 (t) cc_final: 0.9371 (p) REVERT: H 49 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8348 (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: 0.6604 time to fit residues: 188.9533 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 : 0.423 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.074812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.053084 restraints weight = 36758.288| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.14 r_work: 0.2668 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16456 Z= 0.193 Angle : 0.535 6.426 22292 Z= 0.292 Chirality : 0.044 0.137 2500 Planarity : 0.005 0.037 2904 Dihedral : 4.424 29.700 2272 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.88 % Allowed : 8.47 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.18), residues: 2068 helix: 1.79 (0.21), residues: 608 sheet: 0.67 (0.22), residues: 520 loop : -0.36 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 74 TYR 0.015 0.002 TYR C 280 PHE 0.013 0.001 PHE E 127 TRP 0.012 0.001 TRP F 149 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00437 (16456) covalent geometry : angle 0.53490 (22292) hydrogen bonds : bond 0.04691 ( 732) hydrogen bonds : angle 5.54294 ( 2016) *********************** 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 240 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.689 Fit side-chains REVERT: A 49 MET cc_start: 0.9394 (ptm) cc_final: 0.9031 (ptm) REVERT: A 181 ASP cc_start: 0.9022 (t70) cc_final: 0.8761 (t0) REVERT: A 299 SER cc_start: 0.9492 (m) cc_final: 0.9187 (p) REVERT: B 49 MET cc_start: 0.9389 (ptm) cc_final: 0.9014 (ptm) REVERT: B 181 ASP cc_start: 0.9020 (t70) cc_final: 0.8758 (t0) REVERT: B 299 SER cc_start: 0.9491 (m) cc_final: 0.9196 (p) REVERT: B 311 MET cc_start: 0.9194 (ttp) cc_final: 0.8984 (ttt) REVERT: C 49 MET cc_start: 0.9394 (ptm) cc_final: 0.9019 (ptm) REVERT: C 181 ASP cc_start: 0.9019 (t70) cc_final: 0.8757 (t0) REVERT: C 299 SER cc_start: 0.9499 (m) cc_final: 0.9196 (p) REVERT: C 311 MET cc_start: 0.9201 (ttp) cc_final: 0.8994 (ttt) REVERT: D 49 MET cc_start: 0.9404 (ptm) cc_final: 0.9048 (ptm) REVERT: D 181 ASP cc_start: 0.9036 (t70) cc_final: 0.8763 (t0) REVERT: D 299 SER cc_start: 0.9492 (m) cc_final: 0.9191 (p) REVERT: E 1 MET cc_start: 0.9214 (ttm) cc_final: 0.8761 (ttt) REVERT: E 6 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8795 (mt-10) REVERT: E 29 SER cc_start: 0.9638 (t) cc_final: 0.9312 (p) REVERT: E 32 ARG cc_start: 0.9074 (ptp90) cc_final: 0.8820 (mtm110) REVERT: E 49 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8373 (mt-10) REVERT: E 51 THR cc_start: 0.9347 (p) cc_final: 0.8979 (t) REVERT: E 69 LYS cc_start: 0.8811 (mtpm) cc_final: 0.8536 (mtpm) REVERT: E 76 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8636 (tmmt) REVERT: E 77 ASP cc_start: 0.8236 (t70) cc_final: 0.7622 (p0) REVERT: E 89 CYS cc_start: 0.7839 (m) cc_final: 0.7592 (m) REVERT: E 129 GLU cc_start: 0.8924 (tt0) cc_final: 0.8597 (tt0) REVERT: F 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8760 (ttt) REVERT: F 6 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8794 (mt-10) REVERT: F 29 SER cc_start: 0.9637 (t) cc_final: 0.9314 (p) REVERT: F 32 ARG cc_start: 0.9075 (ptp90) cc_final: 0.8821 (mtm110) REVERT: F 49 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8372 (mt-10) REVERT: F 51 THR cc_start: 0.9349 (p) cc_final: 0.8980 (t) REVERT: F 68 GLU cc_start: 0.8033 (pm20) cc_final: 0.7827 (pm20) REVERT: F 69 LYS cc_start: 0.8812 (mtpm) cc_final: 0.8536 (mtpm) REVERT: F 76 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8631 (tmmt) REVERT: F 77 ASP cc_start: 0.8229 (t70) cc_final: 0.7627 (p0) REVERT: F 89 CYS cc_start: 0.7887 (m) cc_final: 0.7641 (m) REVERT: F 129 GLU cc_start: 0.8895 (tt0) cc_final: 0.8566 (tt0) REVERT: G 1 MET cc_start: 0.9204 (ttm) cc_final: 0.8752 (ttt) REVERT: G 6 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8801 (mt-10) REVERT: G 29 SER cc_start: 0.9637 (t) cc_final: 0.9308 (p) REVERT: G 32 ARG cc_start: 0.9075 (ptp90) cc_final: 0.8819 (mtm110) REVERT: G 49 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8377 (mt-10) REVERT: G 51 THR cc_start: 0.9351 (p) cc_final: 0.8984 (t) REVERT: G 68 GLU cc_start: 0.8035 (pm20) cc_final: 0.7827 (pm20) REVERT: G 69 LYS cc_start: 0.8806 (mtpm) cc_final: 0.8527 (mtpm) REVERT: G 76 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8631 (tmmt) REVERT: G 77 ASP cc_start: 0.8233 (t70) cc_final: 0.7633 (p0) REVERT: G 89 CYS cc_start: 0.7840 (m) cc_final: 0.7579 (m) REVERT: G 129 GLU cc_start: 0.8896 (tt0) cc_final: 0.8563 (tt0) REVERT: H 1 MET cc_start: 0.9201 (ttm) cc_final: 0.8754 (ttt) REVERT: H 6 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8807 (mt-10) REVERT: H 29 SER cc_start: 0.9638 (t) cc_final: 0.9313 (p) REVERT: H 32 ARG cc_start: 0.9077 (ptp90) cc_final: 0.8822 (mtm110) REVERT: H 49 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8379 (mt-10) REVERT: H 51 THR cc_start: 0.9353 (p) cc_final: 0.8986 (t) REVERT: H 68 GLU cc_start: 0.8030 (pm20) cc_final: 0.7823 (pm20) REVERT: H 69 LYS cc_start: 0.8809 (mtpm) cc_final: 0.8535 (mtpm) REVERT: H 76 LYS cc_start: 0.9050 (tmmt) cc_final: 0.8634 (tmmt) REVERT: H 77 ASP cc_start: 0.8236 (t70) cc_final: 0.7625 (p0) REVERT: H 89 CYS cc_start: 0.7865 (m) cc_final: 0.7619 (m) REVERT: H 129 GLU cc_start: 0.8899 (tt0) cc_final: 0.8567 (tt0) outliers start: 32 outliers final: 12 residues processed: 224 average time/residue: 0.8025 time to fit residues: 194.0855 Evaluate side-chains 204 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 70 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 47 SER 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 54 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 190 optimal weight: 0.0870 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.074442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.053008 restraints weight = 37277.729| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.15 r_work: 0.2666 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1870 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= 0.192 Angle : 0.533 6.547 22292 Z= 0.285 Chirality : 0.044 0.134 2500 Planarity : 0.004 0.037 2904 Dihedral : 4.344 30.331 2264 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.65 % Allowed : 8.71 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.18), residues: 2068 helix: 1.90 (0.21), residues: 604 sheet: 0.46 (0.22), residues: 520 loop : -0.35 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 74 TYR 0.015 0.002 TYR F 45 PHE 0.011 0.001 PHE E 127 TRP 0.009 0.001 TRP F 149 HIS 0.006 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00437 (16456) covalent geometry : angle 0.53337 (22292) hydrogen bonds : bond 0.04234 ( 732) hydrogen bonds : angle 5.24695 ( 2016) *********************** 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 244 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.665 Fit side-chains REVERT: A 49 MET cc_start: 0.9371 (ptm) cc_final: 0.8945 (ptm) REVERT: A 181 ASP cc_start: 0.9045 (t70) cc_final: 0.8748 (t0) REVERT: A 299 SER cc_start: 0.9485 (m) cc_final: 0.9197 (p) REVERT: B 49 MET cc_start: 0.9375 (ptm) cc_final: 0.8955 (ptm) REVERT: B 181 ASP cc_start: 0.9039 (t70) cc_final: 0.8744 (t0) REVERT: B 299 SER cc_start: 0.9476 (m) cc_final: 0.9197 (p) REVERT: C 49 MET cc_start: 0.9379 (ptm) cc_final: 0.8959 (ptm) REVERT: C 181 ASP cc_start: 0.9053 (t70) cc_final: 0.8769 (t0) REVERT: C 299 SER cc_start: 0.9482 (m) cc_final: 0.9200 (p) REVERT: D 49 MET cc_start: 0.9385 (ptm) cc_final: 0.8967 (ptm) REVERT: D 181 ASP cc_start: 0.9036 (t70) cc_final: 0.8532 (t0) REVERT: D 299 SER cc_start: 0.9469 (m) cc_final: 0.9197 (p) REVERT: E 1 MET cc_start: 0.9215 (ttm) cc_final: 0.8783 (ttt) REVERT: E 19 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8750 (mtt-85) REVERT: E 28 MET cc_start: 0.9252 (tpp) cc_final: 0.8937 (pp-130) REVERT: E 29 SER cc_start: 0.9624 (t) cc_final: 0.9089 (p) REVERT: E 32 ARG cc_start: 0.9087 (ptp90) cc_final: 0.8846 (ptp-110) REVERT: E 39 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8633 (ttm110) REVERT: E 49 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8466 (mt-10) REVERT: E 51 THR cc_start: 0.9191 (p) cc_final: 0.8966 (t) REVERT: E 68 GLU cc_start: 0.8051 (pm20) cc_final: 0.7838 (pm20) REVERT: E 69 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8430 (mtpm) REVERT: E 76 LYS cc_start: 0.9043 (tmmt) cc_final: 0.8654 (tmmt) REVERT: E 77 ASP cc_start: 0.8208 (t70) cc_final: 0.7481 (p0) REVERT: E 89 CYS cc_start: 0.7800 (m) cc_final: 0.7538 (m) REVERT: E 94 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7815 (mm110) REVERT: E 95 ASP cc_start: 0.8317 (p0) cc_final: 0.8041 (p0) REVERT: E 129 GLU cc_start: 0.8889 (tt0) cc_final: 0.8582 (tt0) REVERT: F 1 MET cc_start: 0.9209 (ttm) cc_final: 0.8775 (ttt) REVERT: F 19 ARG cc_start: 0.8976 (mtp85) cc_final: 0.8748 (mtt-85) REVERT: F 29 SER cc_start: 0.9620 (t) cc_final: 0.9320 (p) REVERT: F 39 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8632 (ttm110) REVERT: F 49 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8475 (mt-10) REVERT: F 51 THR cc_start: 0.9197 (p) cc_final: 0.8987 (t) REVERT: F 68 GLU cc_start: 0.8098 (pm20) cc_final: 0.7843 (pm20) REVERT: F 76 LYS cc_start: 0.9043 (tmmt) cc_final: 0.8654 (tmmt) REVERT: F 77 ASP cc_start: 0.8205 (t70) cc_final: 0.7478 (p0) REVERT: F 89 CYS cc_start: 0.7793 (m) cc_final: 0.7534 (m) REVERT: F 94 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7865 (mm110) REVERT: F 95 ASP cc_start: 0.8327 (p0) cc_final: 0.8064 (p0) REVERT: F 129 GLU cc_start: 0.8781 (tt0) cc_final: 0.8471 (tt0) REVERT: G 1 MET cc_start: 0.9210 (ttm) cc_final: 0.8777 (ttt) REVERT: G 19 ARG cc_start: 0.8975 (mtp85) cc_final: 0.8746 (mtt-85) REVERT: G 28 MET cc_start: 0.9250 (tpp) cc_final: 0.8937 (pp-130) REVERT: G 29 SER cc_start: 0.9623 (t) cc_final: 0.9087 (p) REVERT: G 32 ARG cc_start: 0.9084 (ptp90) cc_final: 0.8841 (ptp-110) REVERT: G 39 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8631 (ttm110) REVERT: G 49 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8475 (mt-10) REVERT: G 51 THR cc_start: 0.9197 (p) cc_final: 0.8970 (t) REVERT: G 68 GLU cc_start: 0.8105 (pm20) cc_final: 0.7849 (pm20) REVERT: G 69 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8440 (mtpm) REVERT: G 76 LYS cc_start: 0.9049 (tmmt) cc_final: 0.8662 (tmmt) REVERT: G 77 ASP cc_start: 0.8215 (t70) cc_final: 0.7489 (p0) REVERT: G 89 CYS cc_start: 0.7788 (m) cc_final: 0.7525 (m) REVERT: G 94 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7865 (mm110) REVERT: G 95 ASP cc_start: 0.8289 (p0) cc_final: 0.8032 (p0) REVERT: G 129 GLU cc_start: 0.8784 (tt0) cc_final: 0.8470 (tt0) REVERT: H 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8777 (ttt) REVERT: H 19 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8757 (mtt-85) REVERT: H 28 MET cc_start: 0.9257 (tpp) cc_final: 0.8940 (pp-130) REVERT: H 29 SER cc_start: 0.9625 (t) cc_final: 0.9088 (p) REVERT: H 32 ARG cc_start: 0.9085 (ptp90) cc_final: 0.8844 (ptp-110) REVERT: H 39 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8634 (ttm110) REVERT: H 49 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8485 (mt-10) REVERT: H 51 THR cc_start: 0.9195 (p) cc_final: 0.8986 (t) REVERT: H 68 GLU cc_start: 0.8030 (pm20) cc_final: 0.7792 (pm20) REVERT: H 69 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8423 (mtpm) REVERT: H 76 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8673 (tmmt) REVERT: H 77 ASP cc_start: 0.8196 (t70) cc_final: 0.7435 (p0) REVERT: H 89 CYS cc_start: 0.7780 (m) cc_final: 0.7519 (m) REVERT: H 94 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7862 (mm110) REVERT: H 95 ASP cc_start: 0.8285 (p0) cc_final: 0.8028 (p0) REVERT: H 129 GLU cc_start: 0.8782 (tt0) cc_final: 0.8467 (tt0) outliers start: 28 outliers final: 15 residues processed: 231 average time/residue: 0.8191 time to fit residues: 204.1348 Evaluate side-chains 220 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 69 LYS 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 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 58 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.075536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.054230 restraints weight = 37344.080| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.12 r_work: 0.2698 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16456 Z= 0.178 Angle : 0.521 6.339 22292 Z= 0.278 Chirality : 0.043 0.134 2500 Planarity : 0.004 0.038 2904 Dihedral : 4.320 30.733 2264 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.65 % Allowed : 9.47 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2068 helix: 1.99 (0.22), residues: 600 sheet: 0.36 (0.22), residues: 520 loop : -0.38 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 74 TYR 0.025 0.002 TYR G 118 PHE 0.010 0.001 PHE G 127 TRP 0.007 0.001 TRP G 149 HIS 0.004 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00408 (16456) covalent geometry : angle 0.52147 (22292) hydrogen bonds : bond 0.03901 ( 732) hydrogen bonds : angle 5.00451 ( 2016) *********************** 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 240 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9365 (ptm) cc_final: 0.8928 (ptm) REVERT: A 181 ASP cc_start: 0.9065 (t70) cc_final: 0.8576 (t0) REVERT: A 299 SER cc_start: 0.9461 (m) cc_final: 0.9139 (p) REVERT: B 49 MET cc_start: 0.9373 (ptm) cc_final: 0.8945 (ptm) REVERT: B 181 ASP cc_start: 0.9055 (t70) cc_final: 0.8565 (t0) REVERT: B 299 SER cc_start: 0.9463 (m) cc_final: 0.9142 (p) REVERT: C 49 MET cc_start: 0.9377 (ptm) cc_final: 0.8930 (ptm) REVERT: C 181 ASP cc_start: 0.9054 (t70) cc_final: 0.8743 (t0) REVERT: C 299 SER cc_start: 0.9466 (m) cc_final: 0.9145 (p) REVERT: D 49 MET cc_start: 0.9382 (ptm) cc_final: 0.8939 (ptm) REVERT: D 181 ASP cc_start: 0.9058 (t70) cc_final: 0.8742 (t0) REVERT: D 299 SER cc_start: 0.9456 (m) cc_final: 0.9141 (p) REVERT: E 1 MET cc_start: 0.9198 (ttm) cc_final: 0.8752 (ttt) REVERT: E 29 SER cc_start: 0.9600 (t) cc_final: 0.9275 (p) REVERT: E 32 ARG cc_start: 0.9084 (ptp90) cc_final: 0.8873 (mtm110) REVERT: E 39 ARG cc_start: 0.9037 (ttm-80) cc_final: 0.8643 (ttm110) REVERT: E 49 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8506 (mt-10) REVERT: E 51 THR cc_start: 0.9135 (p) cc_final: 0.8777 (t) REVERT: E 68 GLU cc_start: 0.8018 (pm20) cc_final: 0.7782 (pm20) REVERT: E 69 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8501 (mtpm) REVERT: E 76 LYS cc_start: 0.9049 (tmmt) cc_final: 0.8635 (tmmt) REVERT: E 77 ASP cc_start: 0.8058 (t70) cc_final: 0.7264 (p0) REVERT: E 94 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7763 (mm110) REVERT: E 95 ASP cc_start: 0.8415 (p0) cc_final: 0.8092 (p0) REVERT: E 122 ARG cc_start: 0.8071 (tmm160) cc_final: 0.7607 (tmm160) REVERT: E 129 GLU cc_start: 0.8770 (tt0) cc_final: 0.8481 (tt0) REVERT: F 1 MET cc_start: 0.9200 (ttm) cc_final: 0.8754 (ttt) REVERT: F 29 SER cc_start: 0.9650 (t) cc_final: 0.9319 (p) REVERT: F 39 ARG cc_start: 0.9008 (ttm-80) cc_final: 0.8599 (ttm110) REVERT: F 49 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8497 (mt-10) REVERT: F 51 THR cc_start: 0.9169 (p) cc_final: 0.8895 (t) REVERT: F 68 GLU cc_start: 0.7901 (pm20) cc_final: 0.7647 (pm20) REVERT: F 76 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8635 (tmmt) REVERT: F 77 ASP cc_start: 0.8061 (t70) cc_final: 0.7269 (p0) REVERT: F 94 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7731 (mm110) REVERT: F 95 ASP cc_start: 0.8410 (p0) cc_final: 0.8087 (p0) REVERT: F 122 ARG cc_start: 0.8073 (tmm160) cc_final: 0.7609 (tmm160) REVERT: F 129 GLU cc_start: 0.8744 (tt0) cc_final: 0.8421 (tt0) REVERT: G 1 MET cc_start: 0.9196 (ttm) cc_final: 0.8751 (ttt) REVERT: G 29 SER cc_start: 0.9599 (t) cc_final: 0.9274 (p) REVERT: G 32 ARG cc_start: 0.9083 (ptp90) cc_final: 0.8871 (mtm110) REVERT: G 39 ARG cc_start: 0.9036 (ttm-80) cc_final: 0.8660 (ttm110) REVERT: G 49 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8516 (mt-10) REVERT: G 51 THR cc_start: 0.9139 (p) cc_final: 0.8783 (t) REVERT: G 68 GLU cc_start: 0.8046 (pm20) cc_final: 0.7774 (pm20) REVERT: G 69 LYS cc_start: 0.8740 (mtpm) cc_final: 0.8497 (mtpm) REVERT: G 76 LYS cc_start: 0.9050 (tmmt) cc_final: 0.8637 (tmmt) REVERT: G 77 ASP cc_start: 0.8056 (t70) cc_final: 0.7261 (p0) REVERT: G 94 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7765 (mm110) REVERT: G 95 ASP cc_start: 0.8403 (p0) cc_final: 0.8073 (p0) REVERT: G 122 ARG cc_start: 0.8213 (tmm160) cc_final: 0.7796 (tmm160) REVERT: G 129 GLU cc_start: 0.8741 (tt0) cc_final: 0.8416 (tt0) REVERT: H 1 MET cc_start: 0.9195 (ttm) cc_final: 0.8729 (ttt) REVERT: H 29 SER cc_start: 0.9600 (t) cc_final: 0.9273 (p) REVERT: H 32 ARG cc_start: 0.9086 (ptp90) cc_final: 0.8876 (mtm110) REVERT: H 39 ARG cc_start: 0.9038 (ttm-80) cc_final: 0.8646 (ttm110) REVERT: H 49 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8511 (mt-10) REVERT: H 51 THR cc_start: 0.9131 (p) cc_final: 0.8779 (t) REVERT: H 68 GLU cc_start: 0.8025 (pm20) cc_final: 0.7753 (pm20) REVERT: H 69 LYS cc_start: 0.8734 (mtpm) cc_final: 0.8496 (mtpm) REVERT: H 76 LYS cc_start: 0.9040 (tmmt) cc_final: 0.8624 (tmmt) REVERT: H 77 ASP cc_start: 0.8062 (t70) cc_final: 0.7270 (p0) REVERT: H 94 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7754 (mm110) REVERT: H 95 ASP cc_start: 0.8400 (p0) cc_final: 0.8066 (p0) REVERT: H 122 ARG cc_start: 0.8068 (tmm160) cc_final: 0.7604 (tmm160) REVERT: H 129 GLU cc_start: 0.8742 (tt0) cc_final: 0.8441 (tt0) outliers start: 28 outliers final: 18 residues processed: 227 average time/residue: 0.7540 time to fit residues: 185.0048 Evaluate side-chains 221 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 248 VAL Chi-restraints excluded: chain E residue 47 SER 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 47 SER Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 122 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3338 r_free = 0.3338 target = 0.075344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.054106 restraints weight = 37361.301| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.13 r_work: 0.2698 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2119 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= 0.174 Angle : 0.520 6.344 22292 Z= 0.276 Chirality : 0.044 0.134 2500 Planarity : 0.004 0.039 2904 Dihedral : 4.299 30.891 2264 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.71 % Allowed : 10.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2068 helix: 2.01 (0.22), residues: 600 sheet: 0.32 (0.22), residues: 520 loop : -0.37 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 74 TYR 0.014 0.002 TYR E 45 PHE 0.010 0.001 PHE E 127 TRP 0.005 0.001 TRP E 149 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00397 (16456) covalent geometry : angle 0.51987 (22292) hydrogen bonds : bond 0.03803 ( 732) hydrogen bonds : angle 4.85750 ( 2016) *********************** 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 242 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9363 (ptm) cc_final: 0.8935 (ptm) REVERT: A 181 ASP cc_start: 0.9054 (t70) cc_final: 0.8553 (t0) REVERT: A 299 SER cc_start: 0.9449 (m) cc_final: 0.9163 (p) REVERT: B 49 MET cc_start: 0.9380 (ptm) cc_final: 0.8950 (ptm) REVERT: B 181 ASP cc_start: 0.9054 (t70) cc_final: 0.8556 (t0) REVERT: B 299 SER cc_start: 0.9451 (m) cc_final: 0.9168 (p) REVERT: C 49 MET cc_start: 0.9377 (ptm) cc_final: 0.8942 (ptm) REVERT: C 181 ASP cc_start: 0.9056 (t70) cc_final: 0.8751 (t0) REVERT: C 299 SER cc_start: 0.9446 (m) cc_final: 0.9169 (p) REVERT: D 49 MET cc_start: 0.9376 (ptm) cc_final: 0.8944 (ptm) REVERT: D 181 ASP cc_start: 0.9056 (t70) cc_final: 0.8557 (t0) REVERT: D 299 SER cc_start: 0.9449 (m) cc_final: 0.9169 (p) REVERT: E 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8777 (ttt) REVERT: E 24 ASP cc_start: 0.8576 (t0) cc_final: 0.8323 (t0) REVERT: E 28 MET cc_start: 0.9211 (tpp) cc_final: 0.8965 (pp-130) REVERT: E 29 SER cc_start: 0.9625 (t) cc_final: 0.9050 (p) REVERT: E 32 ARG cc_start: 0.9064 (ptp90) cc_final: 0.8840 (ptp-110) REVERT: E 49 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8460 (mt-10) REVERT: E 51 THR cc_start: 0.9134 (p) cc_final: 0.8908 (t) REVERT: E 68 GLU cc_start: 0.8027 (pm20) cc_final: 0.7744 (pm20) REVERT: E 69 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8559 (tppp) REVERT: E 76 LYS cc_start: 0.9078 (tmmt) cc_final: 0.8664 (tmmt) REVERT: E 77 ASP cc_start: 0.8112 (t70) cc_final: 0.7324 (p0) REVERT: E 94 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7776 (mm110) REVERT: E 95 ASP cc_start: 0.8512 (p0) cc_final: 0.8132 (p0) REVERT: E 122 ARG cc_start: 0.8155 (tmm160) cc_final: 0.7703 (tmm160) REVERT: E 129 GLU cc_start: 0.8800 (tt0) cc_final: 0.8509 (tt0) REVERT: F 1 MET cc_start: 0.9227 (ttm) cc_final: 0.8777 (ttt) REVERT: F 28 MET cc_start: 0.9256 (tpp) cc_final: 0.8665 (tpt) REVERT: F 29 SER cc_start: 0.9627 (t) cc_final: 0.9338 (p) REVERT: F 49 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8447 (mt-10) REVERT: F 51 THR cc_start: 0.9138 (p) cc_final: 0.8893 (t) REVERT: F 68 GLU cc_start: 0.7869 (pm20) cc_final: 0.7619 (pm20) REVERT: F 76 LYS cc_start: 0.9079 (tmmt) cc_final: 0.8664 (tmmt) REVERT: F 77 ASP cc_start: 0.8108 (t70) cc_final: 0.7324 (p0) REVERT: F 94 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7815 (mm110) REVERT: F 95 ASP cc_start: 0.8549 (p0) cc_final: 0.8190 (p0) REVERT: F 122 ARG cc_start: 0.8154 (tmm160) cc_final: 0.7701 (tmm160) REVERT: G 1 MET cc_start: 0.9229 (ttm) cc_final: 0.8779 (ttt) REVERT: G 24 ASP cc_start: 0.8568 (t0) cc_final: 0.8315 (t0) REVERT: G 28 MET cc_start: 0.9201 (tpp) cc_final: 0.8961 (pp-130) REVERT: G 29 SER cc_start: 0.9624 (t) cc_final: 0.9046 (p) REVERT: G 32 ARG cc_start: 0.9062 (ptp90) cc_final: 0.8835 (ptp-110) REVERT: G 49 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8454 (mt-10) REVERT: G 51 THR cc_start: 0.9141 (p) cc_final: 0.8907 (t) REVERT: G 68 GLU cc_start: 0.8039 (pm20) cc_final: 0.7732 (pm20) REVERT: G 69 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8552 (tppp) REVERT: G 76 LYS cc_start: 0.9079 (tmmt) cc_final: 0.8665 (tmmt) REVERT: G 77 ASP cc_start: 0.8106 (t70) cc_final: 0.7322 (p0) REVERT: G 94 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7835 (mm110) REVERT: G 95 ASP cc_start: 0.8500 (p0) cc_final: 0.8124 (p0) REVERT: G 122 ARG cc_start: 0.8228 (tmm160) cc_final: 0.7752 (tmm160) REVERT: G 129 GLU cc_start: 0.8777 (tt0) cc_final: 0.8467 (tt0) REVERT: H 1 MET cc_start: 0.9210 (ttm) cc_final: 0.8780 (ttt) REVERT: H 24 ASP cc_start: 0.8577 (t0) cc_final: 0.8323 (t0) REVERT: H 28 MET cc_start: 0.9203 (tpp) cc_final: 0.8963 (pp-130) REVERT: H 29 SER cc_start: 0.9625 (t) cc_final: 0.9044 (p) REVERT: H 32 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8838 (ptp-110) REVERT: H 49 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8455 (mt-10) REVERT: H 51 THR cc_start: 0.9137 (p) cc_final: 0.8919 (t) REVERT: H 68 GLU cc_start: 0.8024 (pm20) cc_final: 0.7714 (pm20) REVERT: H 69 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (tppp) REVERT: H 76 LYS cc_start: 0.9068 (tmmt) cc_final: 0.8654 (tmmt) REVERT: H 77 ASP cc_start: 0.8105 (t70) cc_final: 0.7322 (p0) REVERT: H 94 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7843 (mm110) REVERT: H 95 ASP cc_start: 0.8497 (p0) cc_final: 0.8125 (p0) REVERT: H 122 ARG cc_start: 0.8155 (tmm160) cc_final: 0.7704 (tmm160) REVERT: H 129 GLU cc_start: 0.8780 (tt0) cc_final: 0.8470 (tt0) outliers start: 29 outliers final: 22 residues processed: 232 average time/residue: 0.7202 time to fit residues: 181.1965 Evaluate side-chains 228 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 187 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 187 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 50 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 50 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 50 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 50 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 69 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 63 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 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 = 0.3382 r_free = 0.3382 target = 0.078088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.056868 restraints weight = 37443.741| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.17 r_work: 0.2777 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16456 Z= 0.099 Angle : 0.487 7.731 22292 Z= 0.258 Chirality : 0.042 0.143 2500 Planarity : 0.004 0.036 2904 Dihedral : 3.971 24.975 2264 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 12.24 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.19), residues: 2068 helix: 2.17 (0.22), residues: 600 sheet: 0.20 (0.22), residues: 524 loop : -0.24 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 74 TYR 0.026 0.002 TYR H 118 PHE 0.009 0.001 PHE B 5 TRP 0.007 0.001 TRP F 92 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00214 (16456) covalent geometry : angle 0.48665 (22292) hydrogen bonds : bond 0.03290 ( 732) hydrogen bonds : angle 4.65562 ( 2016) *********************** 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 238 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9280 (ptm) cc_final: 0.8941 (ptm) REVERT: A 181 ASP cc_start: 0.9049 (t70) cc_final: 0.8588 (t0) REVERT: A 299 SER cc_start: 0.9389 (m) cc_final: 0.9186 (p) REVERT: B 49 MET cc_start: 0.9317 (ptm) cc_final: 0.8960 (ptm) REVERT: B 181 ASP cc_start: 0.9033 (t70) cc_final: 0.8575 (t0) REVERT: C 49 MET cc_start: 0.9333 (ptm) cc_final: 0.8971 (ptm) REVERT: C 181 ASP cc_start: 0.9033 (t70) cc_final: 0.8571 (t0) REVERT: C 299 SER cc_start: 0.9434 (m) cc_final: 0.9217 (p) REVERT: D 49 MET cc_start: 0.9329 (ptm) cc_final: 0.8981 (ptm) REVERT: D 181 ASP cc_start: 0.9034 (t70) cc_final: 0.8564 (t0) REVERT: D 299 SER cc_start: 0.9423 (m) cc_final: 0.9182 (p) REVERT: E 1 MET cc_start: 0.9232 (ttm) cc_final: 0.8757 (ttt) REVERT: E 28 MET cc_start: 0.9228 (tpp) cc_final: 0.8781 (tpp) REVERT: E 29 SER cc_start: 0.9583 (t) cc_final: 0.9155 (p) REVERT: E 32 ARG cc_start: 0.9045 (ptp90) cc_final: 0.8626 (mtm110) REVERT: E 47 SER cc_start: 0.8442 (m) cc_final: 0.7930 (p) REVERT: E 49 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8373 (mt-10) REVERT: E 51 THR cc_start: 0.9073 (p) cc_final: 0.8786 (t) REVERT: E 68 GLU cc_start: 0.8010 (pm20) cc_final: 0.7691 (pm20) REVERT: E 74 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8352 (tmm-80) REVERT: E 75 CYS cc_start: 0.9005 (m) cc_final: 0.8610 (p) REVERT: E 76 LYS cc_start: 0.9089 (tmmt) cc_final: 0.8664 (tmmt) REVERT: E 77 ASP cc_start: 0.8080 (t70) cc_final: 0.7250 (p0) REVERT: E 94 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7703 (mm110) REVERT: E 95 ASP cc_start: 0.8568 (p0) cc_final: 0.8187 (p0) REVERT: E 122 ARG cc_start: 0.8175 (tmm160) cc_final: 0.7731 (tmm160) REVERT: E 129 GLU cc_start: 0.8817 (tt0) cc_final: 0.8564 (tt0) REVERT: F 1 MET cc_start: 0.9227 (ttm) cc_final: 0.8751 (ttt) REVERT: F 24 ASP cc_start: 0.8550 (t0) cc_final: 0.8333 (t0) REVERT: F 29 SER cc_start: 0.9605 (t) cc_final: 0.9008 (p) REVERT: F 47 SER cc_start: 0.8509 (m) cc_final: 0.8023 (p) REVERT: F 49 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8395 (mt-10) REVERT: F 68 GLU cc_start: 0.7658 (pm20) cc_final: 0.7447 (pp20) REVERT: F 74 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8336 (tmm-80) REVERT: F 75 CYS cc_start: 0.8993 (m) cc_final: 0.8601 (p) REVERT: F 76 LYS cc_start: 0.9082 (tmmt) cc_final: 0.8655 (tmmt) REVERT: F 77 ASP cc_start: 0.8070 (t70) cc_final: 0.7244 (p0) REVERT: F 94 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7765 (mm110) REVERT: F 95 ASP cc_start: 0.8564 (p0) cc_final: 0.8201 (p0) REVERT: F 122 ARG cc_start: 0.8170 (tmm160) cc_final: 0.7728 (tmm160) REVERT: F 148 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7608 (mtm180) REVERT: G 1 MET cc_start: 0.9215 (ttm) cc_final: 0.8739 (ttt) REVERT: G 28 MET cc_start: 0.9219 (tpp) cc_final: 0.8769 (tpp) REVERT: G 29 SER cc_start: 0.9583 (t) cc_final: 0.9154 (p) REVERT: G 32 ARG cc_start: 0.9043 (ptp90) cc_final: 0.8617 (mtm110) REVERT: G 47 SER cc_start: 0.8537 (m) cc_final: 0.8051 (p) REVERT: G 49 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8399 (mt-10) REVERT: G 51 THR cc_start: 0.9072 (p) cc_final: 0.8797 (t) REVERT: G 68 GLU cc_start: 0.8016 (pm20) cc_final: 0.7633 (pm20) REVERT: G 74 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8346 (tmm-80) REVERT: G 75 CYS cc_start: 0.8992 (m) cc_final: 0.8609 (p) REVERT: G 76 LYS cc_start: 0.9088 (tmmt) cc_final: 0.8664 (tmmt) REVERT: G 77 ASP cc_start: 0.8070 (t70) cc_final: 0.7250 (p0) REVERT: G 94 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7718 (mm110) REVERT: G 95 ASP cc_start: 0.8508 (p0) cc_final: 0.8145 (p0) REVERT: G 122 ARG cc_start: 0.8232 (tmm160) cc_final: 0.7818 (tmm160) REVERT: G 129 GLU cc_start: 0.8787 (tt0) cc_final: 0.8542 (tt0) REVERT: H 1 MET cc_start: 0.9228 (ttm) cc_final: 0.8760 (ttt) REVERT: H 28 MET cc_start: 0.9221 (tpp) cc_final: 0.8771 (tpp) REVERT: H 29 SER cc_start: 0.9583 (t) cc_final: 0.9155 (p) REVERT: H 32 ARG cc_start: 0.9042 (ptp90) cc_final: 0.8617 (mtm110) REVERT: H 47 SER cc_start: 0.8533 (m) cc_final: 0.8042 (p) REVERT: H 49 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8416 (mt-10) REVERT: H 51 THR cc_start: 0.9073 (p) cc_final: 0.8784 (t) REVERT: H 68 GLU cc_start: 0.7993 (pm20) cc_final: 0.7609 (pm20) REVERT: H 74 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8344 (tmm-80) REVERT: H 75 CYS cc_start: 0.9002 (m) cc_final: 0.8626 (p) REVERT: H 76 LYS cc_start: 0.9074 (tmmt) cc_final: 0.8647 (tmmt) REVERT: H 77 ASP cc_start: 0.8076 (t70) cc_final: 0.7244 (p0) REVERT: H 94 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7731 (mm110) REVERT: H 95 ASP cc_start: 0.8531 (p0) cc_final: 0.8153 (p0) REVERT: H 122 ARG cc_start: 0.8180 (tmm160) cc_final: 0.7734 (tmm160) REVERT: H 129 GLU cc_start: 0.8791 (tt0) cc_final: 0.8547 (tt0) outliers start: 15 outliers final: 12 residues processed: 234 average time/residue: 0.8017 time to fit residues: 203.2167 Evaluate side-chains 223 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain G residue 66 THR 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 165 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.076554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.055520 restraints weight = 37583.095| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.05 r_work: 0.2715 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2306 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= 0.180 Angle : 0.539 7.808 22292 Z= 0.284 Chirality : 0.043 0.150 2500 Planarity : 0.004 0.037 2904 Dihedral : 4.201 28.190 2264 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.18 % Allowed : 13.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.19), residues: 2068 helix: 2.12 (0.22), residues: 600 sheet: 0.25 (0.22), residues: 524 loop : -0.27 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 74 TYR 0.012 0.001 TYR D 280 PHE 0.009 0.001 PHE E 127 TRP 0.007 0.001 TRP F 92 HIS 0.006 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00415 (16456) covalent geometry : angle 0.53922 (22292) hydrogen bonds : bond 0.03762 ( 732) hydrogen bonds : angle 4.69188 ( 2016) *********************** 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 232 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9361 (ptm) cc_final: 0.8926 (ptm) REVERT: A 181 ASP cc_start: 0.9082 (t70) cc_final: 0.8831 (t0) REVERT: A 299 SER cc_start: 0.9427 (m) cc_final: 0.9173 (p) REVERT: B 49 MET cc_start: 0.9369 (ptm) cc_final: 0.8939 (ptm) REVERT: B 181 ASP cc_start: 0.9063 (t70) cc_final: 0.8607 (t0) REVERT: C 49 MET cc_start: 0.9379 (ptm) cc_final: 0.8949 (ptm) REVERT: C 181 ASP cc_start: 0.9064 (t70) cc_final: 0.8811 (t0) REVERT: C 299 SER cc_start: 0.9434 (m) cc_final: 0.9189 (p) REVERT: D 49 MET cc_start: 0.9380 (ptm) cc_final: 0.8951 (ptm) REVERT: D 181 ASP cc_start: 0.9070 (t70) cc_final: 0.8605 (t0) REVERT: D 299 SER cc_start: 0.9416 (m) cc_final: 0.9144 (p) REVERT: E 1 MET cc_start: 0.9228 (ttm) cc_final: 0.8814 (ttt) REVERT: E 28 MET cc_start: 0.9231 (tpp) cc_final: 0.8863 (tpp) REVERT: E 29 SER cc_start: 0.9605 (t) cc_final: 0.9291 (p) REVERT: E 34 MET cc_start: 0.8915 (ttm) cc_final: 0.8693 (ttm) REVERT: E 68 GLU cc_start: 0.7884 (pm20) cc_final: 0.7184 (pm20) REVERT: E 69 LYS cc_start: 0.8956 (tppp) cc_final: 0.8494 (mtpp) REVERT: E 74 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8491 (tmm-80) REVERT: E 75 CYS cc_start: 0.9026 (m) cc_final: 0.8565 (p) REVERT: E 76 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8632 (tmmt) REVERT: E 77 ASP cc_start: 0.8107 (t70) cc_final: 0.7316 (p0) REVERT: E 94 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7837 (mm110) REVERT: E 95 ASP cc_start: 0.8534 (p0) cc_final: 0.8232 (p0) REVERT: E 122 ARG cc_start: 0.8178 (tmm160) cc_final: 0.7721 (tmm160) REVERT: E 129 GLU cc_start: 0.8914 (tt0) cc_final: 0.8609 (tt0) REVERT: F 1 MET cc_start: 0.9231 (ttm) cc_final: 0.8816 (ttt) REVERT: F 19 ARG cc_start: 0.9128 (mtp180) cc_final: 0.8902 (mtp85) REVERT: F 29 SER cc_start: 0.9614 (t) cc_final: 0.9189 (p) REVERT: F 32 ARG cc_start: 0.9002 (ptp-110) cc_final: 0.8746 (ptp-110) REVERT: F 74 ARG cc_start: 0.8773 (ttp80) cc_final: 0.8469 (tmm-80) REVERT: F 75 CYS cc_start: 0.9024 (m) cc_final: 0.8574 (p) REVERT: F 76 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8639 (tmmt) REVERT: F 77 ASP cc_start: 0.8102 (t70) cc_final: 0.7316 (p0) REVERT: F 122 ARG cc_start: 0.8180 (tmm160) cc_final: 0.7723 (tmm160) REVERT: F 147 ARG cc_start: 0.7863 (mpp80) cc_final: 0.7599 (mtm-85) REVERT: G 1 MET cc_start: 0.9221 (ttm) cc_final: 0.8806 (ttt) REVERT: G 28 MET cc_start: 0.9227 (tpp) cc_final: 0.8860 (tpp) REVERT: G 29 SER cc_start: 0.9604 (t) cc_final: 0.9290 (p) REVERT: G 34 MET cc_start: 0.8935 (ttm) cc_final: 0.8689 (ttp) REVERT: G 68 GLU cc_start: 0.7906 (pm20) cc_final: 0.7256 (pm20) REVERT: G 69 LYS cc_start: 0.8956 (tppp) cc_final: 0.8498 (mtpp) REVERT: G 74 ARG cc_start: 0.8784 (ttp80) cc_final: 0.8485 (tmm-80) REVERT: G 75 CYS cc_start: 0.9022 (m) cc_final: 0.8590 (p) REVERT: G 76 LYS cc_start: 0.9056 (tmmt) cc_final: 0.8639 (tmmt) REVERT: G 77 ASP cc_start: 0.8130 (t70) cc_final: 0.7335 (p0) REVERT: G 94 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7830 (mm110) REVERT: G 95 ASP cc_start: 0.8521 (p0) cc_final: 0.8231 (p0) REVERT: G 122 ARG cc_start: 0.8225 (tmm160) cc_final: 0.7796 (tmm160) REVERT: G 129 GLU cc_start: 0.8803 (tt0) cc_final: 0.8510 (tt0) REVERT: H 1 MET cc_start: 0.9224 (ttm) cc_final: 0.8815 (ttt) REVERT: H 28 MET cc_start: 0.9229 (tpp) cc_final: 0.8862 (tpp) REVERT: H 29 SER cc_start: 0.9605 (t) cc_final: 0.9292 (p) REVERT: H 34 MET cc_start: 0.8933 (ttm) cc_final: 0.8691 (ttp) REVERT: H 68 GLU cc_start: 0.7898 (pm20) cc_final: 0.7249 (pm20) REVERT: H 69 LYS cc_start: 0.8953 (tppp) cc_final: 0.8493 (mtpp) REVERT: H 74 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8489 (tmm-80) REVERT: H 75 CYS cc_start: 0.9024 (m) cc_final: 0.8585 (p) REVERT: H 76 LYS cc_start: 0.9044 (tmmt) cc_final: 0.8622 (tmmt) REVERT: H 77 ASP cc_start: 0.8102 (t70) cc_final: 0.7316 (p0) REVERT: H 95 ASP cc_start: 0.8526 (p0) cc_final: 0.8259 (p0) REVERT: H 122 ARG cc_start: 0.8212 (tmm160) cc_final: 0.7749 (tmm160) REVERT: H 129 GLU cc_start: 0.8812 (tt0) cc_final: 0.8521 (tt0) outliers start: 20 outliers final: 16 residues processed: 221 average time/residue: 0.8581 time to fit residues: 205.2058 Evaluate side-chains 224 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 47 SER 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 47 SER 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 133 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 193 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.077160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055859 restraints weight = 37525.381| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.17 r_work: 0.2727 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16456 Z= 0.128 Angle : 0.531 8.292 22292 Z= 0.280 Chirality : 0.043 0.151 2500 Planarity : 0.004 0.033 2904 Dihedral : 4.085 26.230 2264 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.94 % Allowed : 13.29 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.19), residues: 2068 helix: 2.12 (0.22), residues: 600 sheet: 0.24 (0.23), residues: 524 loop : -0.26 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 86 TYR 0.030 0.002 TYR H 118 PHE 0.008 0.001 PHE B 5 TRP 0.007 0.001 TRP G 92 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00293 (16456) covalent geometry : angle 0.53133 (22292) hydrogen bonds : bond 0.03447 ( 732) hydrogen bonds : angle 4.62206 ( 2016) *********************** 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 233 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.660 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: 0.9325 (ptm) cc_final: 0.8901 (ptm) REVERT: A 181 ASP cc_start: 0.9080 (t70) cc_final: 0.8601 (t0) REVERT: A 299 SER cc_start: 0.9424 (m) cc_final: 0.9167 (p) REVERT: B 49 MET cc_start: 0.9360 (ptm) cc_final: 0.9011 (ptm) REVERT: B 181 ASP cc_start: 0.9067 (t70) cc_final: 0.8590 (t0) REVERT: C 49 MET cc_start: 0.9339 (ptm) cc_final: 0.8974 (ptm) REVERT: C 181 ASP cc_start: 0.9068 (t70) cc_final: 0.8589 (t0) REVERT: C 299 SER cc_start: 0.9433 (m) cc_final: 0.9222 (p) REVERT: D 49 MET cc_start: 0.9368 (ptm) cc_final: 0.8984 (ptm) REVERT: D 181 ASP cc_start: 0.9065 (t70) cc_final: 0.8591 (t0) REVERT: D 299 SER cc_start: 0.9437 (m) cc_final: 0.9147 (p) REVERT: E 1 MET cc_start: 0.9194 (ttm) cc_final: 0.8791 (ttt) REVERT: E 28 MET cc_start: 0.9219 (tpp) cc_final: 0.8889 (tpp) REVERT: E 29 SER cc_start: 0.9601 (t) cc_final: 0.9308 (p) REVERT: E 68 GLU cc_start: 0.7773 (pm20) cc_final: 0.7060 (pm20) REVERT: E 69 LYS cc_start: 0.8898 (tppp) cc_final: 0.8566 (tppp) REVERT: E 75 CYS cc_start: 0.8969 (m) cc_final: 0.8541 (p) REVERT: E 76 LYS cc_start: 0.9028 (tmmt) cc_final: 0.8586 (tmmt) REVERT: E 77 ASP cc_start: 0.8020 (t70) cc_final: 0.7218 (p0) REVERT: E 95 ASP cc_start: 0.8546 (p0) cc_final: 0.8223 (p0) REVERT: E 122 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7717 (tmm160) REVERT: E 129 GLU cc_start: 0.8790 (tt0) cc_final: 0.8477 (tt0) REVERT: F 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8802 (ttt) REVERT: F 29 SER cc_start: 0.9610 (t) cc_final: 0.9228 (p) REVERT: F 32 ARG cc_start: 0.9015 (ptp-110) cc_final: 0.8655 (ptp-110) REVERT: F 69 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8508 (ttmm) REVERT: F 75 CYS cc_start: 0.8970 (m) cc_final: 0.8560 (p) REVERT: F 76 LYS cc_start: 0.9038 (tmmt) cc_final: 0.8605 (tmmt) REVERT: F 77 ASP cc_start: 0.8015 (t70) cc_final: 0.7217 (p0) REVERT: F 94 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8108 (mm110) REVERT: F 122 ARG cc_start: 0.8198 (tmm160) cc_final: 0.7746 (tmm160) REVERT: F 148 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7823 (mtm180) REVERT: G 1 MET cc_start: 0.9202 (ttm) cc_final: 0.8789 (ttt) REVERT: G 28 MET cc_start: 0.9213 (tpp) cc_final: 0.8888 (tpp) REVERT: G 29 SER cc_start: 0.9601 (t) cc_final: 0.9308 (p) REVERT: G 68 GLU cc_start: 0.7855 (pm20) cc_final: 0.7197 (pm20) REVERT: G 69 LYS cc_start: 0.8905 (tppp) cc_final: 0.8571 (tppp) REVERT: G 75 CYS cc_start: 0.8985 (m) cc_final: 0.8559 (p) REVERT: G 76 LYS cc_start: 0.9041 (tmmt) cc_final: 0.8608 (tmmt) REVERT: G 77 ASP cc_start: 0.8022 (t70) cc_final: 0.7230 (p0) REVERT: G 95 ASP cc_start: 0.8528 (p0) cc_final: 0.8220 (p0) REVERT: G 122 ARG cc_start: 0.8204 (tmm160) cc_final: 0.7761 (tmm160) REVERT: G 129 GLU cc_start: 0.8772 (tt0) cc_final: 0.8449 (tt0) REVERT: H 1 MET cc_start: 0.9197 (ttm) cc_final: 0.8801 (ttt) REVERT: H 28 MET cc_start: 0.9206 (tpp) cc_final: 0.8878 (tpp) REVERT: H 29 SER cc_start: 0.9601 (t) cc_final: 0.9310 (p) REVERT: H 68 GLU cc_start: 0.7844 (pm20) cc_final: 0.7187 (pm20) REVERT: H 69 LYS cc_start: 0.8902 (tppp) cc_final: 0.8569 (tppp) REVERT: H 75 CYS cc_start: 0.8972 (m) cc_final: 0.8555 (p) REVERT: H 76 LYS cc_start: 0.9031 (tmmt) cc_final: 0.8592 (tmmt) REVERT: H 77 ASP cc_start: 0.8024 (t70) cc_final: 0.7228 (p0) REVERT: H 95 ASP cc_start: 0.8523 (p0) cc_final: 0.8229 (p0) REVERT: H 122 ARG cc_start: 0.8197 (tmm160) cc_final: 0.7714 (tmm160) REVERT: H 129 GLU cc_start: 0.8778 (tt0) cc_final: 0.8460 (tt0) outliers start: 16 outliers final: 15 residues processed: 226 average time/residue: 0.8314 time to fit residues: 203.6392 Evaluate side-chains 223 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 47 SER Chi-restraints excluded: chain E residue 66 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3351 r_free = 0.3351 target = 0.076410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055918 restraints weight = 37533.120| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.02 r_work: 0.2718 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16456 Z= 0.170 Angle : 0.549 8.274 22292 Z= 0.289 Chirality : 0.043 0.144 2500 Planarity : 0.004 0.041 2904 Dihedral : 4.199 28.504 2264 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.12 % Allowed : 13.94 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.19), residues: 2068 helix: 2.06 (0.22), residues: 600 sheet: 0.21 (0.23), residues: 524 loop : -0.30 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 86 TYR 0.028 0.002 TYR G 118 PHE 0.009 0.001 PHE E 127 TRP 0.006 0.001 TRP E 92 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00392 (16456) covalent geometry : angle 0.54873 (22292) hydrogen bonds : bond 0.03670 ( 732) hydrogen bonds : angle 4.65658 ( 2016) *********************** 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 235 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9358 (ptm) cc_final: 0.8929 (ptm) REVERT: A 181 ASP cc_start: 0.9060 (t70) cc_final: 0.8611 (t0) REVERT: B 49 MET cc_start: 0.9368 (ptm) cc_final: 0.8940 (ptm) REVERT: B 181 ASP cc_start: 0.9051 (t70) cc_final: 0.8601 (t0) REVERT: C 49 MET cc_start: 0.9376 (ptm) cc_final: 0.8951 (ptm) REVERT: C 181 ASP cc_start: 0.9055 (t70) cc_final: 0.8586 (t0) REVERT: D 49 MET cc_start: 0.9378 (ptm) cc_final: 0.8951 (ptm) REVERT: D 299 SER cc_start: 0.9414 (m) cc_final: 0.9155 (p) REVERT: E 1 MET cc_start: 0.9218 (ttm) cc_final: 0.8833 (ttt) REVERT: E 29 SER cc_start: 0.9599 (t) cc_final: 0.9318 (p) REVERT: E 32 ARG cc_start: 0.9011 (ptp90) cc_final: 0.8730 (mtm110) REVERT: E 68 GLU cc_start: 0.7751 (pm20) cc_final: 0.7127 (pm20) REVERT: E 69 LYS cc_start: 0.8937 (tppp) cc_final: 0.8651 (tppp) REVERT: E 75 CYS cc_start: 0.8993 (m) cc_final: 0.8570 (p) REVERT: E 76 LYS cc_start: 0.9027 (tmmt) cc_final: 0.8612 (tmmt) REVERT: E 77 ASP cc_start: 0.8101 (t70) cc_final: 0.7336 (p0) REVERT: E 86 ARG cc_start: 0.9081 (tpp80) cc_final: 0.8727 (tpp80) REVERT: E 95 ASP cc_start: 0.8504 (p0) cc_final: 0.8230 (p0) REVERT: E 122 ARG cc_start: 0.8208 (tmm160) cc_final: 0.7723 (tmm160) REVERT: E 129 GLU cc_start: 0.8810 (tt0) cc_final: 0.8513 (tt0) REVERT: F 1 MET cc_start: 0.9222 (ttm) cc_final: 0.8836 (ttt) REVERT: F 29 SER cc_start: 0.9605 (t) cc_final: 0.9209 (p) REVERT: F 32 ARG cc_start: 0.8983 (ptp-110) cc_final: 0.8600 (ptp-110) REVERT: F 68 GLU cc_start: 0.7205 (pm20) cc_final: 0.6986 (pm20) REVERT: F 69 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8682 (ttmm) REVERT: F 75 CYS cc_start: 0.9004 (m) cc_final: 0.8582 (p) REVERT: F 76 LYS cc_start: 0.9022 (tmmt) cc_final: 0.8603 (tmmt) REVERT: F 77 ASP cc_start: 0.8059 (t70) cc_final: 0.7280 (p0) REVERT: F 94 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7783 (mm110) REVERT: F 95 ASP cc_start: 0.8784 (p0) cc_final: 0.8286 (p0) REVERT: F 122 ARG cc_start: 0.8219 (tmm160) cc_final: 0.7730 (tmm160) REVERT: G 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8829 (ttt) REVERT: G 29 SER cc_start: 0.9599 (t) cc_final: 0.9207 (p) REVERT: G 32 ARG cc_start: 0.9007 (ptp90) cc_final: 0.8613 (mtm110) REVERT: G 68 GLU cc_start: 0.7816 (pm20) cc_final: 0.7254 (pm20) REVERT: G 69 LYS cc_start: 0.8950 (tppp) cc_final: 0.8664 (tppp) REVERT: G 75 CYS cc_start: 0.9015 (m) cc_final: 0.8585 (p) REVERT: G 76 LYS cc_start: 0.9059 (tmmt) cc_final: 0.8633 (tmmt) REVERT: G 77 ASP cc_start: 0.8099 (t70) cc_final: 0.7343 (p0) REVERT: G 95 ASP cc_start: 0.8494 (p0) cc_final: 0.8234 (p0) REVERT: G 122 ARG cc_start: 0.8223 (tmm160) cc_final: 0.7784 (tmm160) REVERT: G 129 GLU cc_start: 0.8776 (tt0) cc_final: 0.8465 (tt0) REVERT: H 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8812 (ttt) REVERT: H 29 SER cc_start: 0.9589 (t) cc_final: 0.9270 (p) REVERT: H 32 ARG cc_start: 0.9014 (ptp90) cc_final: 0.8726 (mtm110) REVERT: H 68 GLU cc_start: 0.7802 (pm20) cc_final: 0.7231 (pm20) REVERT: H 69 LYS cc_start: 0.8940 (tppp) cc_final: 0.8654 (tppp) REVERT: H 75 CYS cc_start: 0.9006 (m) cc_final: 0.8578 (p) REVERT: H 76 LYS cc_start: 0.9046 (tmmt) cc_final: 0.8612 (tmmt) REVERT: H 77 ASP cc_start: 0.8096 (t70) cc_final: 0.7333 (p0) REVERT: H 95 ASP cc_start: 0.8498 (p0) cc_final: 0.8251 (p0) REVERT: H 122 ARG cc_start: 0.8224 (tmm160) cc_final: 0.7734 (tmm160) REVERT: H 129 GLU cc_start: 0.8797 (tt0) cc_final: 0.8490 (tt0) outliers start: 19 outliers final: 16 residues processed: 228 average time/residue: 0.8092 time to fit residues: 199.9956 Evaluate side-chains 223 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 47 SER 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 47 SER 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 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 161 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.076918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056186 restraints weight = 37458.120| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.05 r_work: 0.2729 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16456 Z= 0.148 Angle : 0.551 8.330 22292 Z= 0.290 Chirality : 0.043 0.152 2500 Planarity : 0.004 0.042 2904 Dihedral : 4.162 27.868 2264 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.06 % Allowed : 13.88 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.19), residues: 2068 helix: 2.05 (0.22), residues: 600 sheet: 0.27 (0.23), residues: 524 loop : -0.32 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 86 TYR 0.029 0.002 TYR F 118 PHE 0.008 0.001 PHE E 127 TRP 0.009 0.001 TRP F 92 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00342 (16456) covalent geometry : angle 0.55125 (22292) hydrogen bonds : bond 0.03610 ( 732) hydrogen bonds : angle 4.61614 ( 2016) ********************** 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 227 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.639 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: 0.9335 (ptm) cc_final: 0.8925 (ptm) REVERT: A 181 ASP cc_start: 0.9037 (t70) cc_final: 0.8587 (t0) REVERT: B 49 MET cc_start: 0.9349 (ptm) cc_final: 0.8986 (ptm) REVERT: B 181 ASP cc_start: 0.9030 (t70) cc_final: 0.8584 (t0) REVERT: C 49 MET cc_start: 0.9356 (ptm) cc_final: 0.8998 (ptm) REVERT: C 181 ASP cc_start: 0.9035 (t70) cc_final: 0.8566 (t0) REVERT: D 49 MET cc_start: 0.9352 (ptm) cc_final: 0.8991 (ptm) REVERT: D 181 ASP cc_start: 0.9039 (t70) cc_final: 0.8577 (t0) REVERT: D 299 SER cc_start: 0.9405 (m) cc_final: 0.9144 (p) REVERT: E 1 MET cc_start: 0.9224 (ttm) cc_final: 0.8881 (ttt) REVERT: E 24 ASP cc_start: 0.8483 (t0) cc_final: 0.8226 (t0) REVERT: E 28 MET cc_start: 0.9111 (tpp) cc_final: 0.8893 (pp-130) REVERT: E 29 SER cc_start: 0.9605 (t) cc_final: 0.9103 (p) REVERT: E 68 GLU cc_start: 0.7554 (pm20) cc_final: 0.7201 (pm20) REVERT: E 69 LYS cc_start: 0.8834 (tppp) cc_final: 0.8419 (ttmm) REVERT: E 75 CYS cc_start: 0.8986 (m) cc_final: 0.8587 (p) REVERT: E 76 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8618 (tmmt) REVERT: E 77 ASP cc_start: 0.8091 (t70) cc_final: 0.7328 (p0) REVERT: E 86 ARG cc_start: 0.9075 (tpp80) cc_final: 0.8717 (tpp80) REVERT: E 95 ASP cc_start: 0.8508 (p0) cc_final: 0.8235 (p0) REVERT: E 122 ARG cc_start: 0.8215 (tmm160) cc_final: 0.7736 (tmm160) REVERT: E 129 GLU cc_start: 0.8796 (tt0) cc_final: 0.8485 (tt0) REVERT: F 1 MET cc_start: 0.9227 (ttm) cc_final: 0.8881 (ttt) REVERT: F 29 SER cc_start: 0.9608 (t) cc_final: 0.9195 (p) REVERT: F 32 ARG cc_start: 0.9008 (ptp-110) cc_final: 0.8602 (ptp-110) REVERT: F 68 GLU cc_start: 0.6998 (pm20) cc_final: 0.6779 (pm20) REVERT: F 69 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8664 (ttmm) REVERT: F 75 CYS cc_start: 0.8976 (m) cc_final: 0.8588 (p) REVERT: F 76 LYS cc_start: 0.9029 (tmmt) cc_final: 0.8611 (tmmt) REVERT: F 77 ASP cc_start: 0.8081 (t70) cc_final: 0.7312 (p0) REVERT: F 94 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7797 (mm110) REVERT: F 95 ASP cc_start: 0.8793 (p0) cc_final: 0.8304 (p0) REVERT: F 122 ARG cc_start: 0.8217 (tmm160) cc_final: 0.7734 (tmm160) REVERT: F 147 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7687 (mtm-85) REVERT: F 148 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7761 (mtm180) REVERT: G 1 MET cc_start: 0.9216 (ttm) cc_final: 0.8926 (ttt) REVERT: G 24 ASP cc_start: 0.8468 (t0) cc_final: 0.8215 (t0) REVERT: G 28 MET cc_start: 0.9097 (tpp) cc_final: 0.8893 (pp-130) REVERT: G 29 SER cc_start: 0.9606 (t) cc_final: 0.9100 (p) REVERT: G 68 GLU cc_start: 0.7614 (pm20) cc_final: 0.7307 (pm20) REVERT: G 69 LYS cc_start: 0.8853 (tppp) cc_final: 0.8444 (ttmm) REVERT: G 75 CYS cc_start: 0.8994 (m) cc_final: 0.8587 (p) REVERT: G 76 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8619 (tmmt) REVERT: G 77 ASP cc_start: 0.8086 (t70) cc_final: 0.7328 (p0) REVERT: G 95 ASP cc_start: 0.8494 (p0) cc_final: 0.8224 (p0) REVERT: G 122 ARG cc_start: 0.8222 (tmm160) cc_final: 0.7785 (tmm160) REVERT: G 129 GLU cc_start: 0.8775 (tt0) cc_final: 0.8528 (tt0) REVERT: H 1 MET cc_start: 0.9228 (ttm) cc_final: 0.8825 (ttt) REVERT: H 29 SER cc_start: 0.9602 (t) cc_final: 0.9314 (p) REVERT: H 32 ARG cc_start: 0.9012 (ptp90) cc_final: 0.8780 (mtm110) REVERT: H 68 GLU cc_start: 0.7617 (pm20) cc_final: 0.7310 (pm20) REVERT: H 69 LYS cc_start: 0.8860 (tppp) cc_final: 0.8311 (ttmm) REVERT: H 75 CYS cc_start: 0.8998 (m) cc_final: 0.8593 (p) REVERT: H 76 LYS cc_start: 0.9018 (tmmt) cc_final: 0.8592 (tmmt) REVERT: H 77 ASP cc_start: 0.8087 (t70) cc_final: 0.7322 (p0) REVERT: H 95 ASP cc_start: 0.8503 (p0) cc_final: 0.8299 (p0) REVERT: H 122 ARG cc_start: 0.8220 (tmm160) cc_final: 0.7731 (tmm160) REVERT: H 129 GLU cc_start: 0.8773 (tt0) cc_final: 0.8467 (tt0) outliers start: 18 outliers final: 16 residues processed: 218 average time/residue: 0.8123 time to fit residues: 192.0569 Evaluate side-chains 222 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 47 SER 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 47 SER 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 125 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 188 optimal weight: 0.0870 chunk 112 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 135 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.077355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055871 restraints weight = 37144.399| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.17 r_work: 0.2733 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16456 Z= 0.132 Angle : 0.549 8.721 22292 Z= 0.290 Chirality : 0.043 0.151 2500 Planarity : 0.004 0.050 2904 Dihedral : 4.110 26.877 2264 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.00 % Allowed : 14.00 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.19), residues: 2068 helix: 2.00 (0.21), residues: 600 sheet: 0.31 (0.23), residues: 524 loop : -0.31 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 32 TYR 0.029 0.002 TYR F 118 PHE 0.031 0.001 PHE F 145 TRP 0.008 0.001 TRP F 92 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00303 (16456) covalent geometry : angle 0.54941 (22292) hydrogen bonds : bond 0.03571 ( 732) hydrogen bonds : angle 4.61230 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5102.92 seconds wall clock time: 88 minutes 11.59 seconds (5291.59 seconds total)