Starting phenix.real_space_refine on Tue Dec 31 16:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bb1_15953/12_2024/8bb1_15953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bb1_15953/12_2024/8bb1_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_15953/12_2024/8bb1_15953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bb1_15953/12_2024/8bb1_15953.map" model { file = "/net/cci-nas-00/data/ceres_data/8bb1_15953/12_2024/8bb1_15953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bb1_15953/12_2024/8bb1_15953.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 88 5.16 5 Cl 4 4.86 5 C 10180 2.51 5 N 2784 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16168 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2895 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1140 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.88, per 1000 atoms: 0.61 Number of scatterers: 16168 At special positions: 0 Unit cell: (123.487, 150.188, 96.7875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 88 16.00 O 3112 8.00 N 2784 7.00 C 10180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.4 seconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 38.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 14 through 34 removed outlier: 3.657A pdb=" N ASP A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.560A pdb=" N THR A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.601A pdb=" N ILE A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.590A pdb=" N MET A 236 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 269 through 288 removed outlier: 4.798A pdb=" N ALA A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 3.555A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 removed outlier: 4.089A pdb=" N ILE A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.737A pdb=" N ALA A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 356 " --> pdb=" O GLU A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 356' Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.707A pdb=" N LYS A 369 " --> pdb=" O PRO A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'B' and resid 14 through 34 removed outlier: 3.659A pdb=" N ASP B 20 " --> pdb=" O ASP B 16 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 135 through 154 removed outlier: 3.558A pdb=" N THR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.601A pdb=" N ILE B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.576A pdb=" N MET B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 269 through 288 removed outlier: 4.794A pdb=" N ALA B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 removed outlier: 3.556A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 removed outlier: 4.093A pdb=" N ILE B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.740A pdb=" N ALA B 355 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.708A pdb=" N LYS B 369 " --> pdb=" O PRO B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 14 through 34 removed outlier: 3.659A pdb=" N ASP C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 76 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 135 through 154 removed outlier: 3.561A pdb=" N THR C 139 " --> pdb=" O PRO C 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.594A pdb=" N ILE C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.575A pdb=" N MET C 236 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 255' Processing helix chain 'C' and resid 269 through 288 removed outlier: 4.795A pdb=" N ALA C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 3.552A pdb=" N LEU C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 removed outlier: 4.092A pdb=" N ILE C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.733A pdb=" N ALA C 355 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 356' Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.729A pdb=" N LYS C 369 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.658A pdb=" N ASP D 20 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 135 through 154 removed outlier: 3.561A pdb=" N THR D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 206 through 211 removed outlier: 3.601A pdb=" N ILE D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.564A pdb=" N MET D 236 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 252 through 255 removed outlier: 4.253A pdb=" N ALA D 255 " --> pdb=" O GLY D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 269 through 288 removed outlier: 4.794A pdb=" N ALA D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 removed outlier: 3.557A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 removed outlier: 4.090A pdb=" N ILE D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.733A pdb=" N ALA D 355 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 356 " --> pdb=" O GLU D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 352 through 356' Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.710A pdb=" N LYS D 369 " --> pdb=" O PRO D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'E' and resid 23 through 41 removed outlier: 3.546A pdb=" N ALA E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 77 through 92 Processing helix chain 'F' and resid 23 through 41 removed outlier: 3.546A pdb=" N ALA F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 77 through 92 Processing helix chain 'G' and resid 23 through 41 removed outlier: 3.545A pdb=" N ALA G 41 " --> pdb=" O THR G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 77 through 92 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.545A pdb=" N ALA H 41 " --> pdb=" O THR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 77 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 5.445A pdb=" N ASP A 163 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN A 171 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE A 180 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP A 173 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 178 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N LYS A 221 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP A 181 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A 223 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 183 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 98 removed outlier: 6.278A pdb=" N VAL A 50 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 94 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL A 52 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY A 96 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY A 54 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLN A 98 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 56 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 127 removed outlier: 3.639A pdb=" N SER A 309 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 10 removed outlier: 5.441A pdb=" N ASP B 163 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B 171 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE B 180 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP B 173 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 178 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N LYS B 221 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 181 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE B 223 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 183 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 98 removed outlier: 6.275A pdb=" N VAL B 50 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 94 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 52 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY B 96 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY B 54 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLN B 98 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE B 56 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.636A pdb=" N SER B 309 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.439A pdb=" N ASP C 163 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN C 171 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE C 180 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP C 173 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL C 178 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N LYS C 221 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP C 181 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N PHE C 223 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 183 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 98 removed outlier: 6.252A pdb=" N VAL C 50 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ALA C 94 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL C 52 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 96 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY C 54 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLN C 98 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 56 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 127 removed outlier: 3.635A pdb=" N SER C 309 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.437A pdb=" N ASP D 163 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN D 171 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE D 180 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASP D 173 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N LYS D 221 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP D 181 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE D 223 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 183 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 98 removed outlier: 6.265A pdb=" N VAL D 50 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA D 94 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL D 52 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY D 96 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY D 54 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN D 98 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 56 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 127 removed outlier: 3.636A pdb=" N SER D 309 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 47 through 54 removed outlier: 6.702A pdb=" N GLU E 49 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ARG E 74 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR E 51 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG E 72 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 126 through 129 Processing sheet with id=AB6, first strand: chain 'F' and resid 47 through 54 removed outlier: 6.700A pdb=" N GLU F 49 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ARG F 74 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR F 51 " --> pdb=" O ARG F 72 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG F 72 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 126 through 129 Processing sheet with id=AB8, first strand: chain 'G' and resid 47 through 54 removed outlier: 6.700A pdb=" N GLU G 49 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG G 74 " --> pdb=" O GLU G 49 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR G 51 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG G 72 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 126 through 129 Processing sheet with id=AC1, first strand: chain 'H' and resid 47 through 54 removed outlier: 6.699A pdb=" N GLU H 49 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG H 74 " --> pdb=" O GLU H 49 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR H 51 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG H 72 " --> pdb=" O THR H 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 126 through 129 732 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 4.73 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: 0.00 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.800 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.830 ------------------------------------------------------------------------------- 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= 0.201 Angle : 0.416 4.829 22292 Z= 0.218 Chirality : 0.041 0.129 2500 Planarity : 0.005 0.055 2904 Dihedral : 10.046 83.678 6016 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.71 % Allowed : 3.41 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2068 helix: 1.25 (0.21), residues: 612 sheet: 0.54 (0.23), residues: 536 loop : -0.29 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 149 HIS 0.003 0.001 HIS D 189 PHE 0.012 0.001 PHE E 127 TYR 0.008 0.001 TYR F 118 ARG 0.013 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 256 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9418 (ptm) cc_final: 0.9094 (ptm) REVERT: A 82 MET cc_start: 0.8881 (mtt) cc_final: 0.8627 (mtm) REVERT: A 181 ASP cc_start: 0.8942 (t70) cc_final: 0.8661 (t0) REVERT: A 299 SER cc_start: 0.9476 (m) cc_final: 0.9238 (p) REVERT: A 311 MET cc_start: 0.9297 (ttp) cc_final: 0.9077 (ttt) REVERT: B 49 MET cc_start: 0.9411 (ptm) cc_final: 0.9104 (ptm) REVERT: B 82 MET cc_start: 0.8909 (mtt) cc_final: 0.8660 (mtm) REVERT: B 181 ASP cc_start: 0.8930 (t70) cc_final: 0.8654 (t0) REVERT: B 299 SER cc_start: 0.9474 (m) cc_final: 0.9227 (p) REVERT: B 311 MET cc_start: 0.9307 (ttp) cc_final: 0.9085 (ttt) REVERT: C 49 MET cc_start: 0.9409 (ptm) cc_final: 0.9106 (ptm) REVERT: C 82 MET cc_start: 0.8881 (mtt) cc_final: 0.8627 (mtm) REVERT: C 181 ASP cc_start: 0.8932 (t70) cc_final: 0.8651 (t0) REVERT: C 299 SER cc_start: 0.9478 (m) cc_final: 0.9250 (p) REVERT: C 311 MET cc_start: 0.9300 (ttp) cc_final: 0.9068 (ttt) REVERT: D 49 MET cc_start: 0.9416 (ptm) cc_final: 0.9117 (ptm) REVERT: D 82 MET cc_start: 0.8882 (mtt) cc_final: 0.8626 (mtm) REVERT: D 181 ASP cc_start: 0.8957 (t70) cc_final: 0.8682 (t0) REVERT: D 299 SER cc_start: 0.9478 (m) cc_final: 0.9234 (p) REVERT: D 311 MET cc_start: 0.9311 (ttp) cc_final: 0.9068 (ttt) REVERT: E 1 MET cc_start: 0.9261 (ttm) cc_final: 0.8789 (ttt) REVERT: E 24 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8383 (t0) REVERT: E 29 SER cc_start: 0.9670 (t) cc_final: 0.9344 (p) REVERT: E 49 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8353 (mt-10) REVERT: E 51 THR cc_start: 0.9220 (p) cc_final: 0.8984 (m) REVERT: E 89 CYS cc_start: 0.7965 (m) cc_final: 0.7587 (m) REVERT: E 129 GLU cc_start: 0.8799 (tt0) cc_final: 0.8398 (tt0) REVERT: F 1 MET cc_start: 0.9266 (ttm) cc_final: 0.8796 (ttt) REVERT: F 24 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8382 (t0) REVERT: F 29 SER cc_start: 0.9670 (t) cc_final: 0.9344 (p) REVERT: F 49 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8356 (mt-10) REVERT: F 51 THR cc_start: 0.9224 (p) cc_final: 0.8989 (m) REVERT: F 89 CYS cc_start: 0.7969 (m) cc_final: 0.7593 (m) REVERT: F 129 GLU cc_start: 0.8801 (tt0) cc_final: 0.8399 (tt0) REVERT: G 1 MET cc_start: 0.9251 (ttm) cc_final: 0.8770 (ttt) REVERT: G 24 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8375 (t0) REVERT: G 29 SER cc_start: 0.9669 (t) cc_final: 0.9340 (p) REVERT: G 49 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8354 (mt-10) REVERT: G 51 THR cc_start: 0.9219 (p) cc_final: 0.8984 (m) REVERT: G 89 CYS cc_start: 0.7967 (m) cc_final: 0.7587 (m) REVERT: G 129 GLU cc_start: 0.8785 (tt0) cc_final: 0.8388 (tt0) REVERT: H 1 MET cc_start: 0.9248 (ttm) cc_final: 0.8787 (ttt) REVERT: H 24 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8376 (t0) REVERT: H 29 SER cc_start: 0.9670 (t) cc_final: 0.9344 (p) REVERT: H 49 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8347 (mt-10) REVERT: H 51 THR cc_start: 0.9218 (p) cc_final: 0.8982 (m) REVERT: H 89 CYS cc_start: 0.7956 (m) cc_final: 0.7574 (m) REVERT: H 129 GLU cc_start: 0.8803 (tt0) cc_final: 0.8401 (tt0) outliers start: 12 outliers final: 4 residues processed: 264 average time/residue: 1.5871 time to fit residues: 456.7017 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 : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain H residue 24 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0970 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 0.0030 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 21 GLN B 14 HIS B 21 GLN C 14 HIS C 21 GLN D 14 HIS D 21 GLN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16456 Z= 0.223 Angle : 0.514 6.064 22292 Z= 0.280 Chirality : 0.043 0.137 2500 Planarity : 0.004 0.031 2904 Dihedral : 4.308 28.244 2272 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.35 % Allowed : 8.47 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2068 helix: 1.94 (0.21), residues: 604 sheet: 0.69 (0.23), residues: 520 loop : -0.34 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 149 HIS 0.003 0.001 HIS A 189 PHE 0.012 0.001 PHE E 127 TYR 0.013 0.001 TYR C 280 ARG 0.008 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9413 (ptm) cc_final: 0.9133 (ptm) REVERT: A 181 ASP cc_start: 0.9055 (t70) cc_final: 0.8792 (t0) REVERT: A 299 SER cc_start: 0.9522 (m) cc_final: 0.9265 (p) REVERT: A 311 MET cc_start: 0.9231 (ttp) cc_final: 0.9016 (ttt) REVERT: B 49 MET cc_start: 0.9399 (ptm) cc_final: 0.9117 (ptm) REVERT: B 181 ASP cc_start: 0.9046 (t70) cc_final: 0.8781 (t0) REVERT: B 299 SER cc_start: 0.9519 (m) cc_final: 0.9257 (p) REVERT: C 49 MET cc_start: 0.9399 (ptm) cc_final: 0.9123 (ptm) REVERT: C 181 ASP cc_start: 0.9044 (t70) cc_final: 0.8779 (t0) REVERT: C 299 SER cc_start: 0.9541 (m) cc_final: 0.9271 (p) REVERT: D 49 MET cc_start: 0.9407 (ptm) cc_final: 0.9128 (ptm) REVERT: D 181 ASP cc_start: 0.9076 (t70) cc_final: 0.8823 (t0) REVERT: D 299 SER cc_start: 0.9522 (m) cc_final: 0.9266 (p) REVERT: E 1 MET cc_start: 0.9218 (ttm) cc_final: 0.8716 (ttt) REVERT: E 28 MET cc_start: 0.9161 (tpp) cc_final: 0.8579 (tpp) REVERT: E 29 SER cc_start: 0.9667 (t) cc_final: 0.9303 (p) REVERT: E 49 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8466 (mt-10) REVERT: E 51 THR cc_start: 0.9330 (p) cc_final: 0.8919 (t) REVERT: E 68 GLU cc_start: 0.8162 (pm20) cc_final: 0.7959 (pm20) REVERT: E 69 LYS cc_start: 0.8825 (mtpm) cc_final: 0.8501 (mtpm) REVERT: E 76 LYS cc_start: 0.9000 (tmmt) cc_final: 0.8524 (tmmt) REVERT: E 77 ASP cc_start: 0.8212 (t70) cc_final: 0.7597 (p0) REVERT: E 89 CYS cc_start: 0.7875 (m) cc_final: 0.7632 (m) REVERT: E 129 GLU cc_start: 0.8842 (tt0) cc_final: 0.8604 (tt0) REVERT: F 1 MET cc_start: 0.9224 (ttm) cc_final: 0.8723 (ttt) REVERT: F 28 MET cc_start: 0.9168 (tpp) cc_final: 0.8587 (tpp) REVERT: F 29 SER cc_start: 0.9666 (t) cc_final: 0.9304 (p) REVERT: F 49 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8478 (mt-10) REVERT: F 51 THR cc_start: 0.9332 (p) cc_final: 0.8919 (t) REVERT: F 68 GLU cc_start: 0.8156 (pm20) cc_final: 0.7934 (pm20) REVERT: F 69 LYS cc_start: 0.8819 (mtpm) cc_final: 0.8494 (mtpm) REVERT: F 76 LYS cc_start: 0.8995 (tmmt) cc_final: 0.8519 (tmmt) REVERT: F 77 ASP cc_start: 0.8221 (t70) cc_final: 0.7620 (p0) REVERT: F 89 CYS cc_start: 0.7888 (m) cc_final: 0.7649 (m) REVERT: F 129 GLU cc_start: 0.8813 (tt0) cc_final: 0.8573 (tt0) REVERT: G 1 MET cc_start: 0.9213 (ttm) cc_final: 0.8718 (ttt) REVERT: G 28 MET cc_start: 0.9160 (tpp) cc_final: 0.8578 (tpp) REVERT: G 29 SER cc_start: 0.9666 (t) cc_final: 0.9301 (p) REVERT: G 49 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8490 (mt-10) REVERT: G 51 THR cc_start: 0.9330 (p) cc_final: 0.8922 (t) REVERT: G 68 GLU cc_start: 0.8158 (pm20) cc_final: 0.7939 (pm20) REVERT: G 69 LYS cc_start: 0.8826 (mtpm) cc_final: 0.8499 (mtpm) REVERT: G 76 LYS cc_start: 0.9001 (tmmt) cc_final: 0.8523 (tmmt) REVERT: G 77 ASP cc_start: 0.8217 (t70) cc_final: 0.7617 (p0) REVERT: G 89 CYS cc_start: 0.7879 (m) cc_final: 0.7636 (m) REVERT: G 129 GLU cc_start: 0.8812 (tt0) cc_final: 0.8573 (tt0) REVERT: H 1 MET cc_start: 0.9207 (ttm) cc_final: 0.8700 (ttt) REVERT: H 28 MET cc_start: 0.9164 (tpp) cc_final: 0.8584 (tpp) REVERT: H 29 SER cc_start: 0.9667 (t) cc_final: 0.9302 (p) REVERT: H 49 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8450 (mt-10) REVERT: H 51 THR cc_start: 0.9328 (p) cc_final: 0.8915 (t) REVERT: H 68 GLU cc_start: 0.8179 (pm20) cc_final: 0.7975 (pm20) REVERT: H 69 LYS cc_start: 0.8819 (mtpm) cc_final: 0.8494 (mtpm) REVERT: H 76 LYS cc_start: 0.9002 (tmmt) cc_final: 0.8528 (tmmt) REVERT: H 77 ASP cc_start: 0.8216 (t70) cc_final: 0.7599 (p0) REVERT: H 89 CYS cc_start: 0.7864 (m) cc_final: 0.7621 (m) REVERT: H 129 GLU cc_start: 0.8814 (tt0) cc_final: 0.8572 (tt0) outliers start: 23 outliers final: 8 residues processed: 224 average time/residue: 1.8014 time to fit residues: 435.6737 Evaluate side-chains 206 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 0.0770 chunk 165 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16456 Z= 0.170 Angle : 0.499 5.973 22292 Z= 0.265 Chirality : 0.043 0.139 2500 Planarity : 0.004 0.035 2904 Dihedral : 4.106 25.965 2264 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.00 % Allowed : 10.41 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2068 helix: 2.06 (0.21), residues: 604 sheet: 0.55 (0.22), residues: 520 loop : -0.27 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 149 HIS 0.006 0.001 HIS B 189 PHE 0.009 0.001 PHE D 5 TYR 0.013 0.001 TYR H 45 ARG 0.007 0.001 ARG G 74 *********************** 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 236 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 2.057 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: 0.9391 (ptm) cc_final: 0.9047 (ptm) REVERT: A 181 ASP cc_start: 0.9070 (t70) cc_final: 0.8800 (t0) REVERT: A 299 SER cc_start: 0.9511 (m) cc_final: 0.9274 (p) REVERT: B 49 MET cc_start: 0.9380 (ptm) cc_final: 0.9023 (ptm) REVERT: B 181 ASP cc_start: 0.9061 (t70) cc_final: 0.8588 (t0) REVERT: B 299 SER cc_start: 0.9506 (m) cc_final: 0.9264 (p) REVERT: C 49 MET cc_start: 0.9381 (ptm) cc_final: 0.9032 (ptm) REVERT: C 181 ASP cc_start: 0.9062 (t70) cc_final: 0.8790 (t0) REVERT: C 299 SER cc_start: 0.9517 (m) cc_final: 0.9272 (p) REVERT: D 49 MET cc_start: 0.9388 (ptm) cc_final: 0.9028 (ptm) REVERT: D 181 ASP cc_start: 0.9077 (t70) cc_final: 0.8578 (t0) REVERT: D 299 SER cc_start: 0.9509 (m) cc_final: 0.9268 (p) REVERT: E 1 MET cc_start: 0.9190 (ttm) cc_final: 0.8755 (ttt) REVERT: E 19 ARG cc_start: 0.9040 (mtp85) cc_final: 0.8813 (mtt-85) REVERT: E 28 MET cc_start: 0.9199 (tpp) cc_final: 0.8589 (tpp) REVERT: E 29 SER cc_start: 0.9682 (t) cc_final: 0.9312 (p) REVERT: E 49 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 51 THR cc_start: 0.9183 (p) cc_final: 0.8959 (t) REVERT: E 68 GLU cc_start: 0.8046 (pm20) cc_final: 0.7816 (pm20) REVERT: E 69 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8430 (mtpp) REVERT: E 76 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8571 (tmmt) REVERT: E 77 ASP cc_start: 0.8131 (t70) cc_final: 0.7394 (p0) REVERT: E 89 CYS cc_start: 0.7848 (m) cc_final: 0.7594 (m) REVERT: E 94 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7842 (mm110) REVERT: E 95 ASP cc_start: 0.8232 (p0) cc_final: 0.7999 (p0) REVERT: E 129 GLU cc_start: 0.8828 (tt0) cc_final: 0.8493 (tt0) REVERT: F 1 MET cc_start: 0.9196 (ttm) cc_final: 0.8764 (ttt) REVERT: F 19 ARG cc_start: 0.9047 (mtp85) cc_final: 0.8818 (mtt-85) REVERT: F 28 MET cc_start: 0.9206 (tpp) cc_final: 0.8609 (tpp) REVERT: F 29 SER cc_start: 0.9682 (t) cc_final: 0.9313 (p) REVERT: F 49 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8672 (mt-10) REVERT: F 51 THR cc_start: 0.9185 (p) cc_final: 0.8961 (t) REVERT: F 68 GLU cc_start: 0.8127 (pm20) cc_final: 0.7869 (pm20) REVERT: F 69 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8425 (mtpp) REVERT: F 76 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8565 (tmmt) REVERT: F 77 ASP cc_start: 0.8142 (t70) cc_final: 0.7405 (p0) REVERT: F 89 CYS cc_start: 0.7853 (m) cc_final: 0.7602 (m) REVERT: F 94 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7838 (mm110) REVERT: F 95 ASP cc_start: 0.8234 (p0) cc_final: 0.7989 (p0) REVERT: F 129 GLU cc_start: 0.8717 (tt0) cc_final: 0.8380 (tt0) REVERT: G 1 MET cc_start: 0.9183 (ttm) cc_final: 0.8751 (ttt) REVERT: G 19 ARG cc_start: 0.9048 (mtp85) cc_final: 0.8816 (mtt-85) REVERT: G 28 MET cc_start: 0.9198 (tpp) cc_final: 0.8598 (tpp) REVERT: G 29 SER cc_start: 0.9681 (t) cc_final: 0.9308 (p) REVERT: G 49 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8657 (mt-10) REVERT: G 51 THR cc_start: 0.9184 (p) cc_final: 0.8963 (t) REVERT: G 68 GLU cc_start: 0.8048 (pm20) cc_final: 0.7809 (pm20) REVERT: G 69 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: G 76 LYS cc_start: 0.9010 (tmmt) cc_final: 0.8572 (tmmt) REVERT: G 77 ASP cc_start: 0.8138 (t70) cc_final: 0.7402 (p0) REVERT: G 89 CYS cc_start: 0.7851 (m) cc_final: 0.7596 (m) REVERT: G 94 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7830 (mm110) REVERT: G 95 ASP cc_start: 0.8270 (p0) cc_final: 0.8001 (p0) REVERT: G 129 GLU cc_start: 0.8715 (tt0) cc_final: 0.8364 (tt0) REVERT: H 1 MET cc_start: 0.9186 (ttm) cc_final: 0.8753 (ttt) REVERT: H 19 ARG cc_start: 0.9051 (mtp85) cc_final: 0.8822 (mtt-85) REVERT: H 28 MET cc_start: 0.9201 (tpp) cc_final: 0.8592 (tpp) REVERT: H 29 SER cc_start: 0.9683 (t) cc_final: 0.9313 (p) REVERT: H 49 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8648 (mt-10) REVERT: H 51 THR cc_start: 0.9181 (p) cc_final: 0.8956 (t) REVERT: H 68 GLU cc_start: 0.8044 (pm20) cc_final: 0.7803 (pm20) REVERT: H 69 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: H 76 LYS cc_start: 0.9010 (tmmt) cc_final: 0.8573 (tmmt) REVERT: H 77 ASP cc_start: 0.8137 (t70) cc_final: 0.7396 (p0) REVERT: H 89 CYS cc_start: 0.7821 (m) cc_final: 0.7566 (m) REVERT: H 94 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7833 (mm110) REVERT: H 95 ASP cc_start: 0.8269 (p0) cc_final: 0.8007 (p0) REVERT: H 129 GLU cc_start: 0.8719 (tt0) cc_final: 0.8378 (tt0) outliers start: 17 outliers final: 12 residues processed: 228 average time/residue: 1.7882 time to fit residues: 441.5413 Evaluate side-chains 218 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 69 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.1980 chunk 139 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 0.0060 chunk 197 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 GLN D 297 GLN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16456 Z= 0.199 Angle : 0.493 5.754 22292 Z= 0.263 Chirality : 0.043 0.136 2500 Planarity : 0.004 0.036 2904 Dihedral : 4.085 26.081 2264 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 10.76 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2068 helix: 2.21 (0.22), residues: 604 sheet: 0.53 (0.23), residues: 520 loop : -0.26 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 92 HIS 0.004 0.001 HIS D 189 PHE 0.009 0.001 PHE E 127 TYR 0.025 0.002 TYR G 118 ARG 0.009 0.001 ARG E 74 *********************** 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 232 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 2.062 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: 0.9407 (ptm) cc_final: 0.9044 (ptm) REVERT: A 181 ASP cc_start: 0.9087 (t70) cc_final: 0.8586 (t0) REVERT: A 203 MET cc_start: 0.9240 (tpp) cc_final: 0.8990 (tpt) REVERT: A 299 SER cc_start: 0.9523 (m) cc_final: 0.9271 (p) REVERT: B 49 MET cc_start: 0.9394 (ptm) cc_final: 0.9020 (ptm) REVERT: B 181 ASP cc_start: 0.9078 (t70) cc_final: 0.8604 (t0) REVERT: B 299 SER cc_start: 0.9519 (m) cc_final: 0.9263 (p) REVERT: C 49 MET cc_start: 0.9394 (ptm) cc_final: 0.9037 (ptm) REVERT: C 181 ASP cc_start: 0.9081 (t70) cc_final: 0.8582 (t0) REVERT: C 299 SER cc_start: 0.9498 (m) cc_final: 0.9266 (p) REVERT: D 49 MET cc_start: 0.9404 (ptm) cc_final: 0.9044 (ptm) REVERT: D 181 ASP cc_start: 0.9091 (t70) cc_final: 0.8609 (t0) REVERT: D 203 MET cc_start: 0.9245 (tpp) cc_final: 0.8991 (tpt) REVERT: D 299 SER cc_start: 0.9494 (m) cc_final: 0.9261 (p) REVERT: E 1 MET cc_start: 0.9166 (ttm) cc_final: 0.8727 (ttt) REVERT: E 28 MET cc_start: 0.9197 (tpp) cc_final: 0.8642 (tpt) REVERT: E 29 SER cc_start: 0.9671 (t) cc_final: 0.9302 (p) REVERT: E 49 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8661 (mt-10) REVERT: E 51 THR cc_start: 0.9176 (p) cc_final: 0.8787 (t) REVERT: E 68 GLU cc_start: 0.8087 (pm20) cc_final: 0.7835 (pm20) REVERT: E 69 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: E 76 LYS cc_start: 0.8992 (tmmt) cc_final: 0.8536 (tmmt) REVERT: E 77 ASP cc_start: 0.8122 (t70) cc_final: 0.7397 (p0) REVERT: E 89 CYS cc_start: 0.7688 (m) cc_final: 0.7479 (m) REVERT: E 94 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7835 (mm110) REVERT: E 95 ASP cc_start: 0.8386 (p0) cc_final: 0.8087 (p0) REVERT: E 122 ARG cc_start: 0.8167 (tmm160) cc_final: 0.7746 (tmm160) REVERT: F 1 MET cc_start: 0.9170 (ttm) cc_final: 0.8755 (ttt) REVERT: F 19 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8781 (mtt-85) REVERT: F 28 MET cc_start: 0.9202 (tpp) cc_final: 0.8648 (tpt) REVERT: F 29 SER cc_start: 0.9672 (t) cc_final: 0.9304 (p) REVERT: F 49 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8672 (mt-10) REVERT: F 51 THR cc_start: 0.9177 (p) cc_final: 0.8786 (t) REVERT: F 68 GLU cc_start: 0.8094 (pm20) cc_final: 0.7825 (pm20) REVERT: F 69 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8324 (mtpp) REVERT: F 76 LYS cc_start: 0.8983 (tmmt) cc_final: 0.8525 (tmmt) REVERT: F 77 ASP cc_start: 0.8135 (t70) cc_final: 0.7412 (p0) REVERT: F 89 CYS cc_start: 0.7696 (m) cc_final: 0.7483 (m) REVERT: F 94 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7860 (mm110) REVERT: F 95 ASP cc_start: 0.8388 (p0) cc_final: 0.8081 (p0) REVERT: F 122 ARG cc_start: 0.8171 (tmm160) cc_final: 0.7747 (tmm160) REVERT: F 129 GLU cc_start: 0.8825 (tt0) cc_final: 0.8510 (tt0) REVERT: G 1 MET cc_start: 0.9167 (ttm) cc_final: 0.8756 (ttt) REVERT: G 28 MET cc_start: 0.9195 (tpp) cc_final: 0.8640 (tpt) REVERT: G 29 SER cc_start: 0.9670 (t) cc_final: 0.9299 (p) REVERT: G 49 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8677 (mt-10) REVERT: G 51 THR cc_start: 0.9173 (p) cc_final: 0.8790 (t) REVERT: G 68 GLU cc_start: 0.8088 (pm20) cc_final: 0.7829 (pm20) REVERT: G 69 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: G 76 LYS cc_start: 0.8990 (tmmt) cc_final: 0.8534 (tmmt) REVERT: G 77 ASP cc_start: 0.8129 (t70) cc_final: 0.7407 (p0) REVERT: G 89 CYS cc_start: 0.7687 (m) cc_final: 0.7473 (m) REVERT: G 94 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7827 (mm110) REVERT: G 95 ASP cc_start: 0.8378 (p0) cc_final: 0.8045 (p0) REVERT: G 122 ARG cc_start: 0.8207 (tmm160) cc_final: 0.7781 (tmm160) REVERT: G 129 GLU cc_start: 0.8824 (tt0) cc_final: 0.8490 (tt0) REVERT: H 1 MET cc_start: 0.9161 (ttm) cc_final: 0.8736 (ttt) REVERT: H 28 MET cc_start: 0.9194 (tpp) cc_final: 0.8642 (tpt) REVERT: H 29 SER cc_start: 0.9673 (t) cc_final: 0.9303 (p) REVERT: H 49 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8680 (mt-10) REVERT: H 51 THR cc_start: 0.9173 (p) cc_final: 0.8778 (t) REVERT: H 68 GLU cc_start: 0.8084 (pm20) cc_final: 0.7824 (pm20) REVERT: H 69 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: H 76 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8534 (tmmt) REVERT: H 77 ASP cc_start: 0.8124 (t70) cc_final: 0.7397 (p0) REVERT: H 89 CYS cc_start: 0.7659 (m) cc_final: 0.7446 (m) REVERT: H 94 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7830 (mm110) REVERT: H 95 ASP cc_start: 0.8381 (p0) cc_final: 0.8041 (p0) REVERT: H 122 ARG cc_start: 0.8175 (tmm160) cc_final: 0.7754 (tmm160) REVERT: H 129 GLU cc_start: 0.8828 (tt0) cc_final: 0.8509 (tt0) outliers start: 24 outliers final: 9 residues processed: 223 average time/residue: 1.7150 time to fit residues: 415.1428 Evaluate side-chains 218 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 69 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16456 Z= 0.201 Angle : 0.491 5.734 22292 Z= 0.262 Chirality : 0.043 0.136 2500 Planarity : 0.004 0.038 2904 Dihedral : 4.081 26.423 2264 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.76 % Allowed : 11.35 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 2068 helix: 2.27 (0.22), residues: 600 sheet: 0.50 (0.23), residues: 520 loop : -0.29 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 92 HIS 0.003 0.001 HIS D 189 PHE 0.009 0.001 PHE G 127 TYR 0.013 0.001 TYR F 45 ARG 0.008 0.001 ARG G 74 *********************** 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 222 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 2.033 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: 0.9408 (ptm) cc_final: 0.9031 (ptm) REVERT: A 181 ASP cc_start: 0.9099 (t70) cc_final: 0.8868 (t0) REVERT: A 203 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9026 (tpt) REVERT: A 299 SER cc_start: 0.9508 (m) cc_final: 0.9262 (p) REVERT: B 49 MET cc_start: 0.9396 (ptm) cc_final: 0.9016 (ptm) REVERT: B 181 ASP cc_start: 0.9076 (t70) cc_final: 0.8625 (t0) REVERT: B 299 SER cc_start: 0.9505 (m) cc_final: 0.9253 (p) REVERT: C 49 MET cc_start: 0.9394 (ptm) cc_final: 0.9059 (ptm) REVERT: C 181 ASP cc_start: 0.9092 (t70) cc_final: 0.8862 (t0) REVERT: C 299 SER cc_start: 0.9513 (m) cc_final: 0.9277 (p) REVERT: D 49 MET cc_start: 0.9398 (ptm) cc_final: 0.9043 (ptm) REVERT: D 181 ASP cc_start: 0.9100 (t70) cc_final: 0.8661 (t0) REVERT: D 203 MET cc_start: 0.9275 (tpp) cc_final: 0.9031 (tpt) REVERT: D 299 SER cc_start: 0.9495 (m) cc_final: 0.9265 (p) REVERT: E 1 MET cc_start: 0.9170 (ttm) cc_final: 0.8743 (ttt) REVERT: E 28 MET cc_start: 0.9209 (tpp) cc_final: 0.8667 (tpp) REVERT: E 29 SER cc_start: 0.9692 (t) cc_final: 0.9318 (p) REVERT: E 49 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8678 (mt-10) REVERT: E 51 THR cc_start: 0.9138 (p) cc_final: 0.8861 (t) REVERT: E 68 GLU cc_start: 0.8098 (pm20) cc_final: 0.7800 (pm20) REVERT: E 76 LYS cc_start: 0.9004 (tmmt) cc_final: 0.8520 (tmmt) REVERT: E 77 ASP cc_start: 0.8124 (t70) cc_final: 0.7399 (p0) REVERT: E 89 CYS cc_start: 0.7753 (m) cc_final: 0.7530 (m) REVERT: E 94 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7835 (mm110) REVERT: E 95 ASP cc_start: 0.8472 (p0) cc_final: 0.8149 (p0) REVERT: E 122 ARG cc_start: 0.8199 (tmm160) cc_final: 0.7753 (tmm160) REVERT: E 129 GLU cc_start: 0.8765 (tt0) cc_final: 0.8480 (tt0) REVERT: F 1 MET cc_start: 0.9179 (ttm) cc_final: 0.8751 (ttt) REVERT: F 28 MET cc_start: 0.9212 (tpp) cc_final: 0.8674 (tpp) REVERT: F 29 SER cc_start: 0.9672 (t) cc_final: 0.9319 (p) REVERT: F 49 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8683 (mt-10) REVERT: F 51 THR cc_start: 0.9136 (p) cc_final: 0.8852 (t) REVERT: F 68 GLU cc_start: 0.8067 (pm20) cc_final: 0.7774 (pm20) REVERT: F 76 LYS cc_start: 0.8996 (tmmt) cc_final: 0.8511 (tmmt) REVERT: F 77 ASP cc_start: 0.8146 (t70) cc_final: 0.7430 (p0) REVERT: F 89 CYS cc_start: 0.7727 (m) cc_final: 0.7514 (m) REVERT: F 122 ARG cc_start: 0.8202 (tmm160) cc_final: 0.7754 (tmm160) REVERT: F 129 GLU cc_start: 0.8820 (tt0) cc_final: 0.8494 (tt0) REVERT: F 148 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7561 (mtm180) REVERT: G 1 MET cc_start: 0.9170 (ttm) cc_final: 0.8743 (ttt) REVERT: G 28 MET cc_start: 0.9206 (tpp) cc_final: 0.8664 (tpp) REVERT: G 29 SER cc_start: 0.9701 (t) cc_final: 0.9336 (p) REVERT: G 49 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8679 (mt-10) REVERT: G 51 THR cc_start: 0.9137 (p) cc_final: 0.8871 (t) REVERT: G 68 GLU cc_start: 0.8098 (pm20) cc_final: 0.7800 (pm20) REVERT: G 76 LYS cc_start: 0.9004 (tmmt) cc_final: 0.8520 (tmmt) REVERT: G 77 ASP cc_start: 0.8129 (t70) cc_final: 0.7407 (p0) REVERT: G 89 CYS cc_start: 0.7744 (m) cc_final: 0.7527 (m) REVERT: G 94 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7825 (mm110) REVERT: G 95 ASP cc_start: 0.8467 (p0) cc_final: 0.8114 (p0) REVERT: G 122 ARG cc_start: 0.8201 (tmm160) cc_final: 0.7752 (tmm160) REVERT: G 129 GLU cc_start: 0.8820 (tt0) cc_final: 0.8509 (tt0) REVERT: G 148 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7562 (mtm180) REVERT: H 1 MET cc_start: 0.9171 (ttm) cc_final: 0.8756 (ttt) REVERT: H 28 MET cc_start: 0.9208 (tpp) cc_final: 0.8668 (tpp) REVERT: H 29 SER cc_start: 0.9703 (t) cc_final: 0.9339 (p) REVERT: H 49 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8679 (mt-10) REVERT: H 51 THR cc_start: 0.9137 (p) cc_final: 0.8872 (t) REVERT: H 68 GLU cc_start: 0.8086 (pm20) cc_final: 0.7785 (pm20) REVERT: H 76 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8518 (tmmt) REVERT: H 77 ASP cc_start: 0.8138 (t70) cc_final: 0.7419 (p0) REVERT: H 89 CYS cc_start: 0.7708 (m) cc_final: 0.7495 (m) REVERT: H 94 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7827 (mm110) REVERT: H 95 ASP cc_start: 0.8467 (p0) cc_final: 0.8115 (p0) REVERT: H 122 ARG cc_start: 0.8205 (tmm160) cc_final: 0.7761 (tmm160) REVERT: H 129 GLU cc_start: 0.8823 (tt0) cc_final: 0.8495 (tt0) outliers start: 13 outliers final: 11 residues processed: 217 average time/residue: 1.7718 time to fit residues: 416.3160 Evaluate side-chains 214 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 203 MET 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 66 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 197 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16456 Z= 0.247 Angle : 0.520 6.336 22292 Z= 0.274 Chirality : 0.043 0.136 2500 Planarity : 0.004 0.038 2904 Dihedral : 4.135 27.995 2264 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.29 % Allowed : 11.29 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 2068 helix: 2.25 (0.22), residues: 600 sheet: 0.24 (0.22), residues: 544 loop : -0.18 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 149 HIS 0.002 0.001 HIS A 189 PHE 0.009 0.001 PHE H 127 TYR 0.026 0.002 TYR F 118 ARG 0.009 0.001 ARG E 74 *********************** 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 232 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.9422 (ptm) cc_final: 0.9038 (ptm) REVERT: A 181 ASP cc_start: 0.9106 (t70) cc_final: 0.8875 (t0) REVERT: A 203 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8965 (mmm) REVERT: A 299 SER cc_start: 0.9513 (m) cc_final: 0.9263 (p) REVERT: B 49 MET cc_start: 0.9415 (ptm) cc_final: 0.9028 (ptm) REVERT: B 181 ASP cc_start: 0.9083 (t70) cc_final: 0.8637 (t0) REVERT: B 299 SER cc_start: 0.9509 (m) cc_final: 0.9253 (p) REVERT: C 49 MET cc_start: 0.9409 (ptm) cc_final: 0.9063 (ptm) REVERT: C 181 ASP cc_start: 0.9097 (t70) cc_final: 0.8645 (t0) REVERT: C 299 SER cc_start: 0.9508 (m) cc_final: 0.9270 (p) REVERT: D 49 MET cc_start: 0.9412 (ptm) cc_final: 0.9027 (ptm) REVERT: D 181 ASP cc_start: 0.9107 (t70) cc_final: 0.8673 (t0) REVERT: D 203 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8970 (mmm) REVERT: D 299 SER cc_start: 0.9502 (m) cc_final: 0.9264 (p) REVERT: E 1 MET cc_start: 0.9157 (ttm) cc_final: 0.8732 (ttt) REVERT: E 29 SER cc_start: 0.9685 (t) cc_final: 0.9305 (p) REVERT: E 49 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8674 (mt-10) REVERT: E 68 GLU cc_start: 0.8028 (pm20) cc_final: 0.7305 (pm20) REVERT: E 69 LYS cc_start: 0.8990 (tppp) cc_final: 0.8589 (mtpp) REVERT: E 76 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8549 (tmmt) REVERT: E 77 ASP cc_start: 0.8099 (t70) cc_final: 0.7341 (p0) REVERT: E 89 CYS cc_start: 0.7758 (m) cc_final: 0.7539 (m) REVERT: E 122 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7713 (tmm160) REVERT: E 129 GLU cc_start: 0.8751 (tt0) cc_final: 0.8451 (tt0) REVERT: F 1 MET cc_start: 0.9162 (ttm) cc_final: 0.8735 (ttt) REVERT: F 29 SER cc_start: 0.9687 (t) cc_final: 0.9297 (p) REVERT: F 49 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8679 (mt-10) REVERT: F 68 GLU cc_start: 0.8047 (pm20) cc_final: 0.7315 (pm20) REVERT: F 69 LYS cc_start: 0.8982 (tppp) cc_final: 0.8577 (mtpp) REVERT: F 76 LYS cc_start: 0.9007 (tmmt) cc_final: 0.8542 (tmmt) REVERT: F 77 ASP cc_start: 0.8112 (t70) cc_final: 0.7359 (p0) REVERT: F 89 CYS cc_start: 0.7762 (m) cc_final: 0.7547 (m) REVERT: F 122 ARG cc_start: 0.8179 (tmm160) cc_final: 0.7714 (tmm160) REVERT: F 129 GLU cc_start: 0.8828 (tt0) cc_final: 0.8499 (tt0) REVERT: G 1 MET cc_start: 0.9152 (ttm) cc_final: 0.8723 (ttt) REVERT: G 29 SER cc_start: 0.9684 (t) cc_final: 0.9287 (p) REVERT: G 49 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8685 (mt-10) REVERT: G 68 GLU cc_start: 0.8045 (pm20) cc_final: 0.7757 (pm20) REVERT: G 69 LYS cc_start: 0.9001 (tppp) cc_final: 0.8592 (mtpp) REVERT: G 76 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8550 (tmmt) REVERT: G 77 ASP cc_start: 0.8104 (t70) cc_final: 0.7354 (p0) REVERT: G 89 CYS cc_start: 0.7747 (m) cc_final: 0.7527 (m) REVERT: G 94 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7737 (mm110) REVERT: G 95 ASP cc_start: 0.8489 (p0) cc_final: 0.8126 (p0) REVERT: G 122 ARG cc_start: 0.8199 (tmm160) cc_final: 0.7716 (tmm160) REVERT: G 129 GLU cc_start: 0.8826 (tt0) cc_final: 0.8498 (tt0) REVERT: H 1 MET cc_start: 0.9152 (ttm) cc_final: 0.8729 (ttt) REVERT: H 29 SER cc_start: 0.9685 (t) cc_final: 0.9289 (p) REVERT: H 49 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8675 (mt-10) REVERT: H 68 GLU cc_start: 0.8029 (pm20) cc_final: 0.7740 (pm20) REVERT: H 69 LYS cc_start: 0.8996 (tppp) cc_final: 0.8588 (mtpp) REVERT: H 76 LYS cc_start: 0.9012 (tmmt) cc_final: 0.8547 (tmmt) REVERT: H 77 ASP cc_start: 0.8104 (t70) cc_final: 0.7346 (p0) REVERT: H 89 CYS cc_start: 0.7719 (m) cc_final: 0.7504 (m) REVERT: H 94 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7733 (mm110) REVERT: H 95 ASP cc_start: 0.8490 (p0) cc_final: 0.8131 (p0) REVERT: H 122 ARG cc_start: 0.8184 (tmm160) cc_final: 0.7721 (tmm160) REVERT: H 129 GLU cc_start: 0.8829 (tt0) cc_final: 0.8499 (tt0) outliers start: 22 outliers final: 17 residues processed: 219 average time/residue: 1.6384 time to fit residues: 390.2735 Evaluate side-chains 222 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 203 MET 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 203 MET 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 6 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 196 optimal weight: 0.1980 chunk 123 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 94 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.003 0.034 16456 Z= 0.189 Angle : 0.519 7.131 22292 Z= 0.272 Chirality : 0.042 0.137 2500 Planarity : 0.004 0.038 2904 Dihedral : 4.051 26.443 2264 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.29 % Allowed : 12.53 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2068 helix: 2.31 (0.22), residues: 600 sheet: 0.18 (0.22), residues: 544 loop : -0.19 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 149 HIS 0.002 0.001 HIS D 189 PHE 0.008 0.001 PHE A 5 TYR 0.027 0.001 TYR G 118 ARG 0.009 0.001 ARG E 74 *********************** 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 229 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 1.956 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: 0.9387 (ptm) cc_final: 0.9056 (ptm) REVERT: A 181 ASP cc_start: 0.9095 (t70) cc_final: 0.8650 (t0) REVERT: A 203 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8985 (mmm) REVERT: A 299 SER cc_start: 0.9483 (m) cc_final: 0.9275 (p) REVERT: B 49 MET cc_start: 0.9389 (ptm) cc_final: 0.9066 (ptm) REVERT: B 181 ASP cc_start: 0.9086 (t70) cc_final: 0.8645 (t0) REVERT: B 299 SER cc_start: 0.9480 (m) cc_final: 0.9267 (p) REVERT: C 49 MET cc_start: 0.9384 (ptm) cc_final: 0.9064 (ptm) REVERT: C 181 ASP cc_start: 0.9085 (t70) cc_final: 0.8642 (t0) REVERT: C 299 SER cc_start: 0.9503 (m) cc_final: 0.9278 (p) REVERT: D 49 MET cc_start: 0.9390 (ptm) cc_final: 0.9030 (ptm) REVERT: D 181 ASP cc_start: 0.9096 (t70) cc_final: 0.8668 (t0) REVERT: D 203 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8676 (tpp) REVERT: D 299 SER cc_start: 0.9498 (m) cc_final: 0.9272 (p) REVERT: E 1 MET cc_start: 0.9167 (ttm) cc_final: 0.8747 (ttt) REVERT: E 28 MET cc_start: 0.9205 (tpp) cc_final: 0.8647 (tpt) REVERT: E 29 SER cc_start: 0.9674 (t) cc_final: 0.9308 (p) REVERT: E 49 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8709 (mt-10) REVERT: E 68 GLU cc_start: 0.7953 (pm20) cc_final: 0.7295 (pm20) REVERT: E 69 LYS cc_start: 0.8961 (tppp) cc_final: 0.8550 (mtpp) REVERT: E 75 CYS cc_start: 0.9054 (m) cc_final: 0.8543 (p) REVERT: E 76 LYS cc_start: 0.9022 (tmmt) cc_final: 0.8573 (tmmt) REVERT: E 77 ASP cc_start: 0.8060 (t70) cc_final: 0.7248 (p0) REVERT: E 89 CYS cc_start: 0.7764 (m) cc_final: 0.7536 (m) REVERT: E 122 ARG cc_start: 0.8181 (tmm160) cc_final: 0.7754 (tmm160) REVERT: E 129 GLU cc_start: 0.8730 (tt0) cc_final: 0.8428 (tt0) REVERT: F 1 MET cc_start: 0.9175 (ttm) cc_final: 0.8752 (ttt) REVERT: F 28 MET cc_start: 0.9213 (tpp) cc_final: 0.8656 (tpt) REVERT: F 29 SER cc_start: 0.9676 (t) cc_final: 0.9314 (p) REVERT: F 49 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8713 (mt-10) REVERT: F 68 GLU cc_start: 0.7966 (pm20) cc_final: 0.7668 (pm20) REVERT: F 69 LYS cc_start: 0.8981 (tppp) cc_final: 0.8577 (mtpp) REVERT: F 75 CYS cc_start: 0.9047 (m) cc_final: 0.8564 (p) REVERT: F 76 LYS cc_start: 0.9014 (tmmt) cc_final: 0.8567 (tmmt) REVERT: F 77 ASP cc_start: 0.8074 (t70) cc_final: 0.7265 (p0) REVERT: F 89 CYS cc_start: 0.7722 (m) cc_final: 0.7509 (m) REVERT: F 122 ARG cc_start: 0.8166 (tmm160) cc_final: 0.7750 (tmm160) REVERT: F 129 GLU cc_start: 0.8839 (tt0) cc_final: 0.8512 (tt0) REVERT: G 1 MET cc_start: 0.9163 (ttm) cc_final: 0.8740 (ttt) REVERT: G 28 MET cc_start: 0.9201 (tpp) cc_final: 0.8643 (tpt) REVERT: G 29 SER cc_start: 0.9676 (t) cc_final: 0.9308 (p) REVERT: G 49 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8704 (mt-10) REVERT: G 68 GLU cc_start: 0.8027 (pm20) cc_final: 0.7718 (pm20) REVERT: G 69 LYS cc_start: 0.8976 (tppp) cc_final: 0.8557 (mtpp) REVERT: G 75 CYS cc_start: 0.9048 (m) cc_final: 0.8549 (p) REVERT: G 76 LYS cc_start: 0.9021 (tmmt) cc_final: 0.8574 (tmmt) REVERT: G 77 ASP cc_start: 0.8078 (t70) cc_final: 0.7265 (p0) REVERT: G 89 CYS cc_start: 0.7726 (m) cc_final: 0.7499 (m) REVERT: G 122 ARG cc_start: 0.8206 (tmm160) cc_final: 0.7776 (tmm160) REVERT: G 129 GLU cc_start: 0.8836 (tt0) cc_final: 0.8511 (tt0) REVERT: H 1 MET cc_start: 0.9162 (ttm) cc_final: 0.8748 (ttt) REVERT: H 28 MET cc_start: 0.9201 (tpp) cc_final: 0.8644 (tpt) REVERT: H 29 SER cc_start: 0.9677 (t) cc_final: 0.9311 (p) REVERT: H 49 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8707 (mt-10) REVERT: H 68 GLU cc_start: 0.8016 (pm20) cc_final: 0.7707 (pm20) REVERT: H 69 LYS cc_start: 0.8971 (tppp) cc_final: 0.8551 (mtpp) REVERT: H 75 CYS cc_start: 0.9054 (m) cc_final: 0.8544 (p) REVERT: H 76 LYS cc_start: 0.9021 (tmmt) cc_final: 0.8573 (tmmt) REVERT: H 77 ASP cc_start: 0.8065 (t70) cc_final: 0.7253 (p0) REVERT: H 89 CYS cc_start: 0.7692 (m) cc_final: 0.7464 (m) REVERT: H 122 ARG cc_start: 0.8188 (tmm160) cc_final: 0.7760 (tmm160) REVERT: H 129 GLU cc_start: 0.8837 (tt0) cc_final: 0.8513 (tt0) outliers start: 22 outliers final: 16 residues processed: 223 average time/residue: 1.6259 time to fit residues: 395.3989 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 : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 MET 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 203 MET 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 121 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.0570 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 GLN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16456 Z= 0.227 Angle : 0.540 8.647 22292 Z= 0.282 Chirality : 0.043 0.135 2500 Planarity : 0.004 0.041 2904 Dihedral : 4.082 27.054 2264 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.00 % Allowed : 12.53 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2068 helix: 2.27 (0.22), residues: 600 sheet: 0.17 (0.22), residues: 544 loop : -0.21 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 92 HIS 0.002 0.000 HIS D 189 PHE 0.009 0.001 PHE F 127 TYR 0.028 0.002 TYR E 118 ARG 0.009 0.001 ARG H 74 *********************** 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 223 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 2.032 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: 0.9413 (ptm) cc_final: 0.9035 (ptm) REVERT: A 181 ASP cc_start: 0.9097 (t70) cc_final: 0.8650 (t0) REVERT: A 203 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8974 (mmm) REVERT: A 299 SER cc_start: 0.9494 (m) cc_final: 0.9264 (p) REVERT: B 49 MET cc_start: 0.9406 (ptm) cc_final: 0.9067 (ptm) REVERT: B 181 ASP cc_start: 0.9088 (t70) cc_final: 0.8648 (t0) REVERT: B 299 SER cc_start: 0.9495 (m) cc_final: 0.9263 (p) REVERT: C 49 MET cc_start: 0.9398 (ptm) cc_final: 0.9064 (ptm) REVERT: C 181 ASP cc_start: 0.9083 (t70) cc_final: 0.8638 (t0) REVERT: C 299 SER cc_start: 0.9485 (m) cc_final: 0.9244 (p) REVERT: D 49 MET cc_start: 0.9407 (ptm) cc_final: 0.9071 (ptm) REVERT: D 181 ASP cc_start: 0.9098 (t70) cc_final: 0.8667 (t0) REVERT: D 203 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8978 (mmm) REVERT: D 299 SER cc_start: 0.9477 (m) cc_final: 0.9235 (p) REVERT: E 1 MET cc_start: 0.9147 (ttm) cc_final: 0.8726 (ttt) REVERT: E 28 MET cc_start: 0.9200 (tpp) cc_final: 0.8640 (tpt) REVERT: E 29 SER cc_start: 0.9667 (t) cc_final: 0.9307 (p) REVERT: E 49 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8747 (mt-10) REVERT: E 68 GLU cc_start: 0.7890 (pm20) cc_final: 0.7585 (pm20) REVERT: E 69 LYS cc_start: 0.8974 (tppp) cc_final: 0.8679 (tppp) REVERT: E 75 CYS cc_start: 0.9054 (m) cc_final: 0.8541 (p) REVERT: E 76 LYS cc_start: 0.9024 (tmmt) cc_final: 0.8569 (tmmt) REVERT: E 77 ASP cc_start: 0.8015 (t70) cc_final: 0.7239 (p0) REVERT: E 122 ARG cc_start: 0.8180 (tmm160) cc_final: 0.7766 (tmm160) REVERT: E 129 GLU cc_start: 0.8748 (tt0) cc_final: 0.8449 (tt0) REVERT: F 1 MET cc_start: 0.9162 (ttm) cc_final: 0.8737 (ttt) REVERT: F 28 MET cc_start: 0.9208 (tpp) cc_final: 0.8648 (tpt) REVERT: F 29 SER cc_start: 0.9670 (t) cc_final: 0.9312 (p) REVERT: F 68 GLU cc_start: 0.7927 (pm20) cc_final: 0.7602 (pm20) REVERT: F 69 LYS cc_start: 0.8967 (tppp) cc_final: 0.8675 (tppp) REVERT: F 75 CYS cc_start: 0.9059 (m) cc_final: 0.8552 (p) REVERT: F 76 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8563 (tmmt) REVERT: F 77 ASP cc_start: 0.8030 (t70) cc_final: 0.7256 (p0) REVERT: F 89 CYS cc_start: 0.7744 (m) cc_final: 0.7522 (m) REVERT: F 122 ARG cc_start: 0.8185 (tmm160) cc_final: 0.7766 (tmm160) REVERT: F 129 GLU cc_start: 0.8833 (tt0) cc_final: 0.8520 (tt0) REVERT: G 1 MET cc_start: 0.9153 (ttm) cc_final: 0.8730 (ttt) REVERT: G 28 MET cc_start: 0.9200 (tpp) cc_final: 0.8641 (tpt) REVERT: G 29 SER cc_start: 0.9668 (t) cc_final: 0.9305 (p) REVERT: G 49 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8745 (mt-10) REVERT: G 68 GLU cc_start: 0.7938 (pm20) cc_final: 0.7627 (pm20) REVERT: G 69 LYS cc_start: 0.8964 (tppp) cc_final: 0.8669 (tppp) REVERT: G 75 CYS cc_start: 0.9053 (m) cc_final: 0.8548 (p) REVERT: G 76 LYS cc_start: 0.9016 (tmmt) cc_final: 0.8558 (tmmt) REVERT: G 77 ASP cc_start: 0.8016 (t70) cc_final: 0.7243 (p0) REVERT: G 89 CYS cc_start: 0.7813 (m) cc_final: 0.7609 (m) REVERT: G 122 ARG cc_start: 0.8188 (tmm160) cc_final: 0.7767 (tmm160) REVERT: G 129 GLU cc_start: 0.8832 (tt0) cc_final: 0.8521 (tt0) REVERT: H 1 MET cc_start: 0.9152 (ttm) cc_final: 0.8741 (ttt) REVERT: H 28 MET cc_start: 0.9200 (tpp) cc_final: 0.8641 (tpt) REVERT: H 29 SER cc_start: 0.9670 (t) cc_final: 0.9309 (p) REVERT: H 49 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8728 (mt-10) REVERT: H 68 GLU cc_start: 0.7954 (pm20) cc_final: 0.7644 (pm20) REVERT: H 69 LYS cc_start: 0.8967 (tppp) cc_final: 0.8669 (tppp) REVERT: H 75 CYS cc_start: 0.9054 (m) cc_final: 0.8540 (p) REVERT: H 76 LYS cc_start: 0.9022 (tmmt) cc_final: 0.8567 (tmmt) REVERT: H 77 ASP cc_start: 0.8017 (t70) cc_final: 0.7239 (p0) REVERT: H 89 CYS cc_start: 0.7776 (m) cc_final: 0.7573 (m) REVERT: H 122 ARG cc_start: 0.8189 (tmm160) cc_final: 0.7772 (tmm160) REVERT: H 129 GLU cc_start: 0.8750 (tt0) cc_final: 0.8429 (tt0) outliers start: 17 outliers final: 15 residues processed: 216 average time/residue: 1.7017 time to fit residues: 404.6943 Evaluate side-chains 221 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 MET 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 203 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 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 188 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 94 GLN G 152 GLN H 94 GLN H 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16456 Z= 0.207 Angle : 0.539 9.298 22292 Z= 0.282 Chirality : 0.042 0.139 2500 Planarity : 0.004 0.043 2904 Dihedral : 4.038 26.241 2264 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.06 % Allowed : 12.71 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2068 helix: 2.32 (0.22), residues: 600 sheet: 0.15 (0.22), residues: 544 loop : -0.23 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 149 HIS 0.002 0.000 HIS D 189 PHE 0.008 0.001 PHE E 127 TYR 0.028 0.002 TYR G 118 ARG 0.009 0.001 ARG F 74 *********************** 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 229 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.848 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: 0.9389 (ptm) cc_final: 0.9057 (ptm) REVERT: A 181 ASP cc_start: 0.9087 (t70) cc_final: 0.8643 (t0) REVERT: A 203 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8983 (mmm) REVERT: B 49 MET cc_start: 0.9393 (ptm) cc_final: 0.9069 (ptm) REVERT: B 181 ASP cc_start: 0.9078 (t70) cc_final: 0.8663 (t0) REVERT: C 49 MET cc_start: 0.9385 (ptm) cc_final: 0.9065 (ptm) REVERT: C 181 ASP cc_start: 0.9070 (t70) cc_final: 0.8646 (t0) REVERT: C 299 SER cc_start: 0.9477 (m) cc_final: 0.9273 (p) REVERT: D 49 MET cc_start: 0.9394 (ptm) cc_final: 0.9073 (ptm) REVERT: D 181 ASP cc_start: 0.9088 (t70) cc_final: 0.8661 (t0) REVERT: D 203 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8984 (mmm) REVERT: D 299 SER cc_start: 0.9478 (m) cc_final: 0.9277 (p) REVERT: E 1 MET cc_start: 0.9151 (ttm) cc_final: 0.8731 (ttt) REVERT: E 28 MET cc_start: 0.9190 (tpp) cc_final: 0.8627 (tpt) REVERT: E 29 SER cc_start: 0.9677 (t) cc_final: 0.9310 (p) REVERT: E 68 GLU cc_start: 0.7816 (pm20) cc_final: 0.7498 (pm20) REVERT: E 69 LYS cc_start: 0.8960 (tppp) cc_final: 0.8670 (tppp) REVERT: E 75 CYS cc_start: 0.9071 (m) cc_final: 0.8617 (p) REVERT: E 76 LYS cc_start: 0.9021 (tmmt) cc_final: 0.8559 (tmmt) REVERT: E 77 ASP cc_start: 0.8040 (t70) cc_final: 0.7271 (p0) REVERT: E 122 ARG cc_start: 0.8175 (tmm160) cc_final: 0.7763 (tmm160) REVERT: E 129 GLU cc_start: 0.8715 (tt0) cc_final: 0.8463 (tt0) REVERT: F 1 MET cc_start: 0.9170 (ttm) cc_final: 0.8746 (ttt) REVERT: F 28 MET cc_start: 0.9194 (tpp) cc_final: 0.8632 (tpt) REVERT: F 29 SER cc_start: 0.9667 (t) cc_final: 0.9312 (p) REVERT: F 49 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8760 (mt-10) REVERT: F 68 GLU cc_start: 0.7854 (pm20) cc_final: 0.7527 (pm20) REVERT: F 69 LYS cc_start: 0.8944 (tppp) cc_final: 0.8646 (tppp) REVERT: F 75 CYS cc_start: 0.9067 (m) cc_final: 0.8631 (p) REVERT: F 76 LYS cc_start: 0.9018 (tmmt) cc_final: 0.8559 (tmmt) REVERT: F 77 ASP cc_start: 0.8035 (t70) cc_final: 0.7277 (p0) REVERT: F 89 CYS cc_start: 0.7742 (m) cc_final: 0.7537 (m) REVERT: F 122 ARG cc_start: 0.8179 (tmm160) cc_final: 0.7761 (tmm160) REVERT: F 129 GLU cc_start: 0.8831 (tt0) cc_final: 0.8514 (tt0) REVERT: G 1 MET cc_start: 0.9159 (ttm) cc_final: 0.8736 (ttt) REVERT: G 29 SER cc_start: 0.9665 (t) cc_final: 0.9275 (p) REVERT: G 49 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8759 (mt-10) REVERT: G 68 GLU cc_start: 0.7856 (pm20) cc_final: 0.7528 (pm20) REVERT: G 69 LYS cc_start: 0.8966 (tppp) cc_final: 0.8735 (tppp) REVERT: G 75 CYS cc_start: 0.9068 (m) cc_final: 0.8626 (p) REVERT: G 76 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8562 (tmmt) REVERT: G 77 ASP cc_start: 0.8035 (t70) cc_final: 0.7270 (p0) REVERT: G 89 CYS cc_start: 0.7743 (m) cc_final: 0.7527 (m) REVERT: G 122 ARG cc_start: 0.8201 (tmm160) cc_final: 0.7764 (tmm160) REVERT: G 129 GLU cc_start: 0.8736 (tt0) cc_final: 0.8421 (tt0) REVERT: H 1 MET cc_start: 0.9158 (ttm) cc_final: 0.8742 (ttt) REVERT: H 29 SER cc_start: 0.9678 (t) cc_final: 0.9281 (p) REVERT: H 68 GLU cc_start: 0.7862 (pm20) cc_final: 0.7480 (pm20) REVERT: H 69 LYS cc_start: 0.8960 (tppp) cc_final: 0.8727 (tppp) REVERT: H 75 CYS cc_start: 0.9073 (m) cc_final: 0.8619 (p) REVERT: H 76 LYS cc_start: 0.9021 (tmmt) cc_final: 0.8562 (tmmt) REVERT: H 77 ASP cc_start: 0.8034 (t70) cc_final: 0.7264 (p0) REVERT: H 89 CYS cc_start: 0.7659 (m) cc_final: 0.7445 (m) REVERT: H 122 ARG cc_start: 0.8183 (tmm160) cc_final: 0.7767 (tmm160) REVERT: H 129 GLU cc_start: 0.8745 (tt0) cc_final: 0.8428 (tt0) outliers start: 18 outliers final: 16 residues processed: 222 average time/residue: 1.6395 time to fit residues: 396.2286 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 : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 MET 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 203 MET 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 6 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 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 193 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 0.0010 chunk 128 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16456 Z= 0.214 Angle : 0.550 9.415 22292 Z= 0.287 Chirality : 0.043 0.154 2500 Planarity : 0.004 0.042 2904 Dihedral : 4.044 26.258 2264 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.06 % Allowed : 12.94 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2068 helix: 2.30 (0.22), residues: 600 sheet: 0.23 (0.22), residues: 524 loop : -0.27 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 92 HIS 0.002 0.000 HIS D 189 PHE 0.008 0.001 PHE G 127 TYR 0.028 0.002 TYR F 118 ARG 0.009 0.001 ARG E 74 ********************** 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 225 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 2.020 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: 0.9393 (ptm) cc_final: 0.9055 (ptm) REVERT: A 181 ASP cc_start: 0.9086 (t70) cc_final: 0.8641 (t0) REVERT: A 203 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8981 (mmm) REVERT: B 49 MET cc_start: 0.9396 (ptm) cc_final: 0.9067 (ptm) REVERT: B 181 ASP cc_start: 0.9076 (t70) cc_final: 0.8639 (t0) REVERT: C 49 MET cc_start: 0.9388 (ptm) cc_final: 0.9063 (ptm) REVERT: C 181 ASP cc_start: 0.9065 (t70) cc_final: 0.8641 (t0) REVERT: D 49 MET cc_start: 0.9399 (ptm) cc_final: 0.9071 (ptm) REVERT: D 181 ASP cc_start: 0.9086 (t70) cc_final: 0.8660 (t0) REVERT: D 203 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8983 (mmm) REVERT: E 1 MET cc_start: 0.9155 (ttm) cc_final: 0.8737 (ttt) REVERT: E 29 SER cc_start: 0.9673 (t) cc_final: 0.9284 (p) REVERT: E 68 GLU cc_start: 0.7521 (pm20) cc_final: 0.7123 (pm20) REVERT: E 69 LYS cc_start: 0.8941 (tppp) cc_final: 0.8712 (tppp) REVERT: E 75 CYS cc_start: 0.9065 (m) cc_final: 0.8628 (p) REVERT: E 76 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8590 (tmmt) REVERT: E 77 ASP cc_start: 0.8062 (t70) cc_final: 0.7303 (p0) REVERT: E 95 ASP cc_start: 0.8758 (p0) cc_final: 0.8370 (p0) REVERT: E 122 ARG cc_start: 0.8173 (tmm160) cc_final: 0.7762 (tmm160) REVERT: E 129 GLU cc_start: 0.8728 (tt0) cc_final: 0.8487 (tt0) REVERT: F 1 MET cc_start: 0.9167 (ttm) cc_final: 0.8743 (ttt) REVERT: F 29 SER cc_start: 0.9667 (t) cc_final: 0.9283 (p) REVERT: F 49 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8797 (mt-10) REVERT: F 68 GLU cc_start: 0.7681 (pm20) cc_final: 0.7350 (pm20) REVERT: F 69 LYS cc_start: 0.8925 (tppp) cc_final: 0.8689 (tppp) REVERT: F 75 CYS cc_start: 0.9112 (m) cc_final: 0.8626 (p) REVERT: F 76 LYS cc_start: 0.9018 (tmmt) cc_final: 0.8615 (tmmt) REVERT: F 77 ASP cc_start: 0.8069 (t70) cc_final: 0.7320 (p0) REVERT: F 89 CYS cc_start: 0.7749 (m) cc_final: 0.7542 (m) REVERT: F 122 ARG cc_start: 0.8178 (tmm160) cc_final: 0.7763 (tmm160) REVERT: F 129 GLU cc_start: 0.8734 (tt0) cc_final: 0.8415 (tt0) REVERT: G 1 MET cc_start: 0.9157 (ttm) cc_final: 0.8734 (ttt) REVERT: G 28 MET cc_start: 0.9123 (tpp) cc_final: 0.8638 (tpt) REVERT: G 29 SER cc_start: 0.9667 (t) cc_final: 0.9304 (p) REVERT: G 68 GLU cc_start: 0.7639 (pm20) cc_final: 0.7399 (pp20) REVERT: G 69 LYS cc_start: 0.8937 (tppp) cc_final: 0.8074 (ttmm) REVERT: G 75 CYS cc_start: 0.9073 (m) cc_final: 0.8620 (p) REVERT: G 76 LYS cc_start: 0.9009 (tmmt) cc_final: 0.8600 (tmmt) REVERT: G 77 ASP cc_start: 0.8064 (t70) cc_final: 0.7306 (p0) REVERT: G 89 CYS cc_start: 0.7743 (m) cc_final: 0.7533 (m) REVERT: G 122 ARG cc_start: 0.8197 (tmm160) cc_final: 0.7762 (tmm160) REVERT: G 129 GLU cc_start: 0.8734 (tt0) cc_final: 0.8420 (tt0) REVERT: H 1 MET cc_start: 0.9155 (ttm) cc_final: 0.8745 (ttt) REVERT: H 28 MET cc_start: 0.9127 (tpp) cc_final: 0.8638 (tpt) REVERT: H 29 SER cc_start: 0.9671 (t) cc_final: 0.9308 (p) REVERT: H 68 GLU cc_start: 0.7654 (pm20) cc_final: 0.7324 (pm20) REVERT: H 69 LYS cc_start: 0.8936 (tppp) cc_final: 0.8364 (ttmm) REVERT: H 75 CYS cc_start: 0.9063 (m) cc_final: 0.8630 (p) REVERT: H 76 LYS cc_start: 0.9031 (tmmt) cc_final: 0.8611 (tmmt) REVERT: H 77 ASP cc_start: 0.8058 (t70) cc_final: 0.7298 (p0) REVERT: H 89 CYS cc_start: 0.7716 (m) cc_final: 0.7504 (m) REVERT: H 122 ARG cc_start: 0.8183 (tmm160) cc_final: 0.7769 (tmm160) REVERT: H 129 GLU cc_start: 0.8745 (tt0) cc_final: 0.8487 (tt0) outliers start: 18 outliers final: 16 residues processed: 218 average time/residue: 1.6470 time to fit residues: 391.2701 Evaluate side-chains 222 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 MET 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 203 MET 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 6 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 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 172 optimal weight: 0.0370 chunk 49 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 0.0770 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN E 152 GLN F 152 GLN G 152 GLN H 152 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.057278 restraints weight = 37424.580| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.04 r_work: 0.2786 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16456 Z= 0.176 Angle : 0.544 9.245 22292 Z= 0.283 Chirality : 0.042 0.156 2500 Planarity : 0.004 0.041 2904 Dihedral : 3.922 23.744 2264 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.06 % Allowed : 13.29 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2068 helix: 2.35 (0.22), residues: 600 sheet: 0.30 (0.23), residues: 524 loop : -0.27 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 149 HIS 0.002 0.000 HIS C 79 PHE 0.007 0.001 PHE F 127 TYR 0.028 0.001 TYR H 118 ARG 0.009 0.001 ARG H 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6448.27 seconds wall clock time: 116 minutes 26.23 seconds (6986.23 seconds total)