Starting phenix.real_space_refine on Wed May 21 07:45:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emw_28267/05_2025/8emw_28267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emw_28267/05_2025/8emw_28267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8emw_28267/05_2025/8emw_28267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emw_28267/05_2025/8emw_28267.map" model { file = "/net/cci-nas-00/data/ceres_data/8emw_28267/05_2025/8emw_28267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emw_28267/05_2025/8emw_28267.cif" } resolution = 3.5 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11633 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 79 5.16 5 C 7373 2.51 5 N 2034 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5926 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 47, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2512 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2516 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 339 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.57 Number of scatterers: 11714 At special positions: 0 Unit cell: (83.061, 132.562, 119.977, 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) Ca 1 19.99 S 79 16.00 O 2227 8.00 N 2034 7.00 C 7373 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: 2.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 30 sheets defined 21.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.545A pdb=" N ARG A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.509A pdb=" N TRP A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 157 through 163 removed outlier: 3.873A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.766A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.969A pdb=" N VAL A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.612A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.762A pdb=" N ASP A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.667A pdb=" N PHE A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.009A pdb=" N LEU A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 347 through 357 removed outlier: 4.021A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.578A pdb=" N GLU A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.714A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 removed outlier: 4.006A pdb=" N LEU A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 437' Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.542A pdb=" N THR A 592 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.635A pdb=" N ALA A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.665A pdb=" N PHE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.698A pdb=" N ASN A 666 " --> pdb=" O GLN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.698A pdb=" N ARG A 874 " --> pdb=" O ASP A 870 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN A 875 " --> pdb=" O GLN A 871 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 878 " --> pdb=" O ARG A 874 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.170A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.029A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.800A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.535A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.600A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.513A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.604A pdb=" N SER A 26 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 54 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.989A pdb=" N ASP A 71 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 104 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 330 through 331 removed outlier: 7.430A pdb=" N SER A 330 " --> pdb=" O LEU A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA8, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.601A pdb=" N VAL A 408 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LYS A 466 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 410 " --> pdb=" O LYS A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 620 through 621 removed outlier: 6.441A pdb=" N PHE A 620 " --> pdb=" O TYR A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.376A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.376A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 745 through 752 removed outlier: 5.097A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 824 through 826 removed outlier: 5.553A pdb=" N LEU A 825 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.018A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.846A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.272A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.733A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.569A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.623A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.663A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.732A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.572A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.572A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.589A pdb=" N VAL C 112 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC8, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.902A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 167 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.630A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AD2, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.683A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 320 removed outlier: 3.534A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 768 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: 4.20 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3660 1.33 - 1.45: 2007 1.45 - 1.57: 6153 1.57 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 11939 Sorted by residual: bond pdb=" CA SER A 37 " pdb=" CB SER A 37 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.58e-02 4.01e+03 8.68e+00 bond pdb=" N ASP C 291 " pdb=" CA ASP C 291 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.26e-02 6.30e+03 6.27e+00 bond pdb=" N ASP C 290 " pdb=" CA ASP C 290 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.11e+00 bond pdb=" N ASP A 125 " pdb=" CA ASP A 125 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.98e+00 bond pdb=" N SER A 37 " pdb=" CA SER A 37 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.63e+00 ... (remaining 11934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15473 1.98 - 3.95: 621 3.95 - 5.93: 61 5.93 - 7.90: 15 7.90 - 9.88: 8 Bond angle restraints: 16178 Sorted by residual: angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 113.89 105.90 7.99 1.58e+00 4.01e-01 2.56e+01 angle pdb=" C ASN A 39 " pdb=" CA ASN A 39 " pdb=" CB ASN A 39 " ideal model delta sigma weight residual 113.45 103.94 9.51 1.98e+00 2.55e-01 2.31e+01 angle pdb=" C ASP C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.92 108.08 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" C TYR C 289 " pdb=" CA TYR C 289 " pdb=" CB TYR C 289 " ideal model delta sigma weight residual 114.10 105.86 8.24 2.11e+00 2.25e-01 1.53e+01 ... (remaining 16173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6314 17.36 - 34.73: 738 34.73 - 52.09: 135 52.09 - 69.46: 14 69.46 - 86.82: 15 Dihedral angle restraints: 7216 sinusoidal: 2845 harmonic: 4371 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A 702 " pdb=" C PRO A 702 " pdb=" N GLU A 703 " pdb=" CA GLU A 703 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN C 313 " pdb=" C ASN C 313 " pdb=" N ARG C 314 " pdb=" CA ARG C 314 " ideal model delta harmonic sigma weight residual -180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1512 0.071 - 0.142: 283 0.142 - 0.212: 24 0.212 - 0.283: 6 0.283 - 0.354: 1 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA ASP A 126 " pdb=" N ASP A 126 " pdb=" C ASP A 126 " pdb=" CB ASP A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN A 39 " pdb=" N ASN A 39 " pdb=" C ASN A 39 " pdb=" CB ASN A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A 347 " pdb=" CA VAL A 347 " pdb=" CG1 VAL A 347 " pdb=" CG2 VAL A 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1823 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 370 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 371 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 369 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 370 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 455 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 456 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.038 5.00e-02 4.00e+02 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2838 2.78 - 3.31: 9861 3.31 - 3.84: 18694 3.84 - 4.37: 21694 4.37 - 4.90: 37965 Nonbonded interactions: 91052 Sorted by model distance: nonbonded pdb=" OH TYR A 240 " pdb=" OD2 ASP C 186 " model vdw 2.248 3.040 nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.262 3.040 nonbonded pdb=" O VAL A 361 " pdb=" OG SER A 411 " model vdw 2.275 3.040 nonbonded pdb=" OG SER C 161 " pdb=" O THR C 165 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.288 3.040 ... (remaining 91047 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 'B' and (resid 4 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 51 or (resi \ d 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throug \ h 152 or (resid 153 and (name N or name CA or name C or name O or name CB )) or \ resid 154 through 174 or (resid 175 and (name N or name CA or name C or name O o \ r name CB )) or resid 176 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB )) or resid 198 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 340)) selection = (chain 'C' and (resid 4 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 213 or (resid 214 through 215 an \ d (name N or name CA or name C or name O or name CB )) or resid 216 through 258 \ or (resid 259 and (name N or name CA or name C or name O or name CB )) or resid \ 260 through 282 or (resid 283 and (name N or name CA or name C or name O or name \ CB )) or resid 284 through 340)) } 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 group one per residue 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 11939 Z= 0.352 Angle : 0.908 9.878 16178 Z= 0.503 Chirality : 0.056 0.354 1826 Planarity : 0.007 0.102 2098 Dihedral : 15.242 86.819 4384 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Cbeta Deviations : 0.07 % 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: -5.07 (0.17), residues: 1486 helix: -4.92 (0.10), residues: 308 sheet: -3.25 (0.24), residues: 374 loop : -2.74 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.011 0.002 HIS A 332 PHE 0.033 0.003 PHE B 199 TYR 0.021 0.003 TYR A 692 ARG 0.006 0.001 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.30325 ( 270) hydrogen bonds : angle 10.71339 ( 768) covalent geometry : bond 0.00819 (11939) covalent geometry : angle 0.90832 (16178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8030 (p0) cc_final: 0.7789 (p0) REVERT: A 173 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8117 (tppt) REVERT: A 215 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7707 (ttp80) REVERT: A 236 LYS cc_start: 0.7854 (tptt) cc_final: 0.7580 (mttp) REVERT: A 247 MET cc_start: 0.7560 (ttp) cc_final: 0.7159 (ttp) REVERT: A 290 GLN cc_start: 0.7581 (mt0) cc_final: 0.7325 (mt0) REVERT: A 341 LEU cc_start: 0.8880 (mp) cc_final: 0.8677 (mp) REVERT: A 374 GLU cc_start: 0.8306 (pm20) cc_final: 0.7672 (pm20) REVERT: A 460 MET cc_start: 0.8644 (ttp) cc_final: 0.8215 (ttp) REVERT: A 577 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 583 GLU cc_start: 0.7749 (tt0) cc_final: 0.7542 (mt-10) REVERT: A 870 ASP cc_start: 0.7837 (t0) cc_final: 0.7603 (t0) REVERT: B 12 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 325 MET cc_start: 0.7238 (mmp) cc_final: 0.6568 (mtp) REVERT: B 340 ASN cc_start: 0.8139 (t0) cc_final: 0.7894 (t0) REVERT: C 78 LYS cc_start: 0.8212 (tttm) cc_final: 0.7940 (mtpp) REVERT: C 188 MET cc_start: 0.7864 (mmm) cc_final: 0.7557 (mmm) REVERT: C 312 ASP cc_start: 0.7021 (p0) cc_final: 0.6798 (p0) REVERT: D 44 HIS cc_start: 0.7815 (m-70) cc_final: 0.7613 (m-70) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2910 time to fit residues: 97.0127 Evaluate side-chains 176 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 124 GLN A 163 GLN A 379 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 GLN B 35 ASN B 91 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN C 16 ASN C 230 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108145 restraints weight = 17319.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112209 restraints weight = 9507.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114795 restraints weight = 6532.779| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11939 Z= 0.159 Angle : 0.598 7.404 16178 Z= 0.317 Chirality : 0.044 0.145 1826 Planarity : 0.005 0.058 2098 Dihedral : 5.440 23.047 1630 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.13 % Allowed : 15.86 % Favored : 82.00 % 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: -4.16 (0.18), residues: 1486 helix: -3.52 (0.20), residues: 327 sheet: -2.89 (0.24), residues: 367 loop : -2.29 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 332 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.001 TYR A 822 ARG 0.003 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 270) hydrogen bonds : angle 6.22772 ( 768) covalent geometry : bond 0.00366 (11939) covalent geometry : angle 0.59764 (16178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.269 Fit side-chains REVERT: A 46 ASP cc_start: 0.8134 (p0) cc_final: 0.7812 (p0) REVERT: A 173 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7961 (tppt) REVERT: A 215 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7410 (ttp-170) REVERT: A 236 LYS cc_start: 0.7925 (tptt) cc_final: 0.7615 (mttp) REVERT: A 283 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 290 GLN cc_start: 0.7582 (mt0) cc_final: 0.7315 (mt0) REVERT: A 374 GLU cc_start: 0.8159 (pm20) cc_final: 0.7809 (pm20) REVERT: A 439 ILE cc_start: 0.8680 (pt) cc_final: 0.8440 (mt) REVERT: A 869 MET cc_start: 0.7856 (mmp) cc_final: 0.7574 (mmp) REVERT: A 870 ASP cc_start: 0.8056 (t0) cc_final: 0.7678 (t0) REVERT: B 12 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 45 MET cc_start: 0.7803 (mtm) cc_final: 0.7462 (mtm) REVERT: B 325 MET cc_start: 0.7213 (mmp) cc_final: 0.6632 (mtp) REVERT: C 78 LYS cc_start: 0.8218 (tttm) cc_final: 0.7903 (mtpp) REVERT: C 82 TRP cc_start: 0.8613 (m100) cc_final: 0.8326 (m100) REVERT: C 156 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7026 (mm-40) REVERT: C 234 PHE cc_start: 0.7836 (m-80) cc_final: 0.7616 (m-80) REVERT: C 312 ASP cc_start: 0.7185 (p0) cc_final: 0.6968 (p0) REVERT: D 44 HIS cc_start: 0.7866 (m-70) cc_final: 0.7635 (m-70) outliers start: 27 outliers final: 19 residues processed: 228 average time/residue: 0.2459 time to fit residues: 79.0390 Evaluate side-chains 204 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 120 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.0060 chunk 147 optimal weight: 0.2980 chunk 146 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN A 821 HIS A 871 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 340 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113447 restraints weight = 17682.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117516 restraints weight = 9522.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120176 restraints weight = 6457.013| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11939 Z= 0.139 Angle : 0.543 7.852 16178 Z= 0.284 Chirality : 0.043 0.144 1826 Planarity : 0.004 0.047 2098 Dihedral : 4.878 24.383 1630 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.16 % Allowed : 17.76 % Favored : 79.08 % 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: -3.47 (0.19), residues: 1486 helix: -2.65 (0.23), residues: 330 sheet: -2.63 (0.25), residues: 367 loop : -1.91 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS A 379 PHE 0.016 0.001 PHE B 199 TYR 0.014 0.001 TYR A 822 ARG 0.004 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 270) hydrogen bonds : angle 5.36637 ( 768) covalent geometry : bond 0.00333 (11939) covalent geometry : angle 0.54313 (16178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 1.239 Fit side-chains REVERT: A 46 ASP cc_start: 0.8028 (p0) cc_final: 0.7742 (p0) REVERT: A 173 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7982 (tppt) REVERT: A 215 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7457 (ttp-170) REVERT: A 236 LYS cc_start: 0.8000 (tptt) cc_final: 0.7624 (mttp) REVERT: A 341 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 374 GLU cc_start: 0.7945 (pm20) cc_final: 0.7188 (pm20) REVERT: A 413 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7098 (mt-10) REVERT: A 422 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8120 (mt0) REVERT: A 736 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: A 869 MET cc_start: 0.7585 (mmp) cc_final: 0.6777 (mmp) REVERT: A 870 ASP cc_start: 0.7965 (t0) cc_final: 0.7582 (t0) REVERT: B 45 MET cc_start: 0.7735 (mtm) cc_final: 0.7411 (mtm) REVERT: B 325 MET cc_start: 0.7226 (mmp) cc_final: 0.6608 (mtp) REVERT: C 82 TRP cc_start: 0.8652 (m100) cc_final: 0.8387 (m100) REVERT: C 156 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7137 (mm-40) REVERT: C 222 PHE cc_start: 0.7235 (m-80) cc_final: 0.7032 (m-80) REVERT: C 312 ASP cc_start: 0.7241 (p0) cc_final: 0.7015 (p0) REVERT: C 317 CYS cc_start: 0.8352 (p) cc_final: 0.8063 (p) REVERT: C 331 SER cc_start: 0.8880 (m) cc_final: 0.8591 (t) REVERT: D 14 LYS cc_start: 0.8554 (tmtt) cc_final: 0.8025 (ttmt) outliers start: 40 outliers final: 29 residues processed: 231 average time/residue: 0.2349 time to fit residues: 77.4573 Evaluate side-chains 218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 871 GLN B 340 ASN G 44 HIS D 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115049 restraints weight = 17420.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119109 restraints weight = 9428.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121755 restraints weight = 6404.143| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11939 Z= 0.110 Angle : 0.523 8.510 16178 Z= 0.270 Chirality : 0.042 0.138 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.541 22.787 1630 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.24 % Allowed : 19.10 % Favored : 77.66 % 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: -3.06 (0.20), residues: 1486 helix: -2.04 (0.26), residues: 324 sheet: -2.47 (0.26), residues: 351 loop : -1.77 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.002 0.001 HIS D 44 PHE 0.014 0.001 PHE C 253 TYR 0.011 0.001 TYR A 822 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 270) hydrogen bonds : angle 5.04113 ( 768) covalent geometry : bond 0.00259 (11939) covalent geometry : angle 0.52268 (16178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 1.393 Fit side-chains REVERT: A 46 ASP cc_start: 0.7986 (p0) cc_final: 0.7696 (p0) REVERT: A 125 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 173 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7954 (tppt) REVERT: A 215 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7409 (ttp-170) REVERT: A 236 LYS cc_start: 0.7999 (tptt) cc_final: 0.7653 (mttp) REVERT: A 252 GLN cc_start: 0.8191 (mt0) cc_final: 0.7652 (mt0) REVERT: A 283 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 364 ASP cc_start: 0.8136 (m-30) cc_final: 0.7814 (m-30) REVERT: A 374 GLU cc_start: 0.7876 (pm20) cc_final: 0.7417 (pm20) REVERT: A 422 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8106 (mt0) REVERT: A 869 MET cc_start: 0.7528 (mmp) cc_final: 0.6777 (mmp) REVERT: A 870 ASP cc_start: 0.7943 (t0) cc_final: 0.7539 (t0) REVERT: B 45 MET cc_start: 0.7633 (mtm) cc_final: 0.7181 (mtm) REVERT: B 325 MET cc_start: 0.7237 (mmp) cc_final: 0.6657 (mtp) REVERT: C 13 GLN cc_start: 0.8731 (tt0) cc_final: 0.8453 (pt0) REVERT: C 82 TRP cc_start: 0.8628 (m100) cc_final: 0.8290 (m-10) REVERT: C 156 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7041 (mm-40) REVERT: C 298 ASP cc_start: 0.8023 (t0) cc_final: 0.6601 (p0) REVERT: C 317 CYS cc_start: 0.8365 (p) cc_final: 0.8033 (p) REVERT: C 331 SER cc_start: 0.8832 (m) cc_final: 0.8536 (t) REVERT: D 44 HIS cc_start: 0.7618 (m90) cc_final: 0.7084 (m90) outliers start: 41 outliers final: 32 residues processed: 233 average time/residue: 0.2326 time to fit residues: 77.0412 Evaluate side-chains 231 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 340 ASN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107073 restraints weight = 17686.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110869 restraints weight = 9845.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113363 restraints weight = 6833.498| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 11939 Z= 0.367 Angle : 0.735 9.668 16178 Z= 0.377 Chirality : 0.050 0.187 1826 Planarity : 0.005 0.067 2098 Dihedral : 5.374 27.614 1630 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.34 % Allowed : 21.07 % Favored : 74.59 % 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: -3.29 (0.20), residues: 1486 helix: -1.95 (0.27), residues: 318 sheet: -2.79 (0.24), residues: 372 loop : -1.91 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.008 0.002 HIS A 808 PHE 0.028 0.003 PHE A 636 TYR 0.024 0.002 TYR A 692 ARG 0.007 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 270) hydrogen bonds : angle 5.64272 ( 768) covalent geometry : bond 0.00884 (11939) covalent geometry : angle 0.73471 (16178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8348 (p0) cc_final: 0.8014 (p0) REVERT: A 173 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8122 (tppt) REVERT: A 206 ASP cc_start: 0.8195 (p0) cc_final: 0.7957 (p0) REVERT: A 215 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7592 (ttp-170) REVERT: A 252 GLN cc_start: 0.8206 (mt0) cc_final: 0.7613 (mt0) REVERT: A 364 ASP cc_start: 0.8244 (m-30) cc_final: 0.8033 (m-30) REVERT: A 374 GLU cc_start: 0.8221 (pm20) cc_final: 0.7865 (pm20) REVERT: A 422 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8160 (mt0) REVERT: A 869 MET cc_start: 0.7551 (mmp) cc_final: 0.6873 (mmp) REVERT: A 870 ASP cc_start: 0.8030 (t0) cc_final: 0.7674 (t0) REVERT: B 45 MET cc_start: 0.7758 (mtm) cc_final: 0.7541 (mtm) REVERT: B 325 MET cc_start: 0.7387 (mmp) cc_final: 0.6590 (mtp) REVERT: C 78 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8269 (tttp) REVERT: C 82 TRP cc_start: 0.8715 (m100) cc_final: 0.8425 (m100) REVERT: C 233 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7504 (p) REVERT: C 253 PHE cc_start: 0.8319 (m-10) cc_final: 0.8019 (m-10) REVERT: D 44 HIS cc_start: 0.7627 (m90) cc_final: 0.7145 (m90) outliers start: 55 outliers final: 44 residues processed: 235 average time/residue: 0.2434 time to fit residues: 81.7405 Evaluate side-chains 229 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 0.0170 chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 736 GLN A 871 GLN B 239 ASN B 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.149438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114581 restraints weight = 17561.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118700 restraints weight = 9509.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121426 restraints weight = 6463.195| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11939 Z= 0.106 Angle : 0.553 12.604 16178 Z= 0.280 Chirality : 0.043 0.156 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.585 27.318 1630 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.55 % Allowed : 22.65 % Favored : 73.80 % 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: -2.77 (0.20), residues: 1486 helix: -1.54 (0.27), residues: 325 sheet: -2.47 (0.26), residues: 342 loop : -1.62 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS B 311 PHE 0.018 0.001 PHE A 381 TYR 0.015 0.001 TYR G 40 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 270) hydrogen bonds : angle 4.94317 ( 768) covalent geometry : bond 0.00251 (11939) covalent geometry : angle 0.55318 (16178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7977 (p0) cc_final: 0.7663 (p0) REVERT: A 76 ARG cc_start: 0.8396 (ptt90) cc_final: 0.7899 (ptt90) REVERT: A 100 GLU cc_start: 0.7134 (pt0) cc_final: 0.6775 (pm20) REVERT: A 121 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7244 (ttt) REVERT: A 173 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7918 (tppt) REVERT: A 252 GLN cc_start: 0.8179 (mt0) cc_final: 0.7744 (mt0) REVERT: A 374 GLU cc_start: 0.7948 (pm20) cc_final: 0.7459 (pm20) REVERT: A 413 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 422 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7973 (mt0) REVERT: A 736 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: A 869 MET cc_start: 0.7466 (mmp) cc_final: 0.6727 (mmp) REVERT: B 45 MET cc_start: 0.7655 (mtm) cc_final: 0.7253 (mtm) REVERT: B 75 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7489 (tt0) REVERT: B 297 TRP cc_start: 0.8760 (m100) cc_final: 0.8319 (m100) REVERT: B 325 MET cc_start: 0.7271 (mmp) cc_final: 0.6705 (mtp) REVERT: C 13 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: C 82 TRP cc_start: 0.8679 (m100) cc_final: 0.8262 (m-10) REVERT: C 259 GLN cc_start: 0.7501 (tt0) cc_final: 0.6786 (tm-30) REVERT: C 317 CYS cc_start: 0.8226 (p) cc_final: 0.7944 (p) REVERT: C 331 SER cc_start: 0.8911 (m) cc_final: 0.8484 (t) REVERT: D 14 LYS cc_start: 0.8475 (tmtt) cc_final: 0.7998 (ttmt) REVERT: D 44 HIS cc_start: 0.7626 (m90) cc_final: 0.6975 (m90) outliers start: 45 outliers final: 27 residues processed: 228 average time/residue: 0.2324 time to fit residues: 76.3521 Evaluate side-chains 217 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN A 871 GLN B 75 GLN B 311 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115130 restraints weight = 17648.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119235 restraints weight = 9570.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121924 restraints weight = 6507.392| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11939 Z= 0.107 Angle : 0.546 12.145 16178 Z= 0.276 Chirality : 0.043 0.219 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.404 26.757 1630 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.00 % Allowed : 23.60 % Favored : 73.40 % 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: -2.52 (0.21), residues: 1486 helix: -1.21 (0.28), residues: 325 sheet: -2.31 (0.26), residues: 355 loop : -1.48 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR A 596 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 270) hydrogen bonds : angle 4.78822 ( 768) covalent geometry : bond 0.00257 (11939) covalent geometry : angle 0.54557 (16178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7942 (p0) cc_final: 0.7620 (p0) REVERT: A 76 ARG cc_start: 0.8396 (ptt90) cc_final: 0.7906 (ptt90) REVERT: A 100 GLU cc_start: 0.7205 (pt0) cc_final: 0.6817 (pm20) REVERT: A 173 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7910 (tppt) REVERT: A 252 GLN cc_start: 0.8160 (mt0) cc_final: 0.7766 (mt0) REVERT: A 374 GLU cc_start: 0.7908 (pm20) cc_final: 0.7181 (pm20) REVERT: A 736 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 869 MET cc_start: 0.7478 (mmp) cc_final: 0.6820 (mmp) REVERT: B 45 MET cc_start: 0.7623 (mtm) cc_final: 0.7236 (mtm) REVERT: B 46 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7492 (mtt90) REVERT: B 75 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8042 (mm110) REVERT: B 297 TRP cc_start: 0.8748 (m100) cc_final: 0.8273 (m100) REVERT: B 325 MET cc_start: 0.7270 (mmp) cc_final: 0.6711 (mtp) REVERT: C 13 GLN cc_start: 0.8803 (tt0) cc_final: 0.8556 (pt0) REVERT: C 49 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7585 (mpt-90) REVERT: C 82 TRP cc_start: 0.8693 (m100) cc_final: 0.8248 (m-10) REVERT: C 259 GLN cc_start: 0.7518 (tt0) cc_final: 0.6774 (tm-30) REVERT: C 317 CYS cc_start: 0.8255 (p) cc_final: 0.7990 (p) REVERT: C 331 SER cc_start: 0.8842 (m) cc_final: 0.8480 (t) REVERT: D 14 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8008 (ttmt) REVERT: D 44 HIS cc_start: 0.7352 (m90) cc_final: 0.6957 (m90) outliers start: 38 outliers final: 28 residues processed: 218 average time/residue: 0.2500 time to fit residues: 77.0661 Evaluate side-chains 218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115246 restraints weight = 17612.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119339 restraints weight = 9618.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122048 restraints weight = 6550.590| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11939 Z= 0.114 Angle : 0.541 11.318 16178 Z= 0.274 Chirality : 0.043 0.162 1826 Planarity : 0.004 0.060 2098 Dihedral : 4.347 25.982 1630 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.16 % Allowed : 22.73 % Favored : 74.11 % 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: -2.33 (0.21), residues: 1486 helix: -0.99 (0.29), residues: 325 sheet: -2.24 (0.26), residues: 348 loop : -1.39 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS B 311 PHE 0.015 0.001 PHE B 199 TYR 0.014 0.001 TYR A 596 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 270) hydrogen bonds : angle 4.74669 ( 768) covalent geometry : bond 0.00277 (11939) covalent geometry : angle 0.54104 (16178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7967 (p0) cc_final: 0.7647 (p0) REVERT: A 100 GLU cc_start: 0.7172 (pt0) cc_final: 0.6631 (pm20) REVERT: A 103 LEU cc_start: 0.8073 (mt) cc_final: 0.7741 (mm) REVERT: A 121 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7171 (tpt) REVERT: A 173 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7858 (tppt) REVERT: A 252 GLN cc_start: 0.8111 (mt0) cc_final: 0.7741 (mt0) REVERT: A 374 GLU cc_start: 0.7856 (pm20) cc_final: 0.7385 (pm20) REVERT: A 641 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7884 (mttp) REVERT: A 869 MET cc_start: 0.7445 (mmp) cc_final: 0.6802 (mmp) REVERT: B 45 MET cc_start: 0.7629 (mtm) cc_final: 0.7261 (mtm) REVERT: B 297 TRP cc_start: 0.8759 (m100) cc_final: 0.8305 (m100) REVERT: B 325 MET cc_start: 0.7250 (mmp) cc_final: 0.6701 (mtp) REVERT: C 13 GLN cc_start: 0.8806 (tt0) cc_final: 0.8566 (pt0) REVERT: C 49 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7602 (mpt-90) REVERT: C 82 TRP cc_start: 0.8685 (m100) cc_final: 0.8213 (m-10) REVERT: C 188 MET cc_start: 0.8422 (mmm) cc_final: 0.8074 (mmt) REVERT: C 259 GLN cc_start: 0.7536 (tt0) cc_final: 0.6787 (tm-30) REVERT: C 317 CYS cc_start: 0.8238 (p) cc_final: 0.7979 (p) REVERT: C 331 SER cc_start: 0.8878 (m) cc_final: 0.8510 (t) REVERT: D 14 LYS cc_start: 0.8495 (tmtt) cc_final: 0.8025 (ttmt) REVERT: D 44 HIS cc_start: 0.7311 (m90) cc_final: 0.6950 (m90) outliers start: 40 outliers final: 30 residues processed: 220 average time/residue: 0.2633 time to fit residues: 82.8814 Evaluate side-chains 214 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.0070 chunk 128 optimal weight: 8.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 871 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117885 restraints weight = 17533.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122078 restraints weight = 9526.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124838 restraints weight = 6472.597| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11939 Z= 0.094 Angle : 0.538 12.664 16178 Z= 0.270 Chirality : 0.043 0.211 1826 Planarity : 0.003 0.055 2098 Dihedral : 4.141 29.187 1630 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 23.60 % Favored : 73.95 % 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: -2.06 (0.21), residues: 1486 helix: -0.69 (0.30), residues: 326 sheet: -2.08 (0.27), residues: 337 loop : -1.27 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE C 253 TYR 0.013 0.001 TYR G 40 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 270) hydrogen bonds : angle 4.60087 ( 768) covalent geometry : bond 0.00223 (11939) covalent geometry : angle 0.53783 (16178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7936 (p0) cc_final: 0.7622 (p0) REVERT: A 100 GLU cc_start: 0.7140 (pt0) cc_final: 0.6585 (pm20) REVERT: A 374 GLU cc_start: 0.7744 (pm20) cc_final: 0.7288 (pm20) REVERT: A 595 ASN cc_start: 0.7677 (p0) cc_final: 0.7374 (p0) REVERT: A 869 MET cc_start: 0.7490 (mmp) cc_final: 0.6800 (mmp) REVERT: B 13 GLN cc_start: 0.8681 (pp30) cc_final: 0.8457 (pp30) REVERT: B 45 MET cc_start: 0.7585 (mtm) cc_final: 0.7257 (mtm) REVERT: B 297 TRP cc_start: 0.8715 (m100) cc_final: 0.8242 (m100) REVERT: B 325 MET cc_start: 0.7252 (mmp) cc_final: 0.6701 (mtp) REVERT: C 13 GLN cc_start: 0.8805 (tt0) cc_final: 0.8512 (pt0) REVERT: C 82 TRP cc_start: 0.8666 (m100) cc_final: 0.8151 (m-10) REVERT: C 259 GLN cc_start: 0.7585 (tt0) cc_final: 0.6878 (tm-30) REVERT: C 317 CYS cc_start: 0.8224 (p) cc_final: 0.7983 (p) REVERT: C 331 SER cc_start: 0.8742 (m) cc_final: 0.8437 (t) REVERT: D 14 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8059 (ttmt) REVERT: D 44 HIS cc_start: 0.7399 (m90) cc_final: 0.7045 (m90) outliers start: 31 outliers final: 26 residues processed: 219 average time/residue: 0.2459 time to fit residues: 75.9348 Evaluate side-chains 205 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 118 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 44 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 640 ASN B 311 HIS C 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111906 restraints weight = 17611.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115852 restraints weight = 9726.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118420 restraints weight = 6685.288| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11939 Z= 0.213 Angle : 0.621 10.700 16178 Z= 0.314 Chirality : 0.047 0.333 1826 Planarity : 0.004 0.057 2098 Dihedral : 4.614 25.910 1630 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.68 % Allowed : 24.07 % Favored : 73.24 % 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: -2.30 (0.21), residues: 1486 helix: -0.85 (0.29), residues: 331 sheet: -2.33 (0.24), residues: 386 loop : -1.29 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.005 0.001 HIS A 808 PHE 0.018 0.002 PHE B 199 TYR 0.020 0.002 TYR A 596 ARG 0.003 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 270) hydrogen bonds : angle 4.96898 ( 768) covalent geometry : bond 0.00515 (11939) covalent geometry : angle 0.62070 (16178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8114 (p0) cc_final: 0.7799 (p0) REVERT: A 60 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7537 (mp0) REVERT: A 173 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7848 (tppt) REVERT: A 252 GLN cc_start: 0.8103 (mt0) cc_final: 0.7740 (mt0) REVERT: A 290 GLN cc_start: 0.7416 (mt0) cc_final: 0.6764 (mt0) REVERT: A 374 GLU cc_start: 0.7966 (pm20) cc_final: 0.7460 (pm20) REVERT: A 869 MET cc_start: 0.7506 (mmp) cc_final: 0.6808 (mmp) REVERT: B 45 MET cc_start: 0.7670 (mtm) cc_final: 0.7310 (mtm) REVERT: B 325 MET cc_start: 0.7303 (mmp) cc_final: 0.6701 (mtp) REVERT: C 17 GLN cc_start: 0.7990 (mt0) cc_final: 0.7768 (tm-30) REVERT: C 49 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7643 (mpt-90) REVERT: C 66 ASP cc_start: 0.7444 (p0) cc_final: 0.7070 (p0) REVERT: C 82 TRP cc_start: 0.8714 (m100) cc_final: 0.8184 (m-10) REVERT: C 255 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7347 (mt) REVERT: C 317 CYS cc_start: 0.8277 (p) cc_final: 0.7993 (p) REVERT: C 331 SER cc_start: 0.8977 (m) cc_final: 0.8571 (t) REVERT: D 44 HIS cc_start: 0.7434 (m90) cc_final: 0.7036 (m90) outliers start: 34 outliers final: 27 residues processed: 205 average time/residue: 0.2480 time to fit residues: 72.1350 Evaluate side-chains 205 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114932 restraints weight = 17363.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118983 restraints weight = 9503.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121676 restraints weight = 6484.145| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11939 Z= 0.118 Angle : 0.574 10.880 16178 Z= 0.288 Chirality : 0.044 0.250 1826 Planarity : 0.003 0.050 2098 Dihedral : 4.384 29.460 1630 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.21 % Allowed : 24.55 % Favored : 73.24 % 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: -2.08 (0.21), residues: 1486 helix: -0.68 (0.30), residues: 332 sheet: -2.15 (0.26), residues: 359 loop : -1.22 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.001 PHE A 381 TYR 0.020 0.001 TYR A 596 ARG 0.007 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 270) hydrogen bonds : angle 4.76000 ( 768) covalent geometry : bond 0.00285 (11939) covalent geometry : angle 0.57398 (16178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3941.62 seconds wall clock time: 69 minutes 45.99 seconds (4185.99 seconds total)