Starting phenix.real_space_refine on Wed Jun 18 11:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emw_28267/06_2025/8emw_28267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emw_28267/06_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_28267/06_2025/8emw_28267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emw_28267/06_2025/8emw_28267.map" model { file = "/net/cci-nas-00/data/ceres_data/8emw_28267/06_2025/8emw_28267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emw_28267/06_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-5710/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: 6.45, per 1000 atoms: 0.55 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: 2.57 Conformation dependent library (CDL) restraints added in 1.5 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: 1.59 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: 3.82 Time building geometry restraints manager: 3.09 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.800 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- 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 : 1.346 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: 0.2938 time to fit residues: 98.1498 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 : 1.346 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108164 restraints weight = 17319.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112233 restraints weight = 9493.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114888 restraints weight = 6521.417| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 1.322 Fit side-chains REVERT: A 46 ASP cc_start: 0.8129 (p0) cc_final: 0.7807 (p0) REVERT: A 173 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7949 (tppt) REVERT: A 215 ARG cc_start: 0.7790 (ttp80) cc_final: 0.7406 (ttp-170) REVERT: A 236 LYS cc_start: 0.7929 (tptt) cc_final: 0.7614 (mttp) REVERT: A 283 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 290 GLN cc_start: 0.7577 (mt0) cc_final: 0.7309 (mt0) REVERT: A 374 GLU cc_start: 0.8157 (pm20) cc_final: 0.7810 (pm20) REVERT: A 439 ILE cc_start: 0.8679 (pt) cc_final: 0.8436 (mt) REVERT: A 869 MET cc_start: 0.7866 (mmp) cc_final: 0.7585 (mmp) REVERT: A 870 ASP cc_start: 0.8064 (t0) cc_final: 0.7684 (t0) REVERT: B 12 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 45 MET cc_start: 0.7809 (mtm) cc_final: 0.7464 (mtm) REVERT: B 325 MET cc_start: 0.7213 (mmp) cc_final: 0.6629 (mtp) REVERT: C 78 LYS cc_start: 0.8207 (tttm) cc_final: 0.7890 (mtpp) REVERT: C 82 TRP cc_start: 0.8617 (m100) cc_final: 0.8324 (m100) REVERT: C 156 GLN cc_start: 0.7331 (mm-40) cc_final: 0.7023 (mm-40) REVERT: C 234 PHE cc_start: 0.7836 (m-80) cc_final: 0.7616 (m-80) REVERT: C 312 ASP cc_start: 0.7192 (p0) cc_final: 0.6976 (p0) REVERT: D 44 HIS cc_start: 0.7862 (m-70) cc_final: 0.7636 (m-70) outliers start: 27 outliers final: 19 residues processed: 228 average time/residue: 0.2495 time to fit residues: 80.5783 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 : 1.378 ------------------------------------------------------------------------------- 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: 6.9990 chunk 144 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 147 optimal weight: 0.2980 chunk 146 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** C 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112244 restraints weight = 17736.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116283 restraints weight = 9619.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118948 restraints weight = 6535.968| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11939 Z= 0.166 Angle : 0.563 8.285 16178 Z= 0.294 Chirality : 0.044 0.142 1826 Planarity : 0.004 0.047 2098 Dihedral : 5.000 23.805 1630 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.39 % Allowed : 18.00 % Favored : 78.61 % 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: -3.51 (0.19), residues: 1486 helix: -2.64 (0.24), residues: 324 sheet: -2.67 (0.25), residues: 361 loop : -1.96 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS A 808 PHE 0.019 0.002 PHE A 636 TYR 0.015 0.001 TYR A 692 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 270) hydrogen bonds : angle 5.44977 ( 768) covalent geometry : bond 0.00399 (11939) covalent geometry : angle 0.56257 (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 246 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.280 Fit side-chains REVERT: A 46 ASP cc_start: 0.8094 (p0) cc_final: 0.7805 (p0) REVERT: A 173 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8003 (tppt) REVERT: A 215 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7477 (ttp-170) REVERT: A 236 LYS cc_start: 0.8076 (tptt) cc_final: 0.7643 (mttp) REVERT: A 341 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 374 GLU cc_start: 0.7978 (pm20) cc_final: 0.7191 (pm20) REVERT: A 413 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 422 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8128 (mt0) REVERT: A 736 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: A 869 MET cc_start: 0.7610 (mmp) cc_final: 0.6814 (mmp) REVERT: A 870 ASP cc_start: 0.8013 (t0) cc_final: 0.7612 (t0) REVERT: B 45 MET cc_start: 0.7751 (mtm) cc_final: 0.7414 (mtm) REVERT: B 325 MET cc_start: 0.7218 (mmp) cc_final: 0.6591 (mtp) REVERT: C 82 TRP cc_start: 0.8655 (m100) cc_final: 0.8374 (m100) REVERT: C 156 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7118 (mm-40) REVERT: C 222 PHE cc_start: 0.7255 (m-80) cc_final: 0.7043 (m-80) REVERT: C 331 SER cc_start: 0.8862 (m) cc_final: 0.8555 (t) REVERT: D 14 LYS cc_start: 0.8542 (tmtt) cc_final: 0.7991 (ttmt) outliers start: 43 outliers final: 33 residues processed: 230 average time/residue: 0.2496 time to fit residues: 81.6596 Evaluate side-chains 223 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 193 CYS 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 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 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 213 VAL 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 275 SER 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: 0.7980 chunk 87 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.150201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115692 restraints weight = 17385.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119768 restraints weight = 9398.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122480 restraints weight = 6373.540| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11939 Z= 0.098 Angle : 0.519 7.958 16178 Z= 0.269 Chirality : 0.042 0.142 1826 Planarity : 0.004 0.062 2098 Dihedral : 4.531 23.339 1630 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.68 % Allowed : 20.28 % Favored : 77.03 % 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: -3.03 (0.20), residues: 1486 helix: -2.02 (0.26), residues: 324 sheet: -2.44 (0.26), residues: 352 loop : -1.74 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.002 0.001 HIS B 54 PHE 0.014 0.001 PHE C 253 TYR 0.010 0.001 TYR A 822 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 270) hydrogen bonds : angle 5.02184 ( 768) covalent geometry : bond 0.00229 (11939) covalent geometry : angle 0.51878 (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 246 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.292 Fit side-chains REVERT: A 46 ASP cc_start: 0.7983 (p0) cc_final: 0.7696 (p0) REVERT: A 125 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7799 (t0) REVERT: A 173 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7943 (tppt) REVERT: A 215 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7397 (ttp-170) REVERT: A 236 LYS cc_start: 0.8004 (tptt) cc_final: 0.7644 (mttp) REVERT: A 252 GLN cc_start: 0.8171 (mt0) cc_final: 0.7641 (mt0) REVERT: A 283 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 364 ASP cc_start: 0.8124 (m-30) cc_final: 0.7849 (m-30) REVERT: A 374 GLU cc_start: 0.7854 (pm20) cc_final: 0.7388 (pm20) REVERT: A 422 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8100 (mt0) REVERT: A 869 MET cc_start: 0.7508 (mmp) cc_final: 0.7083 (mmp) REVERT: A 870 ASP cc_start: 0.7922 (t0) cc_final: 0.7521 (t0) REVERT: B 45 MET cc_start: 0.7583 (mtm) cc_final: 0.7172 (mtm) REVERT: B 325 MET cc_start: 0.7210 (mmp) cc_final: 0.6646 (mtp) REVERT: G 42 GLU cc_start: 0.7379 (mp0) cc_final: 0.7129 (mp0) REVERT: C 13 GLN cc_start: 0.8737 (tt0) cc_final: 0.8457 (pt0) REVERT: C 82 TRP cc_start: 0.8640 (m100) cc_final: 0.8315 (m-10) REVERT: C 156 GLN cc_start: 0.7315 (mm-40) cc_final: 0.7032 (mm-40) REVERT: C 317 CYS cc_start: 0.8322 (p) cc_final: 0.8019 (p) REVERT: C 331 SER cc_start: 0.8813 (m) cc_final: 0.8547 (t) REVERT: D 44 HIS cc_start: 0.7616 (m90) cc_final: 0.7084 (m90) outliers start: 34 outliers final: 26 residues processed: 234 average time/residue: 0.2571 time to fit residues: 86.4071 Evaluate side-chains 224 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 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 764 THR 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 198 LEU 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 198 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR 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: 6.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- 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 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 340 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.143342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108571 restraints weight = 17630.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112420 restraints weight = 9754.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114825 restraints weight = 6738.856| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 11939 Z= 0.309 Angle : 0.675 8.909 16178 Z= 0.346 Chirality : 0.048 0.149 1826 Planarity : 0.005 0.066 2098 Dihedral : 5.168 27.434 1630 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.03 % Allowed : 21.70 % Favored : 74.27 % 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: -3.18 (0.20), residues: 1486 helix: -1.86 (0.27), residues: 324 sheet: -2.72 (0.24), residues: 372 loop : -1.84 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.006 0.001 HIS A 808 PHE 0.025 0.002 PHE A 636 TYR 0.021 0.002 TYR A 692 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 270) hydrogen bonds : angle 5.46408 ( 768) covalent geometry : bond 0.00743 (11939) covalent geometry : angle 0.67480 (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 246 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8286 (p0) cc_final: 0.7956 (p0) REVERT: A 173 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8067 (tppt) REVERT: A 215 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7549 (ttp-170) REVERT: A 252 GLN cc_start: 0.8196 (mt0) cc_final: 0.7603 (mt0) REVERT: A 374 GLU cc_start: 0.8152 (pm20) cc_final: 0.7784 (pm20) REVERT: A 422 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8175 (mt0) REVERT: A 869 MET cc_start: 0.7536 (mmp) cc_final: 0.6836 (mmp) REVERT: A 870 ASP cc_start: 0.8002 (t0) cc_final: 0.7652 (t0) REVERT: B 45 MET cc_start: 0.7736 (mtm) cc_final: 0.7402 (mtm) REVERT: C 253 PHE cc_start: 0.8268 (m-10) cc_final: 0.7964 (m-10) REVERT: C 331 SER cc_start: 0.8979 (m) cc_final: 0.8667 (t) REVERT: D 14 LYS cc_start: 0.8560 (tmtt) cc_final: 0.7995 (ttmt) REVERT: D 44 HIS cc_start: 0.7639 (m90) cc_final: 0.7165 (m90) outliers start: 51 outliers final: 41 residues processed: 229 average time/residue: 0.2387 time to fit residues: 78.2729 Evaluate side-chains 224 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 736 GLN 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 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 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER 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 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 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: 9.9990 chunk 84 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 239 ASN B 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114561 restraints weight = 17562.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118694 restraints weight = 9473.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121464 restraints weight = 6430.174| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2472 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= 0.108 Angle : 0.542 7.710 16178 Z= 0.275 Chirality : 0.043 0.141 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.561 26.704 1630 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.47 % Allowed : 22.57 % 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: -2.75 (0.21), residues: 1486 helix: -1.45 (0.28), residues: 325 sheet: -2.50 (0.26), residues: 347 loop : -1.61 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 311 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR G 40 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 270) hydrogen bonds : angle 4.91441 ( 768) covalent geometry : bond 0.00256 (11939) covalent geometry : angle 0.54166 (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 244 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7975 (p0) cc_final: 0.7662 (p0) REVERT: A 76 ARG cc_start: 0.8397 (ptt90) cc_final: 0.7901 (ptt90) REVERT: A 100 GLU cc_start: 0.7113 (pt0) cc_final: 0.6781 (pm20) REVERT: A 121 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7202 (ttt) REVERT: A 173 LYS cc_start: 0.8332 (ttpt) cc_final: 0.7920 (tppt) REVERT: A 252 GLN cc_start: 0.8164 (mt0) cc_final: 0.7736 (mt0) REVERT: A 364 ASP cc_start: 0.8102 (m-30) cc_final: 0.7385 (m-30) REVERT: A 374 GLU cc_start: 0.7942 (pm20) cc_final: 0.7449 (pm20) REVERT: A 413 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 422 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7976 (mt0) REVERT: A 736 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: A 869 MET cc_start: 0.7428 (mmp) cc_final: 0.6654 (mmp) REVERT: B 14 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8708 (mm) REVERT: B 45 MET cc_start: 0.7652 (mtm) cc_final: 0.7217 (mtm) REVERT: B 297 TRP cc_start: 0.8763 (m100) cc_final: 0.8325 (m100) REVERT: B 325 MET cc_start: 0.7283 (mmp) cc_final: 0.6706 (mtp) REVERT: G 38 MET cc_start: 0.8249 (tpp) cc_final: 0.7602 (mmm) REVERT: C 13 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (pt0) REVERT: C 82 TRP cc_start: 0.8685 (m100) cc_final: 0.8278 (m-10) REVERT: C 317 CYS cc_start: 0.8213 (p) cc_final: 0.7934 (p) REVERT: C 331 SER cc_start: 0.8839 (m) cc_final: 0.8537 (t) REVERT: D 14 LYS cc_start: 0.8487 (tmtt) cc_final: 0.7997 (ttmt) REVERT: D 44 HIS cc_start: 0.7626 (m90) cc_final: 0.7073 (m90) outliers start: 44 outliers final: 25 residues processed: 228 average time/residue: 0.2364 time to fit residues: 77.3011 Evaluate side-chains 219 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 121 MET 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 711 SER 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 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 227 SER Chi-restraints excluded: chain B residue 250 CYS 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 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 243 THR 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: 6.9990 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 640 ASN A 736 GLN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110823 restraints weight = 17785.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114814 restraints weight = 9742.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117472 restraints weight = 6674.487| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11939 Z= 0.216 Angle : 0.614 10.861 16178 Z= 0.311 Chirality : 0.046 0.236 1826 Planarity : 0.004 0.065 2098 Dihedral : 4.776 25.966 1630 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.03 % Allowed : 22.65 % Favored : 73.32 % 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 (0.21), residues: 1486 helix: -1.36 (0.28), residues: 325 sheet: -2.59 (0.24), residues: 367 loop : -1.59 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.005 0.001 HIS A 808 PHE 0.019 0.002 PHE B 199 TYR 0.016 0.002 TYR A 692 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 270) hydrogen bonds : angle 5.10259 ( 768) covalent geometry : bond 0.00524 (11939) covalent geometry : angle 0.61418 (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 244 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 1.349 Fit side-chains REVERT: A 46 ASP cc_start: 0.8153 (p0) cc_final: 0.7843 (p0) REVERT: A 121 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7501 (ttt) REVERT: A 125 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7823 (t0) REVERT: A 173 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8019 (tppt) REVERT: A 252 GLN cc_start: 0.8175 (mt0) cc_final: 0.7651 (mt0) REVERT: A 374 GLU cc_start: 0.8045 (pm20) cc_final: 0.7507 (pm20) REVERT: A 413 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 422 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8138 (mt0) REVERT: A 869 MET cc_start: 0.7427 (mmp) cc_final: 0.6787 (mmp) REVERT: A 874 ARG cc_start: 0.8389 (ptp-170) cc_final: 0.7791 (ptp-170) REVERT: B 13 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8571 (pp30) REVERT: B 45 MET cc_start: 0.7712 (mtm) cc_final: 0.7321 (mtm) REVERT: B 325 MET cc_start: 0.7343 (mmp) cc_final: 0.6715 (mtp) REVERT: C 13 GLN cc_start: 0.8802 (tt0) cc_final: 0.8523 (pt0) REVERT: C 49 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7595 (mpt-90) REVERT: C 82 TRP cc_start: 0.8732 (m100) cc_final: 0.8285 (m-10) REVERT: C 331 SER cc_start: 0.8938 (m) cc_final: 0.8629 (t) REVERT: D 44 HIS cc_start: 0.7623 (m90) cc_final: 0.7134 (m90) outliers start: 51 outliers final: 42 residues processed: 231 average time/residue: 0.2519 time to fit residues: 82.9034 Evaluate side-chains 236 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 A residue 711 SER 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 14 LEU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 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 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 276 VAL 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 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 MET 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 Chi-restraints excluded: chain C residue 322 ASP 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: 10.0000 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113761 restraints weight = 17558.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117809 restraints weight = 9580.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120564 restraints weight = 6547.889| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2601 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= 0.124 Angle : 0.563 10.701 16178 Z= 0.284 Chirality : 0.044 0.165 1826 Planarity : 0.004 0.064 2098 Dihedral : 4.535 27.775 1630 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.55 % Allowed : 23.60 % Favored : 72.85 % 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: -2.50 (0.21), residues: 1486 helix: -1.13 (0.29), residues: 326 sheet: -2.39 (0.26), residues: 346 loop : -1.48 (0.21), residues: 814 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 0.016 0.001 PHE B 199 TYR 0.015 0.001 TYR G 40 ARG 0.008 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 270) hydrogen bonds : angle 4.89840 ( 768) covalent geometry : bond 0.00301 (11939) covalent geometry : angle 0.56272 (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 240 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8008 (p0) cc_final: 0.7679 (p0) REVERT: A 76 ARG cc_start: 0.8409 (ptt90) cc_final: 0.7946 (ptt90) REVERT: A 121 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7311 (ttt) REVERT: A 173 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7922 (tppt) REVERT: A 252 GLN cc_start: 0.8146 (mt0) cc_final: 0.7762 (mt0) REVERT: A 273 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6828 (ttm110) REVERT: A 374 GLU cc_start: 0.7932 (pm20) cc_final: 0.7433 (pm20) REVERT: A 413 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7063 (mt-10) REVERT: A 641 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8019 (mttp) REVERT: A 869 MET cc_start: 0.7438 (mmp) cc_final: 0.6722 (mmp) REVERT: B 45 MET cc_start: 0.7669 (mtm) cc_final: 0.7295 (mtm) REVERT: B 297 TRP cc_start: 0.8786 (m100) cc_final: 0.8311 (m100) REVERT: B 325 MET cc_start: 0.7295 (mmp) cc_final: 0.6713 (mtp) REVERT: C 13 GLN cc_start: 0.8825 (tt0) cc_final: 0.8507 (pt0) REVERT: C 49 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7622 (mpt-90) REVERT: C 82 TRP cc_start: 0.8686 (m100) cc_final: 0.8224 (m-10) REVERT: C 259 GLN cc_start: 0.7495 (tt0) cc_final: 0.6839 (tm-30) REVERT: C 317 CYS cc_start: 0.8251 (p) cc_final: 0.7983 (p) REVERT: C 331 SER cc_start: 0.8859 (m) cc_final: 0.8574 (t) REVERT: D 14 LYS cc_start: 0.8446 (tmtt) cc_final: 0.7969 (ttmt) REVERT: D 44 HIS cc_start: 0.7595 (m90) cc_final: 0.7132 (m90) outliers start: 45 outliers final: 35 residues processed: 226 average time/residue: 0.2681 time to fit residues: 87.3919 Evaluate side-chains 225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 20 ASP 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 B residue 307 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 143 THR Chi-restraints excluded: chain C residue 189 SER 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 C residue 322 ASP Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 128 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111700 restraints weight = 17585.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115749 restraints weight = 9648.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118375 restraints weight = 6605.300| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11939 Z= 0.186 Angle : 0.598 12.050 16178 Z= 0.303 Chirality : 0.045 0.269 1826 Planarity : 0.004 0.063 2098 Dihedral : 4.685 27.061 1630 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.63 % Allowed : 23.84 % Favored : 72.53 % 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: -2.50 (0.21), residues: 1486 helix: -1.07 (0.29), residues: 326 sheet: -2.40 (0.26), residues: 350 loop : -1.49 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS B 311 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.002 TYR A 692 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 270) hydrogen bonds : angle 5.02210 ( 768) covalent geometry : bond 0.00452 (11939) covalent geometry : angle 0.59814 (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 234 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8123 (p0) cc_final: 0.7794 (p0) REVERT: A 76 ARG cc_start: 0.8410 (ptt90) cc_final: 0.7971 (ptt90) REVERT: A 121 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7299 (ttt) REVERT: A 173 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7953 (tppt) REVERT: A 252 GLN cc_start: 0.8156 (mt0) cc_final: 0.7763 (mt0) REVERT: A 273 ARG cc_start: 0.7169 (ttm110) cc_final: 0.6762 (ttm110) REVERT: A 290 GLN cc_start: 0.7256 (mt0) cc_final: 0.6773 (mt0) REVERT: A 374 GLU cc_start: 0.7994 (pm20) cc_final: 0.7468 (pm20) REVERT: A 413 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7115 (mt-10) REVERT: A 641 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8322 (ttmm) REVERT: A 869 MET cc_start: 0.7451 (mmp) cc_final: 0.6759 (mmp) REVERT: B 13 GLN cc_start: 0.8714 (pp30) cc_final: 0.8506 (pp30) REVERT: B 45 MET cc_start: 0.7687 (mtm) cc_final: 0.7304 (mtm) REVERT: B 325 MET cc_start: 0.7310 (mmp) cc_final: 0.6735 (mtp) REVERT: C 49 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7596 (mpt-90) REVERT: C 82 TRP cc_start: 0.8724 (m100) cc_final: 0.8234 (m-10) REVERT: C 331 SER cc_start: 0.8913 (m) cc_final: 0.8609 (t) REVERT: D 14 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8004 (ttmt) REVERT: D 44 HIS cc_start: 0.7633 (m90) cc_final: 0.7195 (m90) outliers start: 46 outliers final: 39 residues processed: 221 average time/residue: 0.2525 time to fit residues: 79.0568 Evaluate side-chains 224 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 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 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR 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 B residue 307 VAL 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 189 SER 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 271 CYS 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 C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.148569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113942 restraints weight = 17374.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118006 restraints weight = 9448.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120656 restraints weight = 6438.640| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11939 Z= 0.133 Angle : 0.569 12.527 16178 Z= 0.287 Chirality : 0.044 0.250 1826 Planarity : 0.004 0.060 2098 Dihedral : 4.503 30.221 1630 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.47 % Allowed : 24.23 % Favored : 72.30 % 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: -2.35 (0.21), residues: 1486 helix: -0.89 (0.29), residues: 329 sheet: -2.30 (0.25), residues: 366 loop : -1.41 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS B 311 PHE 0.017 0.001 PHE B 199 TYR 0.014 0.001 TYR G 40 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 270) hydrogen bonds : angle 4.86732 ( 768) covalent geometry : bond 0.00323 (11939) covalent geometry : angle 0.56926 (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 234 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8008 (p0) cc_final: 0.7688 (p0) REVERT: A 76 ARG cc_start: 0.8399 (ptt90) cc_final: 0.7927 (ptt90) REVERT: A 121 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7259 (ttt) REVERT: A 173 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7849 (tppt) REVERT: A 252 GLN cc_start: 0.8114 (mt0) cc_final: 0.7743 (mt0) REVERT: A 273 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6791 (ttm110) REVERT: A 374 GLU cc_start: 0.7916 (pm20) cc_final: 0.7422 (pm20) REVERT: A 413 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 641 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8292 (ttmm) REVERT: A 869 MET cc_start: 0.7468 (mmp) cc_final: 0.6746 (mmp) REVERT: B 13 GLN cc_start: 0.8686 (pp30) cc_final: 0.8460 (pp30) REVERT: B 45 MET cc_start: 0.7698 (mtm) cc_final: 0.7333 (mtm) REVERT: B 297 TRP cc_start: 0.8768 (m100) cc_final: 0.8299 (m100) REVERT: B 325 MET cc_start: 0.7314 (mmp) cc_final: 0.6702 (mtp) REVERT: C 49 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7616 (mpt-90) REVERT: C 82 TRP cc_start: 0.8707 (m100) cc_final: 0.8212 (m-10) REVERT: C 259 GLN cc_start: 0.7518 (tt0) cc_final: 0.6678 (tm-30) REVERT: C 317 CYS cc_start: 0.8229 (p) cc_final: 0.7976 (p) REVERT: C 331 SER cc_start: 0.8867 (m) cc_final: 0.8559 (t) REVERT: D 14 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8021 (ttmt) REVERT: D 44 HIS cc_start: 0.7700 (m90) cc_final: 0.7258 (m90) outliers start: 44 outliers final: 41 residues processed: 220 average time/residue: 0.2396 time to fit residues: 75.0770 Evaluate side-chains 228 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 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 634 MET Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR 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 B residue 307 VAL 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 189 SER 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 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 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113512 restraints weight = 17386.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117569 restraints weight = 9502.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120229 restraints weight = 6475.541| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11939 Z= 0.149 Angle : 0.581 12.575 16178 Z= 0.293 Chirality : 0.044 0.238 1826 Planarity : 0.004 0.058 2098 Dihedral : 4.520 29.964 1630 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.71 % Allowed : 24.23 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.21), residues: 1486 helix: -0.78 (0.29), residues: 329 sheet: -2.33 (0.25), residues: 371 loop : -1.38 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS B 54 PHE 0.017 0.001 PHE B 199 TYR 0.013 0.001 TYR G 40 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 270) hydrogen bonds : angle 4.85426 ( 768) covalent geometry : bond 0.00364 (11939) covalent geometry : angle 0.58112 (16178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4117.34 seconds wall clock time: 72 minutes 6.46 seconds (4326.46 seconds total)