Starting phenix.real_space_refine on Sun Aug 24 15:59:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emw_28267/08_2025/8emw_28267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emw_28267/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8emw_28267/08_2025/8emw_28267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emw_28267/08_2025/8emw_28267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8emw_28267/08_2025/8emw_28267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emw_28267/08_2025/8emw_28267.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1} 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: {'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} 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: 2.45, per 1000 atoms: 0.21 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: 0.70 Conformation dependent library (CDL) restraints added in 491.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 1.73 Time building geometry restraints manager: 0.94 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- 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 : 6.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.006 0.001 ARG A 359 TYR 0.021 0.003 TYR A 692 PHE 0.033 0.003 PHE B 199 TRP 0.020 0.002 TRP B 339 HIS 0.011 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00819 (11939) covalent geometry : angle 0.90832 (16178) hydrogen bonds : bond 0.30325 ( 270) hydrogen bonds : angle 10.71339 ( 768) *********************** 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 : 0.427 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: 0.7158 (ttp) REVERT: A 290 GLN cc_start: 0.7581 (mt0) cc_final: 0.7326 (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: 0.7670 (pm20) REVERT: A 460 MET cc_start: 0.8644 (ttp) cc_final: 0.8214 (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: 0.7541 (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: 0.1089 time to fit residues: 36.6621 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 585 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3720 r_free = 0.3720 target = 0.141322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105334 restraints weight = 17623.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109288 restraints weight = 9773.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111823 restraints weight = 6761.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113548 restraints weight = 5368.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114685 restraints weight = 4580.942| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11939 Z= 0.251 Angle : 0.661 8.637 16178 Z= 0.349 Chirality : 0.046 0.164 1826 Planarity : 0.005 0.059 2098 Dihedral : 5.717 25.850 1630 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.00 % Allowed : 15.79 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.24 (0.18), residues: 1486 helix: -3.51 (0.20), residues: 327 sheet: -2.93 (0.24), residues: 380 loop : -2.37 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.020 0.002 TYR A 692 PHE 0.026 0.002 PHE A 636 TRP 0.018 0.002 TRP C 169 HIS 0.005 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00595 (11939) covalent geometry : angle 0.66077 (16178) hydrogen bonds : bond 0.04988 ( 270) hydrogen bonds : angle 6.37000 ( 768) *********************** 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 243 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8265 (p0) cc_final: 0.7933 (p0) REVERT: A 173 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8003 (tppt) REVERT: A 215 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7450 (ttp-170) REVERT: A 236 LYS cc_start: 0.8131 (tptt) cc_final: 0.7633 (mttp) REVERT: A 290 GLN cc_start: 0.7452 (mt0) cc_final: 0.7201 (mt0) REVERT: A 374 GLU cc_start: 0.8171 (pm20) cc_final: 0.7848 (pm20) REVERT: A 439 ILE cc_start: 0.8679 (pt) cc_final: 0.8420 (mt) REVERT: A 870 ASP cc_start: 0.8014 (t0) cc_final: 0.7687 (t0) REVERT: B 12 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 45 MET cc_start: 0.7775 (mtm) cc_final: 0.7427 (mtm) REVERT: B 325 MET cc_start: 0.7172 (mmp) cc_final: 0.6453 (mtp) REVERT: C 78 LYS cc_start: 0.8274 (tttm) cc_final: 0.7941 (mtpp) REVERT: C 82 TRP cc_start: 0.8632 (m100) cc_final: 0.8316 (m100) REVERT: C 156 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7048 (mm-40) REVERT: C 233 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7280 (p) REVERT: C 234 PHE cc_start: 0.7863 (m-80) cc_final: 0.7431 (m-80) REVERT: D 44 HIS cc_start: 0.7785 (m-70) cc_final: 0.7562 (m-70) outliers start: 38 outliers final: 25 residues processed: 231 average time/residue: 0.0986 time to fit residues: 32.5786 Evaluate side-chains 215 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 344 THR 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 95 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 112 VAL 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 271 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 331 SER 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 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 736 GLN ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 GLN B 239 ASN B 340 ASN C 230 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114831 restraints weight = 17523.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118949 restraints weight = 9401.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121702 restraints weight = 6368.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123429 restraints weight = 4930.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124526 restraints weight = 4192.794| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1984 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= 0.107 Angle : 0.536 7.886 16178 Z= 0.279 Chirality : 0.042 0.144 1826 Planarity : 0.004 0.063 2098 Dihedral : 4.852 25.332 1630 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.05 % Allowed : 19.65 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.19), residues: 1486 helix: -2.70 (0.23), residues: 330 sheet: -2.64 (0.25), residues: 346 loop : -1.97 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.011 0.001 TYR A 692 PHE 0.018 0.001 PHE A 381 TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00251 (11939) covalent geometry : angle 0.53638 (16178) hydrogen bonds : bond 0.03508 ( 270) hydrogen bonds : angle 5.39921 ( 768) *********************** 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: 26 poor density : 220 time to evaluate : 0.410 Fit side-chains REVERT: A 46 ASP cc_start: 0.8018 (p0) cc_final: 0.7727 (p0) REVERT: A 173 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7940 (tppt) REVERT: A 215 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7426 (ttp-170) REVERT: A 236 LYS cc_start: 0.7960 (tptt) cc_final: 0.7640 (mttp) REVERT: A 341 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 374 GLU cc_start: 0.7892 (pm20) cc_final: 0.7171 (pm20) REVERT: A 422 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8054 (mt0) REVERT: A 869 MET cc_start: 0.7528 (mmp) cc_final: 0.6763 (mmp) REVERT: A 870 ASP cc_start: 0.7926 (t0) cc_final: 0.7562 (t0) REVERT: B 45 MET cc_start: 0.7688 (mtm) cc_final: 0.7352 (mtm) REVERT: B 325 MET cc_start: 0.7151 (mmp) cc_final: 0.6599 (mtp) REVERT: C 82 TRP cc_start: 0.8639 (m100) cc_final: 0.8373 (m100) REVERT: C 156 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7103 (mm-40) REVERT: C 222 PHE cc_start: 0.7189 (m-80) cc_final: 0.6974 (m-80) REVERT: C 233 CYS cc_start: 0.8090 (t) cc_final: 0.7352 (p) REVERT: C 312 ASP cc_start: 0.7180 (p0) cc_final: 0.6969 (p0) REVERT: C 317 CYS cc_start: 0.8366 (p) cc_final: 0.8039 (p) REVERT: D 14 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8004 (ttmt) outliers start: 26 outliers final: 19 residues processed: 236 average time/residue: 0.0917 time to fit residues: 31.4679 Evaluate side-chains 215 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 341 LEU 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 157 ILE 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 157 ILE 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 296 VAL Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 821 HIS A 871 GLN B 75 GLN B 340 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.147678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112884 restraints weight = 17543.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116882 restraints weight = 9536.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119520 restraints weight = 6510.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.121284 restraints weight = 5082.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122288 restraints weight = 4314.982| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11939 Z= 0.159 Angle : 0.558 8.017 16178 Z= 0.289 Chirality : 0.044 0.139 1826 Planarity : 0.004 0.059 2098 Dihedral : 4.750 22.304 1630 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.47 % Allowed : 20.28 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.20), residues: 1486 helix: -2.14 (0.26), residues: 324 sheet: -2.59 (0.25), residues: 352 loop : -1.78 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.014 0.001 TYR A 822 PHE 0.018 0.002 PHE A 381 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00383 (11939) covalent geometry : angle 0.55800 (16178) hydrogen bonds : bond 0.03408 ( 270) hydrogen bonds : angle 5.24718 ( 768) *********************** 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: 44 poor density : 202 time to evaluate : 0.473 Fit side-chains REVERT: A 46 ASP cc_start: 0.8067 (p0) cc_final: 0.7776 (p0) REVERT: A 173 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7966 (tppt) REVERT: A 215 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7430 (ttp-170) REVERT: A 236 LYS cc_start: 0.8073 (tptt) cc_final: 0.7689 (mttp) REVERT: A 252 GLN cc_start: 0.8173 (mt0) cc_final: 0.7597 (mt0) REVERT: A 374 GLU cc_start: 0.7906 (pm20) cc_final: 0.7425 (pm20) REVERT: A 422 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8070 (mt0) REVERT: A 869 MET cc_start: 0.7488 (mmp) cc_final: 0.6774 (mmp) REVERT: A 870 ASP cc_start: 0.7918 (t0) cc_final: 0.7530 (t0) REVERT: B 45 MET cc_start: 0.7630 (mtm) cc_final: 0.7185 (mtm) REVERT: B 325 MET cc_start: 0.7181 (mmp) cc_final: 0.6596 (mtp) REVERT: C 13 GLN cc_start: 0.8754 (tt0) cc_final: 0.8439 (pt0) REVERT: C 82 TRP cc_start: 0.8653 (m100) cc_final: 0.8326 (m-10) REVERT: C 156 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7064 (mm-40) REVERT: C 234 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: D 44 HIS cc_start: 0.7681 (m90) cc_final: 0.7153 (m90) outliers start: 44 outliers final: 36 residues processed: 231 average time/residue: 0.0958 time to fit residues: 31.7978 Evaluate side-chains 228 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 451 VAL 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 65 THR Chi-restraints excluded: chain B residue 87 THR 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 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 234 PHE 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 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 871 GLN B 340 ASN G 44 HIS C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111685 restraints weight = 17523.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115670 restraints weight = 9584.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118343 restraints weight = 6557.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119995 restraints weight = 5115.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120987 restraints weight = 4366.999| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11939 Z= 0.186 Angle : 0.584 8.510 16178 Z= 0.298 Chirality : 0.044 0.138 1826 Planarity : 0.004 0.062 2098 Dihedral : 4.881 41.443 1630 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.18 % Allowed : 21.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.20), residues: 1486 helix: -1.81 (0.27), residues: 321 sheet: -2.64 (0.24), residues: 363 loop : -1.68 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.015 0.002 TYR A 692 PHE 0.018 0.002 PHE A 381 TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00449 (11939) covalent geometry : angle 0.58371 (16178) hydrogen bonds : bond 0.03360 ( 270) hydrogen bonds : angle 5.19832 ( 768) *********************** 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: 53 poor density : 193 time to evaluate : 0.292 Fit side-chains REVERT: A 46 ASP cc_start: 0.8117 (p0) cc_final: 0.7811 (p0) REVERT: A 121 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7554 (ttt) REVERT: A 125 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7761 (t0) REVERT: A 173 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7966 (tppt) REVERT: A 176 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8652 (mt) REVERT: A 215 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7441 (ttp-170) REVERT: A 236 LYS cc_start: 0.8151 (tptt) cc_final: 0.7698 (mttp) REVERT: A 252 GLN cc_start: 0.8182 (mt0) cc_final: 0.7658 (mt0) REVERT: A 374 GLU cc_start: 0.7980 (pm20) cc_final: 0.7653 (pm20) REVERT: A 413 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 422 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8078 (mt0) REVERT: A 828 GLU cc_start: 0.8510 (mp0) cc_final: 0.8292 (mp0) REVERT: A 869 MET cc_start: 0.7472 (mmp) cc_final: 0.6809 (mmp) REVERT: A 870 ASP cc_start: 0.7900 (t0) cc_final: 0.7542 (t0) REVERT: B 45 MET cc_start: 0.7570 (mtm) cc_final: 0.7087 (mtm) REVERT: B 325 MET cc_start: 0.7239 (mmp) cc_final: 0.6659 (mtp) REVERT: C 13 GLN cc_start: 0.8800 (tt0) cc_final: 0.8498 (pt0) REVERT: C 82 TRP cc_start: 0.8667 (m100) cc_final: 0.8321 (m-10) REVERT: C 234 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: D 14 LYS cc_start: 0.8513 (tmtt) cc_final: 0.7947 (ttmt) REVERT: D 44 HIS cc_start: 0.7758 (m90) cc_final: 0.7170 (m90) outliers start: 53 outliers final: 41 residues processed: 225 average time/residue: 0.0869 time to fit residues: 28.4697 Evaluate side-chains 233 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 176 LEU 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 451 VAL 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 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 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 340 ASN 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 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 871 GLN B 35 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113944 restraints weight = 17499.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118035 restraints weight = 9494.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120741 restraints weight = 6441.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122597 restraints weight = 5009.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123747 restraints weight = 4217.195| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11939 Z= 0.121 Angle : 0.538 8.490 16178 Z= 0.274 Chirality : 0.043 0.139 1826 Planarity : 0.004 0.060 2098 Dihedral : 4.697 51.705 1630 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.79 % Allowed : 22.57 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.20), residues: 1486 helix: -1.51 (0.28), residues: 327 sheet: -2.59 (0.25), residues: 355 loop : -1.57 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.012 0.001 TYR A 648 PHE 0.018 0.001 PHE A 381 TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00291 (11939) covalent geometry : angle 0.53817 (16178) hydrogen bonds : bond 0.02968 ( 270) hydrogen bonds : angle 4.96170 ( 768) *********************** 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 247 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8002 (p0) cc_final: 0.7695 (p0) REVERT: A 173 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7932 (tppt) REVERT: A 215 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7470 (ttp-170) REVERT: A 236 LYS cc_start: 0.8151 (tptt) cc_final: 0.7715 (mttp) REVERT: A 252 GLN cc_start: 0.8166 (mt0) cc_final: 0.7761 (mt0) REVERT: A 273 ARG cc_start: 0.7172 (ttm110) cc_final: 0.6769 (ttm110) REVERT: A 364 ASP cc_start: 0.8153 (m-30) cc_final: 0.7529 (m-30) REVERT: A 374 GLU cc_start: 0.7908 (pm20) cc_final: 0.7453 (pm20) REVERT: A 413 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 422 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7980 (mt0) REVERT: A 869 MET cc_start: 0.7401 (mmp) cc_final: 0.6728 (mmp) REVERT: B 45 MET cc_start: 0.7481 (mtm) cc_final: 0.7263 (mtm) REVERT: B 297 TRP cc_start: 0.8766 (m100) cc_final: 0.8367 (m100) REVERT: B 325 MET cc_start: 0.7190 (mmp) cc_final: 0.6640 (mtp) REVERT: C 13 GLN cc_start: 0.8823 (tt0) cc_final: 0.8547 (pt0) REVERT: C 82 TRP cc_start: 0.8653 (m100) cc_final: 0.8267 (m-10) REVERT: C 318 LEU cc_start: 0.9015 (tt) cc_final: 0.8781 (tt) REVERT: D 14 LYS cc_start: 0.8487 (tmtt) cc_final: 0.7967 (ttmt) REVERT: D 44 HIS cc_start: 0.7753 (m90) cc_final: 0.7127 (m90) outliers start: 48 outliers final: 37 residues processed: 235 average time/residue: 0.1102 time to fit residues: 37.4255 Evaluate side-chains 226 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 808 HIS Chi-restraints excluded: chain A residue 824 CYS 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 65 THR Chi-restraints excluded: chain B residue 87 THR 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 B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN 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 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 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 65 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 239 ASN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108385 restraints weight = 17783.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112250 restraints weight = 9825.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114765 restraints weight = 6771.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116435 restraints weight = 5332.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117632 restraints weight = 4548.426| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 11939 Z= 0.305 Angle : 0.679 8.863 16178 Z= 0.348 Chirality : 0.049 0.330 1826 Planarity : 0.005 0.066 2098 Dihedral : 5.161 28.432 1630 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.58 % Allowed : 22.65 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.20), residues: 1486 helix: -1.56 (0.27), residues: 326 sheet: -2.77 (0.24), residues: 374 loop : -1.72 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.021 0.002 TYR A 692 PHE 0.022 0.002 PHE B 199 TRP 0.013 0.002 TRP C 169 HIS 0.007 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00737 (11939) covalent geometry : angle 0.67942 (16178) hydrogen bonds : bond 0.03755 ( 270) hydrogen bonds : angle 5.44150 ( 768) *********************** 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 246 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.484 Fit side-chains REVERT: A 46 ASP cc_start: 0.8309 (p0) cc_final: 0.7963 (p0) REVERT: A 76 ARG cc_start: 0.8463 (ptt90) cc_final: 0.8074 (ptt90) REVERT: A 173 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8061 (tppt) REVERT: A 215 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7532 (ttp-170) REVERT: A 252 GLN cc_start: 0.8161 (mt0) cc_final: 0.7633 (mt0) REVERT: A 290 GLN cc_start: 0.7352 (mt0) cc_final: 0.6896 (mt0) REVERT: A 374 GLU cc_start: 0.8137 (pm20) cc_final: 0.7795 (pm20) REVERT: A 869 MET cc_start: 0.7426 (mmp) cc_final: 0.6777 (mmp) REVERT: A 874 ARG cc_start: 0.8370 (ptp-170) cc_final: 0.7806 (ptp-170) REVERT: B 45 MET cc_start: 0.7687 (mtm) cc_final: 0.7205 (mtm) REVERT: B 325 MET cc_start: 0.7331 (mmp) cc_final: 0.6594 (mtp) REVERT: G 38 MET cc_start: 0.8161 (tpp) cc_final: 0.7599 (mpp) REVERT: C 49 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7527 (mtt90) REVERT: C 82 TRP cc_start: 0.8709 (m100) cc_final: 0.8314 (m-10) REVERT: C 234 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: C 253 PHE cc_start: 0.8318 (m-10) cc_final: 0.8011 (m-10) REVERT: D 44 HIS cc_start: 0.7686 (m90) cc_final: 0.7174 (m90) outliers start: 58 outliers final: 41 residues processed: 229 average time/residue: 0.1143 time to fit residues: 37.4068 Evaluate side-chains 222 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 193 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS 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 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 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN 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 218 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 124 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 871 GLN B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.150041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115614 restraints weight = 17368.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119731 restraints weight = 9405.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122455 restraints weight = 6383.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124236 restraints weight = 4953.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125374 restraints weight = 4197.079| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11939 Z= 0.100 Angle : 0.553 8.993 16178 Z= 0.280 Chirality : 0.043 0.261 1826 Planarity : 0.004 0.062 2098 Dihedral : 4.500 30.794 1630 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 24.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.21), residues: 1486 helix: -1.08 (0.29), residues: 329 sheet: -2.42 (0.26), residues: 339 loop : -1.43 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 273 TYR 0.012 0.001 TYR A 596 PHE 0.018 0.001 PHE A 381 TRP 0.012 0.001 TRP C 211 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00234 (11939) covalent geometry : angle 0.55271 (16178) hydrogen bonds : bond 0.02838 ( 270) hydrogen bonds : angle 4.90311 ( 768) *********************** 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 231 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7931 (p0) cc_final: 0.7616 (p0) REVERT: A 173 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7879 (tppt) REVERT: A 273 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6779 (ttm110) REVERT: A 290 GLN cc_start: 0.7178 (mt0) cc_final: 0.6738 (mt0) REVERT: A 364 ASP cc_start: 0.8279 (m-30) cc_final: 0.7738 (m-30) REVERT: A 374 GLU cc_start: 0.7924 (pm20) cc_final: 0.7440 (pm20) REVERT: A 869 MET cc_start: 0.7359 (mmp) cc_final: 0.6614 (mmp) REVERT: B 45 MET cc_start: 0.7605 (mtm) cc_final: 0.7165 (mtm) REVERT: B 297 TRP cc_start: 0.8745 (m100) cc_final: 0.8309 (m100) REVERT: B 325 MET cc_start: 0.7305 (mmp) cc_final: 0.6737 (mtp) REVERT: C 13 GLN cc_start: 0.8838 (tt0) cc_final: 0.8548 (pt0) REVERT: C 82 TRP cc_start: 0.8689 (m100) cc_final: 0.8241 (m-10) REVERT: C 259 GLN cc_start: 0.7485 (tt0) cc_final: 0.6703 (tm-30) REVERT: C 317 CYS cc_start: 0.8311 (p) cc_final: 0.7950 (p) REVERT: C 318 LEU cc_start: 0.8998 (tt) cc_final: 0.8781 (tt) REVERT: D 14 LYS cc_start: 0.8447 (tmtt) cc_final: 0.7957 (ttmt) REVERT: D 44 HIS cc_start: 0.7625 (m90) cc_final: 0.7221 (m90) outliers start: 31 outliers final: 25 residues processed: 221 average time/residue: 0.1054 time to fit residues: 33.3226 Evaluate side-chains 213 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU 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 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 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 81 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.0000 chunk 107 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116672 restraints weight = 17148.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120791 restraints weight = 9396.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123450 restraints weight = 6407.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125221 restraints weight = 5012.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126432 restraints weight = 4244.868| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2874 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= 0.101 Angle : 0.549 9.598 16178 Z= 0.277 Chirality : 0.043 0.232 1826 Planarity : 0.004 0.060 2098 Dihedral : 4.358 28.761 1630 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.29 % Allowed : 25.26 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.21), residues: 1486 helix: -0.80 (0.29), residues: 327 sheet: -2.27 (0.26), residues: 364 loop : -1.31 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.020 0.001 TYR G 40 PHE 0.019 0.001 PHE C 253 TRP 0.009 0.001 TRP C 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00241 (11939) covalent geometry : angle 0.54884 (16178) hydrogen bonds : bond 0.02822 ( 270) hydrogen bonds : angle 4.80525 ( 768) *********************** 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 222 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7929 (p0) cc_final: 0.7615 (p0) REVERT: A 60 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 173 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7816 (tppt) REVERT: A 252 GLN cc_start: 0.8043 (mt0) cc_final: 0.7695 (mt0) REVERT: A 273 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6876 (ttm110) REVERT: A 290 GLN cc_start: 0.7192 (mt0) cc_final: 0.6798 (mt0) REVERT: A 364 ASP cc_start: 0.8277 (m-30) cc_final: 0.7777 (m-30) REVERT: A 374 GLU cc_start: 0.7885 (pm20) cc_final: 0.7418 (pm20) REVERT: A 641 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8080 (mttp) REVERT: A 869 MET cc_start: 0.7326 (mmp) cc_final: 0.6619 (mmp) REVERT: B 45 MET cc_start: 0.7558 (mtm) cc_final: 0.7137 (mtm) REVERT: B 59 TYR cc_start: 0.8882 (m-80) cc_final: 0.8678 (m-80) REVERT: B 75 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7442 (tt0) REVERT: B 297 TRP cc_start: 0.8746 (m100) cc_final: 0.8231 (m100) REVERT: B 325 MET cc_start: 0.7282 (mmp) cc_final: 0.6719 (mtp) REVERT: C 17 GLN cc_start: 0.7944 (mt0) cc_final: 0.7734 (tm-30) REVERT: C 82 TRP cc_start: 0.8667 (m100) cc_final: 0.8205 (m-10) REVERT: C 259 GLN cc_start: 0.7468 (tt0) cc_final: 0.6762 (tm-30) REVERT: C 317 CYS cc_start: 0.8319 (p) cc_final: 0.7934 (p) REVERT: C 318 LEU cc_start: 0.8912 (tt) cc_final: 0.8711 (tt) REVERT: D 14 LYS cc_start: 0.8439 (tmtt) cc_final: 0.7980 (ttmt) REVERT: D 44 HIS cc_start: 0.7692 (m90) cc_final: 0.7266 (m90) outliers start: 29 outliers final: 22 residues processed: 212 average time/residue: 0.1108 time to fit residues: 33.7137 Evaluate side-chains 208 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU 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 C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 141 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 871 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114349 restraints weight = 17553.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118432 restraints weight = 9526.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121155 restraints weight = 6472.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122908 restraints weight = 5029.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124067 restraints weight = 4265.403| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11939 Z= 0.138 Angle : 0.581 9.027 16178 Z= 0.289 Chirality : 0.044 0.238 1826 Planarity : 0.004 0.059 2098 Dihedral : 4.406 27.949 1630 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.82 % Allowed : 25.81 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.21), residues: 1486 helix: -0.69 (0.30), residues: 327 sheet: -2.26 (0.25), residues: 368 loop : -1.29 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.020 0.001 TYR G 40 PHE 0.016 0.001 PHE B 199 TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00336 (11939) covalent geometry : angle 0.58057 (16178) hydrogen bonds : bond 0.02909 ( 270) hydrogen bonds : angle 4.79502 ( 768) ********************** 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 208 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8022 (p0) cc_final: 0.7695 (p0) REVERT: A 173 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7822 (tppt) REVERT: A 252 GLN cc_start: 0.8031 (mt0) cc_final: 0.7683 (mt0) REVERT: A 273 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6888 (ttm110) REVERT: A 290 GLN cc_start: 0.7211 (mt0) cc_final: 0.6788 (mt0) REVERT: A 374 GLU cc_start: 0.7946 (pm20) cc_final: 0.7464 (pm20) REVERT: A 641 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8317 (ttmm) REVERT: A 869 MET cc_start: 0.7397 (mmp) cc_final: 0.6671 (mmp) REVERT: B 45 MET cc_start: 0.7609 (mtm) cc_final: 0.7170 (mtm) REVERT: B 297 TRP cc_start: 0.8760 (m100) cc_final: 0.8271 (m100) REVERT: B 325 MET cc_start: 0.7313 (mmp) cc_final: 0.6718 (mtp) REVERT: C 49 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7622 (mpt-90) REVERT: C 82 TRP cc_start: 0.8685 (m100) cc_final: 0.8194 (m-10) REVERT: C 259 GLN cc_start: 0.7508 (tt0) cc_final: 0.7116 (tm-30) REVERT: C 318 LEU cc_start: 0.8939 (tt) cc_final: 0.8700 (tt) REVERT: D 14 LYS cc_start: 0.8498 (tmtt) cc_final: 0.8020 (ttmt) REVERT: D 44 HIS cc_start: 0.7754 (m90) cc_final: 0.7328 (m90) outliers start: 23 outliers final: 20 residues processed: 200 average time/residue: 0.1195 time to fit residues: 33.7757 Evaluate side-chains 199 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 49 ARG 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 192 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 77 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116932 restraints weight = 17555.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121099 restraints weight = 9497.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123854 restraints weight = 6407.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125676 restraints weight = 4960.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126786 restraints weight = 4182.325| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11939 Z= 0.099 Angle : 0.561 9.173 16178 Z= 0.278 Chirality : 0.043 0.195 1826 Planarity : 0.003 0.052 2098 Dihedral : 4.241 31.148 1630 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 25.49 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.22), residues: 1486 helix: -0.53 (0.30), residues: 329 sheet: -2.03 (0.27), residues: 356 loop : -1.18 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.020 0.001 TYR G 40 PHE 0.015 0.001 PHE C 253 TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00235 (11939) covalent geometry : angle 0.56128 (16178) hydrogen bonds : bond 0.02727 ( 270) hydrogen bonds : angle 4.66040 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.88 seconds wall clock time: 35 minutes 47.48 seconds (2147.48 seconds total)