Starting phenix.real_space_refine on Tue Aug 26 21:36:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5s_26357/08_2025/7u5s_26357.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5s_26357/08_2025/7u5s_26357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u5s_26357/08_2025/7u5s_26357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5s_26357/08_2025/7u5s_26357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5s_26357/08_2025/7u5s_26357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5s_26357/08_2025/7u5s_26357.map" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 22792 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 14689 2.51 5 N 3897 2.21 5 O 4408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1501, 11524 Classifications: {'peptide': 1501} Link IDs: {'PTRANS': 67, 'TRANS': 1433} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1505, 11553 Classifications: {'peptide': 1505} Link IDs: {'PTRANS': 67, 'TRANS': 1437} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 1505, 11553 Classifications: {'peptide': 1505} Link IDs: {'PTRANS': 67, 'TRANS': 1437} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 11757 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B 11 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 11 " occ=0.50 Time building chain proxies: 6.22, per 1000 atoms: 0.27 Number of scatterers: 23086 At special positions: 0 Unit cell: (118.703, 181.178, 181.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 4408 8.00 N 3897 7.00 C 14689 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: 1.32 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5524 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 32 sheets defined 46.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.805A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.659A pdb=" N SER A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.598A pdb=" N LYS A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.535A pdb=" N ALA A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.521A pdb=" N MET A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.504A pdb=" N ARG A 127 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.786A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 removed outlier: 4.058A pdb=" N GLU A 178 " --> pdb=" O SER A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.502A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 219 removed outlier: 3.722A pdb=" N ASN A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 248 removed outlier: 3.760A pdb=" N GLU A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.696A pdb=" N PHE A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.625A pdb=" N ALA A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 removed outlier: 3.795A pdb=" N CYS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 4.090A pdb=" N VAL A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.103A pdb=" N HIS A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.601A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.596A pdb=" N LEU A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 removed outlier: 3.631A pdb=" N ILE A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 removed outlier: 3.675A pdb=" N LYS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.854A pdb=" N THR A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 564 through 575 removed outlier: 3.897A pdb=" N VAL A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 593 through 607 removed outlier: 3.846A pdb=" N ILE A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 650 removed outlier: 3.770A pdb=" N LEU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 removed outlier: 3.716A pdb=" N ALA A 671 " --> pdb=" O GLN A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 672 through 677 removed outlier: 3.737A pdb=" N VAL A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 725 Processing helix chain 'A' and resid 738 through 742 removed outlier: 3.965A pdb=" N ARG A 742 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.580A pdb=" N ALA A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 removed outlier: 3.915A pdb=" N LEU A 804 " --> pdb=" O MET A 800 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.887A pdb=" N THR A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 821 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 822 " --> pdb=" O SER A 819 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 823 " --> pdb=" O THR A 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 823' Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.796A pdb=" N HIS A 833 " --> pdb=" O TRP A 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.592A pdb=" N GLU A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.971A pdb=" N LEU A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.952A pdb=" N ILE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 901 through 906' Processing helix chain 'A' and resid 909 through 924 removed outlier: 3.669A pdb=" N PHE A 913 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 923 " --> pdb=" O ILE A 919 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 957 removed outlier: 3.552A pdb=" N LEU A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.601A pdb=" N TRP A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG A 993 " --> pdb=" O GLU A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1013 through 1023 Processing helix chain 'A' and resid 1024 through 1031 Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1082 through 1095 removed outlier: 3.530A pdb=" N ALA A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A1093 " --> pdb=" O GLN A1089 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1119 through 1131 removed outlier: 3.645A pdb=" N LEU A1128 " --> pdb=" O SER A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.546A pdb=" N GLU A1149 " --> pdb=" O ASN A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1188 removed outlier: 4.050A pdb=" N LYS A1179 " --> pdb=" O ASN A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1213 removed outlier: 3.992A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1235 Processing helix chain 'A' and resid 1255 through 1266 removed outlier: 3.501A pdb=" N ASN A1260 " --> pdb=" O ILE A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1298 removed outlier: 3.739A pdb=" N LEU A1289 " --> pdb=" O ARG A1285 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 3.513A pdb=" N TYR A1315 " --> pdb=" O VAL A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1334 removed outlier: 3.707A pdb=" N LYS A1334 " --> pdb=" O MET A1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1331 through 1334' Processing helix chain 'A' and resid 1335 through 1340 removed outlier: 3.753A pdb=" N MET A1338 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1339 " --> pdb=" O ASP A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1352 Processing helix chain 'A' and resid 1370 through 1380 removed outlier: 3.790A pdb=" N PHE A1378 " --> pdb=" O ILE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1409 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1445 through 1450 removed outlier: 3.887A pdb=" N LYS A1449 " --> pdb=" O GLN A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1476 removed outlier: 3.864A pdb=" N LYS A1472 " --> pdb=" O GLY A1468 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A1476 " --> pdb=" O LYS A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1510 Processing helix chain 'A' and resid 1519 through 1536 removed outlier: 3.724A pdb=" N ARG A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1546 Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.805A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 30 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.658A pdb=" N SER B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.534A pdb=" N ALA B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 99 removed outlier: 3.724A pdb=" N GLY B 99 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.520A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.786A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 178 removed outlier: 4.057A pdb=" N GLU B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 178' Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.500A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 219 removed outlier: 3.721A pdb=" N ASN B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 removed outlier: 3.691A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.696A pdb=" N PHE B 262 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.625A pdb=" N ALA B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 298 removed outlier: 3.796A pdb=" N CYS B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 4.090A pdb=" N VAL B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.105A pdb=" N HIS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.601A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.595A pdb=" N LEU B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.633A pdb=" N ILE B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.675A pdb=" N LYS B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.854A pdb=" N THR B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 564 through 575 removed outlier: 3.898A pdb=" N VAL B 568 " --> pdb=" O SER B 564 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 593 through 607 removed outlier: 3.908A pdb=" N ILE B 597 " --> pdb=" O SER B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 650 removed outlier: 3.770A pdb=" N LEU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 671 removed outlier: 3.719A pdb=" N ALA B 671 " --> pdb=" O GLN B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 671' Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.738A pdb=" N VAL B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 725 Processing helix chain 'B' and resid 738 through 742 removed outlier: 3.963A pdb=" N ARG B 742 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 760 removed outlier: 3.613A pdb=" N ALA B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 753 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.656A pdb=" N ALA B 799 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 804 " --> pdb=" O MET B 800 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 809 No H-bonds generated for 'chain 'B' and resid 807 through 809' Processing helix chain 'B' and resid 817 through 823 removed outlier: 3.886A pdb=" N THR B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR B 821 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 822 " --> pdb=" O SER B 819 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 823 " --> pdb=" O THR B 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 817 through 823' Processing helix chain 'B' and resid 827 through 835 removed outlier: 3.796A pdb=" N HIS B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 883 removed outlier: 3.527A pdb=" N TRP B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 896 removed outlier: 3.786A pdb=" N GLU B 894 " --> pdb=" O ASP B 890 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 896 " --> pdb=" O TYR B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 905 removed outlier: 3.586A pdb=" N LEU B 904 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 905 " --> pdb=" O LYS B 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 901 through 905' Processing helix chain 'B' and resid 909 through 924 removed outlier: 3.535A pdb=" N PHE B 913 " --> pdb=" O GLY B 909 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 914 " --> pdb=" O TRP B 910 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 918 " --> pdb=" O ARG B 914 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 923 " --> pdb=" O ILE B 919 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 956 removed outlier: 4.053A pdb=" N ARG B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 949 " --> pdb=" O ASP B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1002 removed outlier: 3.995A pdb=" N VAL B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 993 " --> pdb=" O GLU B 989 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 995 " --> pdb=" O TRP B 991 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TRP B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B1000 " --> pdb=" O LYS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1032 removed outlier: 3.822A pdb=" N ARG B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B1025 " --> pdb=" O ARG B1021 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B1026 " --> pdb=" O ARG B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1065 Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1082 through 1091 removed outlier: 4.033A pdb=" N VAL B1086 " --> pdb=" O SER B1082 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B1087 " --> pdb=" O ALA B1083 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B1091 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1107 through 1111 removed outlier: 3.596A pdb=" N GLY B1111 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1132 removed outlier: 3.539A pdb=" N ARG B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1152 removed outlier: 3.906A pdb=" N GLU B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1188 Processing helix chain 'B' and resid 1202 through 1215 removed outlier: 3.613A pdb=" N LEU B1206 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B1210 " --> pdb=" O LEU B1206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B1214 " --> pdb=" O ASN B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1235 removed outlier: 3.707A pdb=" N GLN B1233 " --> pdb=" O GLY B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1266 Processing helix chain 'B' and resid 1285 through 1297 removed outlier: 3.595A pdb=" N ASN B1291 " --> pdb=" O PRO B1287 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B1292 " --> pdb=" O ASN B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.744A pdb=" N ASP B1316 " --> pdb=" O ASP B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1331 through 1335 Processing helix chain 'B' and resid 1336 through 1340 removed outlier: 3.652A pdb=" N LYS B1339 " --> pdb=" O ASP B1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1352 removed outlier: 3.518A pdb=" N GLU B1349 " --> pdb=" O SER B1345 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B1350 " --> pdb=" O ASP B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1380 removed outlier: 4.225A pdb=" N SER B1377 " --> pdb=" O GLY B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1410 removed outlier: 3.787A pdb=" N TYR B1405 " --> pdb=" O ARG B1401 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B1409 " --> pdb=" O TYR B1405 " (cutoff:3.500A) Processing helix chain 'B' and resid 1421 through 1426 Processing helix chain 'B' and resid 1426 through 1431 removed outlier: 3.639A pdb=" N SER B1431 " --> pdb=" O GLU B1427 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1449 removed outlier: 3.673A pdb=" N ALA B1447 " --> pdb=" O THR B1443 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1481 removed outlier: 3.766A pdb=" N ILE B1474 " --> pdb=" O VAL B1470 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B1476 " --> pdb=" O LYS B1472 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B1479 " --> pdb=" O GLU B1475 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN B1480 " --> pdb=" O ARG B1476 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY B1481 " --> pdb=" O ILE B1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1510 removed outlier: 3.669A pdb=" N LYS B1506 " --> pdb=" O THR B1502 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B1507 " --> pdb=" O PRO B1503 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B1510 " --> pdb=" O LYS B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1519 through 1535 removed outlier: 3.682A pdb=" N ASN B1525 " --> pdb=" O GLU B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1548 removed outlier: 3.791A pdb=" N ARG B1546 " --> pdb=" O GLU B1542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.729A pdb=" N ILE A 8 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL A 170 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 13 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 172 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS A 15 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 131 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N PHE A 171 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN A 133 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP A 173 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 134 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 38 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 109 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 40 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR A 37 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR A 74 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 39 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 76 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR A 41 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.669A pdb=" N LYS A 365 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 813 through 815 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 456 removed outlier: 3.882A pdb=" N GLY A 425 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR A 634 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG A 428 " --> pdb=" O TYR A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA8, first strand: chain 'A' and resid 555 through 560 Processing sheet with id=AA9, first strand: chain 'A' and resid 656 through 659 Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.507A pdb=" N GLU A 771 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 863 through 865 Processing sheet with id=AB3, first strand: chain 'A' and resid 885 through 888 removed outlier: 7.072A pdb=" N LYS A 885 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER A 935 " --> pdb=" O LYS A 885 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 887 " --> pdb=" O SER A 935 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 6.534A pdb=" N VAL A1193 " --> pdb=" O ILE A1221 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE A1223 " --> pdb=" O VAL A1193 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A1195 " --> pdb=" O PHE A1223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A1160 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG A1194 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY A1162 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL A1196 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A1164 " --> pdb=" O VAL A1196 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A1071 " --> pdb=" O ILE A1102 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1104 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A1073 " --> pdb=" O THR A1104 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A1045 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU A1072 " --> pdb=" O ALA A1045 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A1047 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG A1074 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A1049 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A1046 " --> pdb=" O ILE A1242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1301 through 1307 removed outlier: 3.534A pdb=" N GLN A1302 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A1278 " --> pdb=" O PHE A1306 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A1273 " --> pdb=" O GLY A1325 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A1327 " --> pdb=" O LYS A1273 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TRP A1275 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE A1329 " --> pdb=" O TRP A1275 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A1277 " --> pdb=" O ILE A1329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1343 through 1344 removed outlier: 6.617A pdb=" N LYS A1343 " --> pdb=" O GLY A1366 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A1363 " --> pdb=" O ILE A1360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1438 through 1440 removed outlier: 6.274A pdb=" N ILE A1415 " --> pdb=" O GLU A1439 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A1391 " --> pdb=" O TYR A1416 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL A1418 " --> pdb=" O GLY A1391 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A1393 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN A1390 " --> pdb=" O VAL A1453 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A1392 " --> pdb=" O LEU A1455 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER A1454 " --> pdb=" O THR A1491 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU A1493 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA A1456 " --> pdb=" O LEU A1493 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.697A pdb=" N GLU B 4 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS B 15 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 6 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 13 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N VAL B 170 " --> pdb=" O ALYS B 11 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 13 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS B 172 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS B 15 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 131 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N PHE B 171 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN B 133 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP B 173 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 134 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 38 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 109 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 40 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR B 37 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR B 74 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 39 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL B 76 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR B 41 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AC1, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AC2, first strand: chain 'B' and resid 363 through 365 removed outlier: 3.669A pdb=" N LYS B 365 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 813 through 815 Processing sheet with id=AC4, first strand: chain 'B' and resid 424 through 429 removed outlier: 3.883A pdb=" N GLY B 425 " --> pdb=" O GLY B 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 478 through 479 Processing sheet with id=AC6, first strand: chain 'B' and resid 555 through 560 Processing sheet with id=AC7, first strand: chain 'B' and resid 656 through 659 Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 735 removed outlier: 3.509A pdb=" N GLU B 771 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 861 through 864 removed outlier: 6.461A pdb=" N ILE B 862 " --> pdb=" O LEU B 961 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 963 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE B 864 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 885 through 886 removed outlier: 6.946A pdb=" N LYS B 885 " --> pdb=" O VAL B 933 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1220 through 1225 removed outlier: 3.525A pdb=" N PHE B1223 " --> pdb=" O LEU B1195 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B1160 " --> pdb=" O ILE B1192 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG B1194 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY B1162 " --> pdb=" O ARG B1194 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL B1196 " --> pdb=" O GLY B1162 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR B1164 " --> pdb=" O VAL B1196 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LYS B1198 " --> pdb=" O TYR B1164 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B1137 " --> pdb=" O ILE B1161 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR B1163 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B1139 " --> pdb=" O THR B1163 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN B1165 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE B1102 " --> pdb=" O ASP B1069 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B1071 " --> pdb=" O ILE B1102 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B1104 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU B1073 " --> pdb=" O THR B1104 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B1045 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU B1072 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B1047 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ARG B1074 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B1049 " --> pdb=" O ARG B1074 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1302 through 1307 removed outlier: 3.676A pdb=" N GLY B1278 " --> pdb=" O PHE B1306 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS B1273 " --> pdb=" O GLY B1325 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B1327 " --> pdb=" O LYS B1273 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP B1275 " --> pdb=" O LEU B1327 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE B1329 " --> pdb=" O TRP B1275 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B1277 " --> pdb=" O ILE B1329 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1343 through 1344 removed outlier: 3.694A pdb=" N GLY B1363 " --> pdb=" O ILE B1360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1438 through 1440 removed outlier: 6.174A pdb=" N ILE B1415 " --> pdb=" O GLU B1439 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B1416 " --> pdb=" O GLY B1391 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN B1390 " --> pdb=" O LEU B1455 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL B1457 " --> pdb=" O ASN B1390 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU B1392 " --> pdb=" O VAL B1457 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 1.88 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: 6654 1.33 - 1.45: 3988 1.45 - 1.57: 12722 1.57 - 1.69: 3 1.69 - 1.82: 148 Bond restraints: 23515 Sorted by residual: bond pdb=" C ASN B 61 " pdb=" N LEU B 62 " ideal model delta sigma weight residual 1.333 1.213 0.120 1.50e-02 4.44e+03 6.37e+01 bond pdb=" C LEU B 62 " pdb=" N SER B 63 " ideal model delta sigma weight residual 1.335 1.419 -0.084 1.38e-02 5.25e+03 3.73e+01 bond pdb=" C SER A 63 " pdb=" N GLU A 64 " ideal model delta sigma weight residual 1.333 1.246 0.087 1.43e-02 4.89e+03 3.71e+01 bond pdb=" C GLU A 64 " pdb=" N LYS A 65 " ideal model delta sigma weight residual 1.333 1.410 -0.077 1.38e-02 5.25e+03 3.15e+01 bond pdb=" C LEU B 536 " pdb=" N ASN B 537 " ideal model delta sigma weight residual 1.332 1.410 -0.078 1.40e-02 5.10e+03 3.10e+01 ... (remaining 23510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 29974 2.01 - 4.01: 1629 4.01 - 6.02: 179 6.02 - 8.02: 38 8.02 - 10.03: 25 Bond angle restraints: 31845 Sorted by residual: angle pdb=" O GLU B 633 " pdb=" C GLU B 633 " pdb=" N TYR B 634 " ideal model delta sigma weight residual 123.31 114.98 8.33 1.17e+00 7.31e-01 5.07e+01 angle pdb=" CA LEU B 536 " pdb=" C LEU B 536 " pdb=" N ASN B 537 " ideal model delta sigma weight residual 116.93 125.64 -8.71 1.26e+00 6.30e-01 4.78e+01 angle pdb=" C LYS B 221 " pdb=" N LYS B 222 " pdb=" CA LYS B 222 " ideal model delta sigma weight residual 121.83 112.03 9.80 1.56e+00 4.11e-01 3.95e+01 angle pdb=" C LYS A 221 " pdb=" N LYS A 222 " pdb=" CA LYS A 222 " ideal model delta sigma weight residual 121.83 112.07 9.76 1.56e+00 4.11e-01 3.92e+01 angle pdb=" N ILE B 777 " pdb=" CA ILE B 777 " pdb=" C ILE B 777 " ideal model delta sigma weight residual 112.35 103.61 8.74 1.41e+00 5.03e-01 3.84e+01 ... (remaining 31840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12751 17.93 - 35.85: 1175 35.85 - 53.77: 219 53.77 - 71.70: 50 71.70 - 89.62: 26 Dihedral angle restraints: 14221 sinusoidal: 5615 harmonic: 8606 Sorted by residual: dihedral pdb=" CA THR A1330 " pdb=" C THR A1330 " pdb=" N MET A1331 " pdb=" CA MET A1331 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL A1038 " pdb=" C VAL A1038 " pdb=" N VAL A1039 " pdb=" CA VAL A1039 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA VAL A1039 " pdb=" C VAL A1039 " pdb=" N PRO A1040 " pdb=" CA PRO A1040 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 14218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2620 0.060 - 0.119: 861 0.119 - 0.179: 172 0.179 - 0.239: 29 0.239 - 0.298: 11 Chirality restraints: 3693 Sorted by residual: chirality pdb=" CB ILE A1281 " pdb=" CA ILE A1281 " pdb=" CG1 ILE A1281 " pdb=" CG2 ILE A1281 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA MET B1331 " pdb=" N MET B1331 " pdb=" C MET B1331 " pdb=" CB MET B1331 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ILE B 749 " pdb=" N ILE B 749 " pdb=" C ILE B 749 " pdb=" CB ILE B 749 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 3690 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 633 " 0.025 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C GLU B 633 " -0.081 2.00e-02 2.50e+03 pdb=" O GLU B 633 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 634 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 63 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C SER A 63 " -0.054 2.00e-02 2.50e+03 pdb=" O SER A 63 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 64 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 791 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER A 791 " 0.053 2.00e-02 2.50e+03 pdb=" O SER A 791 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A 792 " -0.018 2.00e-02 2.50e+03 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5976 2.79 - 3.32: 20590 3.32 - 3.85: 38357 3.85 - 4.37: 46285 4.37 - 4.90: 76662 Nonbonded interactions: 187870 Sorted by model distance: nonbonded pdb=" O MET B 45 " pdb=" OG1 THR B 48 " model vdw 2.265 3.040 nonbonded pdb=" O MET A 45 " pdb=" OG1 THR A 48 " model vdw 2.265 3.040 nonbonded pdb=" OE2 GLU A1072 " pdb=" OG1 THR A1104 " model vdw 2.265 3.040 nonbonded pdb=" O GLY B 938 " pdb=" OH TYR B 998 " model vdw 2.277 3.040 nonbonded pdb=" O MET A 599 " pdb=" CD1 LEU A 667 " model vdw 2.289 3.460 ... (remaining 187865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 10 or resid 12 through 634 or resid 639 through \ 1550)) selection = (chain 'B' and (resid 2 through 10 or resid 12 through 250 or resid 256 through \ 634 or resid 639 through 964 or resid 985 through 1550)) } 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=0.50 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: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.280 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4360 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 0.120 23515 Z= 0.425 Angle : 1.024 10.029 31845 Z= 0.603 Chirality : 0.061 0.298 3693 Planarity : 0.007 0.072 4070 Dihedral : 14.832 89.625 8697 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % 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: -4.93 (0.12), residues: 2985 helix: -4.22 (0.07), residues: 1274 sheet: -2.24 (0.22), residues: 466 loop : -2.36 (0.15), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1546 TYR 0.027 0.003 TYR A 577 PHE 0.025 0.003 PHE B 836 TRP 0.017 0.002 TRP B1371 HIS 0.009 0.002 HIS B 707 Details of bonding type rmsd covalent geometry : bond 0.00840 (23515) covalent geometry : angle 1.02426 (31845) hydrogen bonds : bond 0.30130 ( 798) hydrogen bonds : angle 10.51053 ( 2205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.6778 (tttt) cc_final: 0.6543 (tttt) REVERT: A 117 MET cc_start: 0.6153 (ttp) cc_final: 0.5664 (ttp) REVERT: A 208 GLU cc_start: 0.5450 (mm-30) cc_final: 0.4778 (mm-30) REVERT: A 280 HIS cc_start: 0.5496 (t70) cc_final: 0.5081 (t70) REVERT: A 298 LEU cc_start: 0.7053 (mt) cc_final: 0.6745 (mt) REVERT: A 303 PRO cc_start: 0.7122 (Cg_endo) cc_final: 0.6633 (Cg_exo) REVERT: A 311 LYS cc_start: 0.8213 (tptp) cc_final: 0.7981 (ttmm) REVERT: A 886 MET cc_start: 0.5951 (tmm) cc_final: 0.5482 (tmm) REVERT: A 889 MET cc_start: 0.5590 (mmp) cc_final: 0.4867 (mmp) REVERT: A 932 TYR cc_start: 0.5669 (m-80) cc_final: 0.5445 (m-80) REVERT: A 942 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6231 (tp30) REVERT: A 1009 SER cc_start: 0.8066 (m) cc_final: 0.7422 (t) REVERT: A 1025 VAL cc_start: 0.8239 (t) cc_final: 0.7976 (p) REVERT: A 1043 ARG cc_start: 0.6810 (ttt-90) cc_final: 0.4805 (tmt-80) REVERT: A 1044 SER cc_start: 0.8155 (p) cc_final: 0.7941 (p) REVERT: A 1048 VAL cc_start: 0.8767 (t) cc_final: 0.8472 (m) REVERT: A 1053 ASP cc_start: 0.4810 (t70) cc_final: 0.3507 (t0) REVERT: A 1072 GLU cc_start: 0.6687 (tp30) cc_final: 0.6466 (tp30) REVERT: A 1077 LEU cc_start: 0.7257 (pp) cc_final: 0.6831 (pp) REVERT: A 1078 PHE cc_start: 0.5997 (m-10) cc_final: 0.5790 (m-80) REVERT: A 1093 ILE cc_start: 0.6488 (tt) cc_final: 0.5927 (mm) REVERT: A 1110 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6231 (mp10) REVERT: A 1126 LEU cc_start: 0.8326 (mt) cc_final: 0.7824 (mm) REVERT: A 1128 LEU cc_start: 0.7232 (tp) cc_final: 0.6920 (tp) REVERT: A 1171 LEU cc_start: 0.6886 (mt) cc_final: 0.6542 (mt) REVERT: A 1221 ILE cc_start: 0.7843 (mt) cc_final: 0.7617 (mt) REVERT: A 1224 ASN cc_start: 0.8061 (m-40) cc_final: 0.7831 (m-40) REVERT: A 1231 LEU cc_start: 0.7995 (tp) cc_final: 0.7681 (tt) REVERT: A 1242 ILE cc_start: 0.7554 (pt) cc_final: 0.6989 (mm) REVERT: A 1272 LYS cc_start: 0.8239 (mttp) cc_final: 0.7984 (mmmt) REVERT: A 1327 LEU cc_start: 0.5504 (mt) cc_final: 0.5290 (mm) REVERT: A 1342 THR cc_start: 0.7414 (p) cc_final: 0.7016 (t) REVERT: A 1356 THR cc_start: 0.7095 (m) cc_final: 0.6739 (p) REVERT: A 1409 GLN cc_start: 0.6978 (mt0) cc_final: 0.6200 (tt0) REVERT: A 1410 MET cc_start: 0.5121 (tpp) cc_final: 0.4561 (tpp) REVERT: A 1418 VAL cc_start: 0.8262 (t) cc_final: 0.7659 (t) REVERT: A 1424 LYS cc_start: 0.6600 (tttt) cc_final: 0.6282 (tmtt) REVERT: A 1432 PHE cc_start: 0.6745 (m-80) cc_final: 0.6304 (m-80) REVERT: A 1526 GLN cc_start: 0.6431 (tt0) cc_final: 0.6209 (pt0) REVERT: A 1529 ARG cc_start: 0.6949 (tpt90) cc_final: 0.6685 (mmm-85) REVERT: A 1530 GLN cc_start: 0.6669 (mt0) cc_final: 0.5851 (mt0) REVERT: A 1532 LYS cc_start: 0.8659 (tptp) cc_final: 0.7809 (tppt) REVERT: A 1533 LEU cc_start: 0.7951 (mt) cc_final: 0.7730 (mt) REVERT: A 1538 THR cc_start: 0.8734 (m) cc_final: 0.8138 (p) REVERT: B 94 PHE cc_start: 0.4047 (t80) cc_final: 0.1716 (t80) REVERT: B 141 MET cc_start: 0.5388 (mtt) cc_final: 0.4901 (tmm) REVERT: B 180 LEU cc_start: 0.7155 (tp) cc_final: 0.6865 (tp) REVERT: B 198 ILE cc_start: 0.6837 (pt) cc_final: 0.6112 (mt) REVERT: B 266 ILE cc_start: 0.7596 (mt) cc_final: 0.6337 (mm) REVERT: B 284 VAL cc_start: 0.6564 (t) cc_final: 0.6135 (t) REVERT: B 798 VAL cc_start: 0.5195 (t) cc_final: 0.4119 (t) REVERT: B 1048 VAL cc_start: 0.7469 (t) cc_final: 0.6790 (p) REVERT: B 1078 PHE cc_start: 0.5674 (m-10) cc_final: 0.5381 (m-80) REVERT: B 1090 ILE cc_start: 0.8399 (mt) cc_final: 0.8199 (tt) REVERT: B 1125 LEU cc_start: 0.8065 (mt) cc_final: 0.7434 (mt) REVERT: B 1126 LEU cc_start: 0.7366 (mt) cc_final: 0.6786 (mt) REVERT: B 1152 SER cc_start: 0.8169 (m) cc_final: 0.7910 (p) REVERT: B 1228 GLN cc_start: 0.7571 (mt0) cc_final: 0.7317 (tt0) REVERT: B 1231 LEU cc_start: 0.8012 (tp) cc_final: 0.7388 (tt) REVERT: B 1233 GLN cc_start: 0.7313 (mt0) cc_final: 0.6972 (tt0) REVERT: B 1235 LEU cc_start: 0.8730 (mt) cc_final: 0.8498 (mm) REVERT: B 1242 ILE cc_start: 0.8143 (pt) cc_final: 0.6585 (mm) REVERT: B 1246 LEU cc_start: 0.8394 (mt) cc_final: 0.7991 (mm) REVERT: B 1256 ILE cc_start: 0.8150 (tp) cc_final: 0.6946 (tp) REVERT: B 1260 ASN cc_start: 0.6760 (m-40) cc_final: 0.6193 (m-40) REVERT: B 1290 HIS cc_start: 0.6069 (m-70) cc_final: 0.4598 (m90) REVERT: B 1342 THR cc_start: 0.7821 (m) cc_final: 0.7482 (p) REVERT: B 1409 GLN cc_start: 0.6850 (mm-40) cc_final: 0.6545 (mm-40) REVERT: B 1437 ASN cc_start: 0.6334 (m110) cc_final: 0.5939 (m110) REVERT: B 1438 LEU cc_start: 0.6807 (mt) cc_final: 0.6497 (tt) REVERT: B 1441 VAL cc_start: 0.8357 (t) cc_final: 0.8092 (p) REVERT: B 1505 MET cc_start: 0.5842 (mtp) cc_final: 0.5216 (mtp) REVERT: B 1522 MET cc_start: 0.6176 (ttp) cc_final: 0.5736 (tpt) REVERT: B 1530 GLN cc_start: 0.6830 (mt0) cc_final: 0.6556 (mt0) REVERT: B 1543 ILE cc_start: 0.8098 (mt) cc_final: 0.7675 (tp) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.1560 time to fit residues: 152.9847 Evaluate side-chains 509 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 393 HIS A 431 ASN A 537 ASN A1184 GLN A1203 GLN ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 264 HIS B 393 HIS B 434 HIS B 440 HIS ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1290 HIS ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1376 ASN B1484 GLN B1545 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.217531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.173034 restraints weight = 79306.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.180080 restraints weight = 46213.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.185289 restraints weight = 30971.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.189131 restraints weight = 22181.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.191903 restraints weight = 16864.034| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23515 Z= 0.160 Angle : 0.695 11.564 31845 Z= 0.365 Chirality : 0.046 0.195 3693 Planarity : 0.006 0.064 4070 Dihedral : 5.382 22.047 3187 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.01 % 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: -3.37 (0.13), residues: 2985 helix: -2.57 (0.11), residues: 1326 sheet: -1.57 (0.23), residues: 468 loop : -1.86 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 335 TYR 0.022 0.002 TYR A1164 PHE 0.028 0.002 PHE A 176 TRP 0.030 0.002 TRP A1514 HIS 0.021 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00338 (23515) covalent geometry : angle 0.69506 (31845) hydrogen bonds : bond 0.05099 ( 798) hydrogen bonds : angle 5.93251 ( 2205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 556 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.4413 (t) cc_final: 0.3430 (p) REVERT: A 75 CYS cc_start: 0.7571 (p) cc_final: 0.6785 (m) REVERT: A 80 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 88 LYS cc_start: 0.7988 (tttt) cc_final: 0.7740 (tttt) REVERT: A 117 MET cc_start: 0.7445 (ttp) cc_final: 0.7075 (ttp) REVERT: A 126 MET cc_start: 0.5879 (mmm) cc_final: 0.5474 (mmm) REVERT: A 134 VAL cc_start: 0.7904 (t) cc_final: 0.7645 (p) REVERT: A 160 PHE cc_start: 0.8107 (m-10) cc_final: 0.7774 (m-10) REVERT: A 168 GLU cc_start: 0.7006 (tp30) cc_final: 0.5789 (tp30) REVERT: A 192 VAL cc_start: 0.7932 (p) cc_final: 0.7378 (t) REVERT: A 238 GLU cc_start: 0.7328 (mp0) cc_final: 0.6988 (mp0) REVERT: A 274 LEU cc_start: 0.7708 (mp) cc_final: 0.7444 (mp) REVERT: A 288 MET cc_start: 0.8146 (mtm) cc_final: 0.7350 (mtm) REVERT: A 294 LEU cc_start: 0.8921 (tp) cc_final: 0.8586 (mt) REVERT: A 296 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7436 (mmm-85) REVERT: A 311 LYS cc_start: 0.8994 (tptp) cc_final: 0.8487 (ttmm) REVERT: A 339 GLU cc_start: 0.8223 (mp0) cc_final: 0.7922 (mp0) REVERT: A 800 MET cc_start: 0.6978 (mtt) cc_final: 0.6369 (mtt) REVERT: A 886 MET cc_start: 0.6895 (tmm) cc_final: 0.6197 (tmm) REVERT: A 924 CYS cc_start: 0.7704 (m) cc_final: 0.7291 (t) REVERT: A 932 TYR cc_start: 0.6248 (m-80) cc_final: 0.5635 (m-80) REVERT: A 1009 SER cc_start: 0.7948 (m) cc_final: 0.7077 (t) REVERT: A 1024 PHE cc_start: 0.7872 (t80) cc_final: 0.7454 (t80) REVERT: A 1025 VAL cc_start: 0.8865 (t) cc_final: 0.8524 (p) REVERT: A 1031 ILE cc_start: 0.7057 (pt) cc_final: 0.6824 (pt) REVERT: A 1043 ARG cc_start: 0.6706 (ttt-90) cc_final: 0.6315 (ttt90) REVERT: A 1048 VAL cc_start: 0.8883 (t) cc_final: 0.8503 (m) REVERT: A 1078 PHE cc_start: 0.7063 (m-10) cc_final: 0.6638 (m-80) REVERT: A 1093 ILE cc_start: 0.7644 (tt) cc_final: 0.7048 (mm) REVERT: A 1103 TYR cc_start: 0.6231 (t80) cc_final: 0.5784 (t80) REVERT: A 1158 THR cc_start: 0.7049 (m) cc_final: 0.6737 (p) REVERT: A 1171 LEU cc_start: 0.7029 (mt) cc_final: 0.6634 (mt) REVERT: A 1234 VAL cc_start: 0.8669 (p) cc_final: 0.8458 (p) REVERT: A 1242 ILE cc_start: 0.7664 (pt) cc_final: 0.7224 (mm) REVERT: A 1261 GLN cc_start: 0.7850 (tp40) cc_final: 0.6601 (tp-100) REVERT: A 1262 THR cc_start: 0.7807 (p) cc_final: 0.7508 (t) REVERT: A 1265 ASP cc_start: 0.8218 (m-30) cc_final: 0.7128 (m-30) REVERT: A 1272 LYS cc_start: 0.8324 (mttp) cc_final: 0.7722 (mmmt) REVERT: A 1273 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7884 (mmmm) REVERT: A 1290 HIS cc_start: 0.7380 (m-70) cc_final: 0.6343 (m-70) REVERT: A 1303 PHE cc_start: 0.6998 (t80) cc_final: 0.6698 (t80) REVERT: A 1315 TYR cc_start: 0.7757 (t80) cc_final: 0.7231 (t80) REVERT: A 1327 LEU cc_start: 0.6903 (mt) cc_final: 0.6251 (mm) REVERT: A 1356 THR cc_start: 0.7118 (m) cc_final: 0.6356 (p) REVERT: A 1407 LEU cc_start: 0.8270 (mt) cc_final: 0.8065 (mt) REVERT: A 1410 MET cc_start: 0.6812 (tpp) cc_final: 0.5656 (tpp) REVERT: A 1417 LEU cc_start: 0.8066 (mt) cc_final: 0.7775 (mt) REVERT: A 1428 LEU cc_start: 0.8677 (mt) cc_final: 0.8310 (mt) REVERT: A 1432 PHE cc_start: 0.7148 (m-80) cc_final: 0.6260 (m-80) REVERT: A 1440 ILE cc_start: 0.7184 (tp) cc_final: 0.6519 (mm) REVERT: A 1522 MET cc_start: 0.8329 (ptt) cc_final: 0.7727 (ptt) REVERT: A 1529 ARG cc_start: 0.8021 (tpt90) cc_final: 0.7483 (mmm-85) REVERT: A 1532 LYS cc_start: 0.8964 (tptp) cc_final: 0.8251 (tppt) REVERT: A 1538 THR cc_start: 0.8653 (m) cc_final: 0.8380 (t) REVERT: B 31 ASN cc_start: 0.6448 (p0) cc_final: 0.6157 (p0) REVERT: B 117 MET cc_start: 0.7602 (ttp) cc_final: 0.7311 (ttp) REVERT: B 141 MET cc_start: 0.7030 (mtt) cc_final: 0.5904 (tmm) REVERT: B 184 GLN cc_start: 0.8723 (mt0) cc_final: 0.8131 (mp10) REVERT: B 204 PHE cc_start: 0.6821 (t80) cc_final: 0.6614 (t80) REVERT: B 240 VAL cc_start: 0.7977 (t) cc_final: 0.7073 (m) REVERT: B 243 LYS cc_start: 0.8743 (tttm) cc_final: 0.8506 (ptpt) REVERT: B 266 ILE cc_start: 0.8398 (mt) cc_final: 0.8081 (mm) REVERT: B 288 MET cc_start: 0.8575 (mtt) cc_final: 0.8347 (mtt) REVERT: B 748 ARG cc_start: 0.6668 (ttp80) cc_final: 0.6368 (ttp80) REVERT: B 798 VAL cc_start: 0.7151 (t) cc_final: 0.6053 (t) REVERT: B 866 MET cc_start: 0.7018 (mmt) cc_final: 0.6345 (mmt) REVERT: B 1069 ASP cc_start: 0.8034 (m-30) cc_final: 0.7620 (m-30) REVERT: B 1090 ILE cc_start: 0.8260 (mt) cc_final: 0.7882 (tt) REVERT: B 1098 ASP cc_start: 0.7291 (p0) cc_final: 0.7052 (p0) REVERT: B 1120 ASP cc_start: 0.8496 (t0) cc_final: 0.8159 (p0) REVERT: B 1125 LEU cc_start: 0.8750 (mt) cc_final: 0.8507 (mt) REVERT: B 1126 LEU cc_start: 0.8583 (mt) cc_final: 0.7547 (mt) REVERT: B 1130 ILE cc_start: 0.6507 (mt) cc_final: 0.6140 (mt) REVERT: B 1152 SER cc_start: 0.8769 (m) cc_final: 0.8549 (p) REVERT: B 1170 GLU cc_start: 0.7689 (pm20) cc_final: 0.7256 (pm20) REVERT: B 1178 TRP cc_start: 0.6648 (m100) cc_final: 0.6175 (m100) REVERT: B 1207 ASP cc_start: 0.7460 (t0) cc_final: 0.6742 (t0) REVERT: B 1211 PHE cc_start: 0.7933 (t80) cc_final: 0.7595 (t80) REVERT: B 1228 GLN cc_start: 0.7826 (mt0) cc_final: 0.7240 (tt0) REVERT: B 1233 GLN cc_start: 0.8356 (mt0) cc_final: 0.7549 (tt0) REVERT: B 1235 LEU cc_start: 0.8931 (mt) cc_final: 0.8593 (mm) REVERT: B 1242 ILE cc_start: 0.8374 (pt) cc_final: 0.7035 (mm) REVERT: B 1245 LYS cc_start: 0.9064 (pptt) cc_final: 0.8648 (pptt) REVERT: B 1246 LEU cc_start: 0.8816 (mt) cc_final: 0.8076 (mt) REVERT: B 1256 ILE cc_start: 0.8540 (tp) cc_final: 0.7749 (tp) REVERT: B 1260 ASN cc_start: 0.8164 (m-40) cc_final: 0.7740 (m-40) REVERT: B 1289 LEU cc_start: 0.8243 (tt) cc_final: 0.8029 (tt) REVERT: B 1290 HIS cc_start: 0.7905 (m90) cc_final: 0.6810 (m90) REVERT: B 1303 PHE cc_start: 0.8252 (t80) cc_final: 0.7536 (t80) REVERT: B 1342 THR cc_start: 0.7672 (m) cc_final: 0.7348 (p) REVERT: B 1364 TYR cc_start: 0.7633 (m-80) cc_final: 0.6840 (m-80) REVERT: B 1371 TRP cc_start: 0.8350 (p-90) cc_final: 0.7820 (p-90) REVERT: B 1372 VAL cc_start: 0.8901 (t) cc_final: 0.8576 (t) REVERT: B 1430 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8228 (mmmm) REVERT: B 1441 VAL cc_start: 0.8566 (t) cc_final: 0.8329 (p) REVERT: B 1473 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8226 (mmtp) REVERT: B 1505 MET cc_start: 0.6813 (mtp) cc_final: 0.6244 (mtp) REVERT: B 1522 MET cc_start: 0.7663 (ttp) cc_final: 0.6888 (tpt) REVERT: B 1529 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7787 (mmm160) REVERT: B 1530 GLN cc_start: 0.8478 (mt0) cc_final: 0.7910 (mt0) REVERT: B 1543 ILE cc_start: 0.8221 (mt) cc_final: 0.7770 (mm) outliers start: 4 outliers final: 2 residues processed: 558 average time/residue: 0.1436 time to fit residues: 124.7245 Evaluate side-chains 502 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 179 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS A 964 HIS ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN A1224 ASN A1236 ASN A1260 ASN ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 440 HIS B 668 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1317 ASN B1409 GLN B1484 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.212317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.165020 restraints weight = 91797.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.172272 restraints weight = 52497.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.177726 restraints weight = 34901.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181683 restraints weight = 25129.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.184575 restraints weight = 19126.740| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4435 r_free = 0.4435 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4435 r_free = 0.4435 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23515 Z= 0.190 Angle : 0.696 14.369 31845 Z= 0.363 Chirality : 0.046 0.207 3693 Planarity : 0.005 0.122 4070 Dihedral : 5.164 26.460 3187 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % 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: -2.50 (0.14), residues: 2985 helix: -1.63 (0.13), residues: 1332 sheet: -1.46 (0.23), residues: 478 loop : -1.53 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 335 TYR 0.019 0.002 TYR B 51 PHE 0.029 0.002 PHE A 327 TRP 0.032 0.002 TRP B 828 HIS 0.019 0.002 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00383 (23515) covalent geometry : angle 0.69625 (31845) hydrogen bonds : bond 0.04286 ( 798) hydrogen bonds : angle 5.54627 ( 2205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 554 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.7513 (p) cc_final: 0.6855 (m) REVERT: A 80 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 88 LYS cc_start: 0.7816 (tttt) cc_final: 0.7595 (tttt) REVERT: A 117 MET cc_start: 0.7509 (ttp) cc_final: 0.7183 (ttp) REVERT: A 168 GLU cc_start: 0.6911 (tp30) cc_final: 0.6644 (tp30) REVERT: A 176 PHE cc_start: 0.6593 (m-10) cc_final: 0.5619 (m-10) REVERT: A 192 VAL cc_start: 0.8067 (p) cc_final: 0.7580 (t) REVERT: A 200 ASN cc_start: 0.5856 (t0) cc_final: 0.5567 (t0) REVERT: A 238 GLU cc_start: 0.7730 (mp0) cc_final: 0.7352 (mp0) REVERT: A 288 MET cc_start: 0.8069 (mtm) cc_final: 0.7319 (mtm) REVERT: A 294 LEU cc_start: 0.9004 (tp) cc_final: 0.8750 (mt) REVERT: A 311 LYS cc_start: 0.8996 (tptp) cc_final: 0.8485 (ttmm) REVERT: A 339 GLU cc_start: 0.8090 (mp0) cc_final: 0.7713 (mp0) REVERT: A 886 MET cc_start: 0.7013 (tmm) cc_final: 0.6333 (tmm) REVERT: A 924 CYS cc_start: 0.7667 (m) cc_final: 0.7379 (t) REVERT: A 932 TYR cc_start: 0.6351 (m-80) cc_final: 0.5672 (m-80) REVERT: A 947 ARG cc_start: 0.7094 (mmp80) cc_final: 0.6283 (mmp80) REVERT: A 1007 TYR cc_start: 0.6536 (m-80) cc_final: 0.5969 (m-80) REVERT: A 1009 SER cc_start: 0.7808 (m) cc_final: 0.7027 (t) REVERT: A 1024 PHE cc_start: 0.7970 (t80) cc_final: 0.7602 (t80) REVERT: A 1029 LYS cc_start: 0.8372 (ptmt) cc_final: 0.8169 (ptmt) REVERT: A 1030 LEU cc_start: 0.7521 (tp) cc_final: 0.7213 (tp) REVERT: A 1031 ILE cc_start: 0.7031 (pt) cc_final: 0.6502 (pt) REVERT: A 1043 ARG cc_start: 0.6963 (ttt-90) cc_final: 0.6564 (ttt90) REVERT: A 1048 VAL cc_start: 0.8901 (t) cc_final: 0.8543 (m) REVERT: A 1103 TYR cc_start: 0.6176 (t80) cc_final: 0.5799 (t80) REVERT: A 1125 LEU cc_start: 0.8324 (mt) cc_final: 0.7937 (mp) REVERT: A 1150 GLU cc_start: 0.6589 (tp30) cc_final: 0.6269 (tp30) REVERT: A 1158 THR cc_start: 0.7103 (m) cc_final: 0.6832 (p) REVERT: A 1171 LEU cc_start: 0.7058 (mt) cc_final: 0.6667 (mt) REVERT: A 1180 ASN cc_start: 0.8139 (m-40) cc_final: 0.7889 (t0) REVERT: A 1224 ASN cc_start: 0.8229 (m-40) cc_final: 0.7677 (m110) REVERT: A 1242 ILE cc_start: 0.7708 (pt) cc_final: 0.7196 (mm) REVERT: A 1261 GLN cc_start: 0.7850 (tp40) cc_final: 0.6581 (tp40) REVERT: A 1265 ASP cc_start: 0.8282 (m-30) cc_final: 0.7032 (m-30) REVERT: A 1272 LYS cc_start: 0.8553 (mttp) cc_final: 0.7924 (mmmt) REVERT: A 1273 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8167 (mmmm) REVERT: A 1290 HIS cc_start: 0.6215 (m-70) cc_final: 0.5558 (m-70) REVERT: A 1297 LEU cc_start: 0.8791 (mt) cc_final: 0.8516 (mm) REVERT: A 1327 LEU cc_start: 0.6826 (mt) cc_final: 0.6454 (mm) REVERT: A 1349 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7429 (pp20) REVERT: A 1356 THR cc_start: 0.7473 (m) cc_final: 0.6895 (p) REVERT: A 1361 GLU cc_start: 0.7787 (mp0) cc_final: 0.7448 (mp0) REVERT: A 1408 HIS cc_start: 0.7704 (t-170) cc_final: 0.7479 (t-90) REVERT: A 1410 MET cc_start: 0.7072 (tpp) cc_final: 0.5854 (tpp) REVERT: A 1418 VAL cc_start: 0.7450 (t) cc_final: 0.6903 (p) REVERT: A 1428 LEU cc_start: 0.8658 (mt) cc_final: 0.8328 (mt) REVERT: A 1432 PHE cc_start: 0.7368 (m-80) cc_final: 0.6558 (m-80) REVERT: A 1440 ILE cc_start: 0.6815 (tp) cc_final: 0.6410 (tt) REVERT: A 1474 ILE cc_start: 0.9050 (pt) cc_final: 0.8832 (pt) REVERT: A 1477 ILE cc_start: 0.8792 (tp) cc_final: 0.8290 (pt) REVERT: A 1522 MET cc_start: 0.8360 (ptt) cc_final: 0.7902 (ptt) REVERT: A 1524 VAL cc_start: 0.8019 (t) cc_final: 0.7631 (p) REVERT: A 1526 GLN cc_start: 0.8062 (pt0) cc_final: 0.7316 (pp30) REVERT: A 1528 ASP cc_start: 0.7789 (m-30) cc_final: 0.7166 (m-30) REVERT: A 1529 ARG cc_start: 0.7994 (tpt90) cc_final: 0.7740 (tpt170) REVERT: A 1532 LYS cc_start: 0.8962 (tptp) cc_final: 0.8159 (tppt) REVERT: A 1533 LEU cc_start: 0.8727 (mt) cc_final: 0.8483 (mt) REVERT: B 31 ASN cc_start: 0.6781 (p0) cc_final: 0.6364 (p0) REVERT: B 92 GLU cc_start: 0.8079 (tt0) cc_final: 0.7777 (tt0) REVERT: B 94 PHE cc_start: 0.5621 (t80) cc_final: 0.5177 (t80) REVERT: B 102 ARG cc_start: 0.8013 (ppt170) cc_final: 0.7566 (ttp80) REVERT: B 117 MET cc_start: 0.7647 (ttp) cc_final: 0.7333 (ttp) REVERT: B 141 MET cc_start: 0.7207 (mtt) cc_final: 0.5951 (tmm) REVERT: B 200 ASN cc_start: 0.7252 (p0) cc_final: 0.6958 (p0) REVERT: B 204 PHE cc_start: 0.7029 (t80) cc_final: 0.6678 (t80) REVERT: B 215 LEU cc_start: 0.7197 (mm) cc_final: 0.6886 (mm) REVERT: B 240 VAL cc_start: 0.7941 (t) cc_final: 0.7716 (m) REVERT: B 243 LYS cc_start: 0.8964 (tttm) cc_final: 0.8706 (ptpt) REVERT: B 264 HIS cc_start: 0.7792 (t-90) cc_final: 0.7590 (t70) REVERT: B 288 MET cc_start: 0.8543 (mtt) cc_final: 0.8068 (mtt) REVERT: B 300 ILE cc_start: 0.7920 (mt) cc_final: 0.7714 (mm) REVERT: B 311 LYS cc_start: 0.8994 (pttt) cc_final: 0.8721 (pttp) REVERT: B 312 CYS cc_start: 0.8114 (p) cc_final: 0.7854 (p) REVERT: B 347 MET cc_start: 0.4981 (mmp) cc_final: 0.4674 (mmp) REVERT: B 604 MET cc_start: 0.6527 (ppp) cc_final: 0.5947 (ppp) REVERT: B 798 VAL cc_start: 0.7237 (t) cc_final: 0.6133 (t) REVERT: B 802 PHE cc_start: 0.5688 (m-80) cc_final: 0.5412 (m-80) REVERT: B 862 ILE cc_start: 0.7433 (mm) cc_final: 0.7219 (mm) REVERT: B 965 ARG cc_start: 0.7380 (ttt180) cc_final: 0.7139 (tpt90) REVERT: B 1029 LYS cc_start: 0.8124 (mttt) cc_final: 0.7279 (tppt) REVERT: B 1069 ASP cc_start: 0.8086 (m-30) cc_final: 0.7706 (m-30) REVERT: B 1090 ILE cc_start: 0.8611 (mt) cc_final: 0.8106 (tp) REVERT: B 1098 ASP cc_start: 0.7118 (p0) cc_final: 0.6898 (p0) REVERT: B 1106 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6633 (mmm-85) REVERT: B 1120 ASP cc_start: 0.8507 (t0) cc_final: 0.8302 (p0) REVERT: B 1121 GLU cc_start: 0.8127 (tp30) cc_final: 0.7776 (tm-30) REVERT: B 1125 LEU cc_start: 0.8857 (mt) cc_final: 0.8575 (mt) REVERT: B 1126 LEU cc_start: 0.8473 (mt) cc_final: 0.8096 (mt) REVERT: B 1130 ILE cc_start: 0.6755 (mt) cc_final: 0.6397 (mt) REVERT: B 1149 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 1152 SER cc_start: 0.8777 (m) cc_final: 0.8374 (p) REVERT: B 1178 TRP cc_start: 0.6486 (m100) cc_final: 0.6157 (m100) REVERT: B 1207 ASP cc_start: 0.7548 (t0) cc_final: 0.6880 (t0) REVERT: B 1211 PHE cc_start: 0.8008 (t80) cc_final: 0.7791 (t80) REVERT: B 1213 LYS cc_start: 0.8504 (tmmt) cc_final: 0.8097 (tmmt) REVERT: B 1228 GLN cc_start: 0.7942 (mt0) cc_final: 0.7486 (tt0) REVERT: B 1233 GLN cc_start: 0.8269 (mt0) cc_final: 0.7608 (tt0) REVERT: B 1235 LEU cc_start: 0.8975 (mt) cc_final: 0.8700 (mm) REVERT: B 1245 LYS cc_start: 0.9077 (pptt) cc_final: 0.8501 (pptt) REVERT: B 1246 LEU cc_start: 0.8911 (mt) cc_final: 0.8180 (mt) REVERT: B 1252 GLU cc_start: 0.6855 (mp0) cc_final: 0.6650 (mp0) REVERT: B 1256 ILE cc_start: 0.8832 (tp) cc_final: 0.8192 (tp) REVERT: B 1260 ASN cc_start: 0.8223 (m-40) cc_final: 0.7839 (m-40) REVERT: B 1290 HIS cc_start: 0.8266 (m90) cc_final: 0.7532 (m90) REVERT: B 1297 LEU cc_start: 0.8524 (mt) cc_final: 0.8259 (mt) REVERT: B 1303 PHE cc_start: 0.8234 (t80) cc_final: 0.7586 (t80) REVERT: B 1342 THR cc_start: 0.8014 (m) cc_final: 0.7640 (p) REVERT: B 1351 ILE cc_start: 0.9172 (mt) cc_final: 0.8539 (mm) REVERT: B 1372 VAL cc_start: 0.8940 (t) cc_final: 0.8652 (t) REVERT: B 1376 ASN cc_start: 0.8429 (m110) cc_final: 0.8227 (m110) REVERT: B 1410 MET cc_start: 0.7970 (mtm) cc_final: 0.7738 (mtm) REVERT: B 1417 LEU cc_start: 0.7617 (mt) cc_final: 0.7369 (mt) REVERT: B 1430 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8166 (mmmm) REVERT: B 1441 VAL cc_start: 0.8642 (t) cc_final: 0.7799 (p) REVERT: B 1473 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8041 (mmtp) REVERT: B 1505 MET cc_start: 0.6914 (mtp) cc_final: 0.6167 (mtp) REVERT: B 1522 MET cc_start: 0.7851 (ttp) cc_final: 0.6922 (tpt) REVERT: B 1529 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.7800 (mmm160) REVERT: B 1530 GLN cc_start: 0.8619 (mt0) cc_final: 0.8144 (mt0) REVERT: B 1543 ILE cc_start: 0.8272 (mt) cc_final: 0.7866 (tp) outliers start: 1 outliers final: 1 residues processed: 554 average time/residue: 0.1523 time to fit residues: 131.2610 Evaluate side-chains 519 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 518 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 21 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 228 optimal weight: 0.4980 chunk 214 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 156 optimal weight: 5.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 ASN A1437 ASN ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1302 GLN B1409 GLN B1484 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.211641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.164296 restraints weight = 84021.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.171688 restraints weight = 48933.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.176798 restraints weight = 32555.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.180596 restraints weight = 23682.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.183310 restraints weight = 18182.359| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23515 Z= 0.151 Angle : 0.637 13.689 31845 Z= 0.327 Chirality : 0.045 0.295 3693 Planarity : 0.005 0.100 4070 Dihedral : 4.911 25.627 3187 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -1.99 (0.15), residues: 2985 helix: -1.08 (0.14), residues: 1332 sheet: -1.33 (0.23), residues: 483 loop : -1.38 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 742 TYR 0.020 0.002 TYR A1512 PHE 0.031 0.002 PHE B 717 TRP 0.054 0.002 TRP B 828 HIS 0.007 0.001 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00321 (23515) covalent geometry : angle 0.63746 (31845) hydrogen bonds : bond 0.03648 ( 798) hydrogen bonds : angle 5.23070 ( 2205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.7680 (t70) cc_final: 0.7113 (t70) REVERT: A 75 CYS cc_start: 0.7488 (p) cc_final: 0.6807 (m) REVERT: A 80 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 88 LYS cc_start: 0.7521 (tmmt) cc_final: 0.7028 (tmmt) REVERT: A 117 MET cc_start: 0.7484 (ttp) cc_final: 0.7176 (ttp) REVERT: A 120 PHE cc_start: 0.8729 (t80) cc_final: 0.8207 (t80) REVERT: A 126 MET cc_start: 0.6159 (mmp) cc_final: 0.5804 (mmp) REVERT: A 215 LEU cc_start: 0.8809 (mt) cc_final: 0.8593 (mp) REVERT: A 288 MET cc_start: 0.8085 (mtm) cc_final: 0.7264 (mtm) REVERT: A 294 LEU cc_start: 0.9052 (tp) cc_final: 0.8717 (mt) REVERT: A 302 PRO cc_start: 0.6679 (Cg_endo) cc_final: 0.6424 (Cg_exo) REVERT: A 311 LYS cc_start: 0.8936 (tptp) cc_final: 0.8418 (ttmm) REVERT: A 339 GLU cc_start: 0.7951 (mp0) cc_final: 0.7628 (mp0) REVERT: A 681 MET cc_start: 0.7989 (mmp) cc_final: 0.7715 (mmt) REVERT: A 713 MET cc_start: 0.6815 (mmp) cc_final: 0.6509 (mmp) REVERT: A 794 ASP cc_start: 0.8199 (t0) cc_final: 0.7987 (m-30) REVERT: A 878 LEU cc_start: 0.8280 (tp) cc_final: 0.8078 (tp) REVERT: A 886 MET cc_start: 0.7016 (tmm) cc_final: 0.6656 (tmm) REVERT: A 924 CYS cc_start: 0.7700 (m) cc_final: 0.7491 (t) REVERT: A 947 ARG cc_start: 0.7205 (mmp80) cc_final: 0.6325 (mmp80) REVERT: A 1003 ASN cc_start: 0.7478 (t0) cc_final: 0.7240 (t0) REVERT: A 1005 HIS cc_start: 0.5063 (m170) cc_final: 0.4617 (m-70) REVERT: A 1007 TYR cc_start: 0.6634 (m-80) cc_final: 0.6184 (m-80) REVERT: A 1009 SER cc_start: 0.7767 (m) cc_final: 0.6949 (t) REVERT: A 1024 PHE cc_start: 0.7951 (t80) cc_final: 0.7525 (t80) REVERT: A 1029 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7543 (ptmt) REVERT: A 1030 LEU cc_start: 0.7514 (tp) cc_final: 0.7264 (tp) REVERT: A 1031 ILE cc_start: 0.7240 (pt) cc_final: 0.6814 (pt) REVERT: A 1035 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 1043 ARG cc_start: 0.6737 (ttt-90) cc_final: 0.6330 (ttt90) REVERT: A 1048 VAL cc_start: 0.8879 (t) cc_final: 0.8465 (m) REVERT: A 1103 TYR cc_start: 0.6353 (t80) cc_final: 0.5953 (t80) REVERT: A 1125 LEU cc_start: 0.8228 (mt) cc_final: 0.7867 (mp) REVERT: A 1158 THR cc_start: 0.7213 (m) cc_final: 0.6843 (p) REVERT: A 1171 LEU cc_start: 0.6769 (mt) cc_final: 0.6369 (mt) REVERT: A 1180 ASN cc_start: 0.8086 (m-40) cc_final: 0.7804 (t0) REVERT: A 1202 ILE cc_start: 0.8266 (tt) cc_final: 0.8013 (mm) REVERT: A 1224 ASN cc_start: 0.8117 (m-40) cc_final: 0.7683 (m110) REVERT: A 1261 GLN cc_start: 0.7809 (tp40) cc_final: 0.6487 (tp40) REVERT: A 1265 ASP cc_start: 0.8176 (m-30) cc_final: 0.6681 (m-30) REVERT: A 1272 LYS cc_start: 0.8563 (mttp) cc_final: 0.7992 (mmmt) REVERT: A 1273 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8073 (mmmm) REVERT: A 1290 HIS cc_start: 0.6620 (m-70) cc_final: 0.5690 (m-70) REVERT: A 1295 LYS cc_start: 0.8855 (pttm) cc_final: 0.8336 (ptpt) REVERT: A 1297 LEU cc_start: 0.8769 (mt) cc_final: 0.8441 (mm) REVERT: A 1327 LEU cc_start: 0.6619 (mt) cc_final: 0.6066 (mm) REVERT: A 1344 LEU cc_start: 0.8131 (tp) cc_final: 0.6928 (tp) REVERT: A 1356 THR cc_start: 0.7641 (m) cc_final: 0.6930 (p) REVERT: A 1361 GLU cc_start: 0.7764 (mp0) cc_final: 0.7451 (mp0) REVERT: A 1407 LEU cc_start: 0.8074 (mt) cc_final: 0.7810 (mt) REVERT: A 1410 MET cc_start: 0.6953 (tpp) cc_final: 0.5712 (tpp) REVERT: A 1417 LEU cc_start: 0.8185 (mt) cc_final: 0.7930 (mt) REVERT: A 1418 VAL cc_start: 0.7452 (t) cc_final: 0.6910 (p) REVERT: A 1428 LEU cc_start: 0.8699 (mt) cc_final: 0.8268 (mt) REVERT: A 1432 PHE cc_start: 0.7341 (m-80) cc_final: 0.6567 (m-80) REVERT: A 1437 ASN cc_start: 0.8006 (t160) cc_final: 0.7671 (t160) REVERT: A 1439 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 1440 ILE cc_start: 0.6717 (tp) cc_final: 0.6322 (tp) REVERT: A 1477 ILE cc_start: 0.8722 (tp) cc_final: 0.8325 (pt) REVERT: A 1522 MET cc_start: 0.8342 (ptt) cc_final: 0.7906 (ptt) REVERT: A 1524 VAL cc_start: 0.7961 (t) cc_final: 0.7636 (p) REVERT: A 1528 ASP cc_start: 0.7793 (m-30) cc_final: 0.7092 (m-30) REVERT: A 1529 ARG cc_start: 0.7969 (tpt90) cc_final: 0.7730 (tpt170) REVERT: A 1532 LYS cc_start: 0.8978 (tptp) cc_final: 0.8248 (tppt) REVERT: A 1534 HIS cc_start: 0.7778 (m170) cc_final: 0.7558 (m170) REVERT: B 31 ASN cc_start: 0.6733 (p0) cc_final: 0.6418 (p0) REVERT: B 45 MET cc_start: 0.6885 (ttm) cc_final: 0.6609 (ttm) REVERT: B 92 GLU cc_start: 0.8079 (tt0) cc_final: 0.7772 (tt0) REVERT: B 117 MET cc_start: 0.7543 (ttp) cc_final: 0.7185 (ttp) REVERT: B 141 MET cc_start: 0.7139 (mtt) cc_final: 0.5862 (tmm) REVERT: B 184 GLN cc_start: 0.8753 (mt0) cc_final: 0.8348 (mp10) REVERT: B 200 ASN cc_start: 0.7506 (p0) cc_final: 0.7197 (p0) REVERT: B 204 PHE cc_start: 0.7102 (t80) cc_final: 0.6818 (t80) REVERT: B 240 VAL cc_start: 0.7964 (t) cc_final: 0.7735 (m) REVERT: B 243 LYS cc_start: 0.8976 (tttm) cc_final: 0.8661 (ptpt) REVERT: B 288 MET cc_start: 0.8483 (mtt) cc_final: 0.8013 (mtt) REVERT: B 290 LYS cc_start: 0.7000 (pttm) cc_final: 0.6715 (pttm) REVERT: B 296 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7681 (mmm-85) REVERT: B 297 TYR cc_start: 0.7455 (t80) cc_final: 0.7221 (t80) REVERT: B 300 ILE cc_start: 0.8010 (mt) cc_final: 0.7807 (mm) REVERT: B 301 LEU cc_start: 0.7182 (tp) cc_final: 0.6967 (tp) REVERT: B 567 TYR cc_start: 0.6751 (m-80) cc_final: 0.6270 (m-80) REVERT: B 604 MET cc_start: 0.6526 (ppp) cc_final: 0.5927 (ppp) REVERT: B 748 ARG cc_start: 0.6380 (tmm160) cc_final: 0.6083 (tmm160) REVERT: B 798 VAL cc_start: 0.7550 (t) cc_final: 0.6520 (t) REVERT: B 800 MET cc_start: 0.5458 (mtp) cc_final: 0.4790 (mtp) REVERT: B 862 ILE cc_start: 0.7503 (mm) cc_final: 0.7262 (mm) REVERT: B 1029 LYS cc_start: 0.8224 (mttt) cc_final: 0.7525 (mmtt) REVERT: B 1069 ASP cc_start: 0.8051 (m-30) cc_final: 0.7691 (m-30) REVERT: B 1085 PHE cc_start: 0.7468 (t80) cc_final: 0.6813 (t80) REVERT: B 1090 ILE cc_start: 0.8614 (mt) cc_final: 0.8097 (tp) REVERT: B 1106 ARG cc_start: 0.7339 (mmt90) cc_final: 0.6748 (mmm-85) REVERT: B 1120 ASP cc_start: 0.8457 (t0) cc_final: 0.8190 (p0) REVERT: B 1121 GLU cc_start: 0.8028 (tp30) cc_final: 0.7663 (tm-30) REVERT: B 1126 LEU cc_start: 0.8429 (mt) cc_final: 0.7744 (mt) REVERT: B 1130 ILE cc_start: 0.7043 (mt) cc_final: 0.6681 (mt) REVERT: B 1152 SER cc_start: 0.8819 (m) cc_final: 0.8425 (p) REVERT: B 1178 TRP cc_start: 0.6505 (m100) cc_final: 0.6127 (m100) REVERT: B 1207 ASP cc_start: 0.7553 (t0) cc_final: 0.6918 (t0) REVERT: B 1211 PHE cc_start: 0.8112 (t80) cc_final: 0.7891 (t80) REVERT: B 1213 LYS cc_start: 0.8509 (tmmt) cc_final: 0.8072 (tmmt) REVERT: B 1221 ILE cc_start: 0.8075 (mt) cc_final: 0.7875 (mt) REVERT: B 1228 GLN cc_start: 0.7865 (mt0) cc_final: 0.7546 (tt0) REVERT: B 1233 GLN cc_start: 0.8150 (mt0) cc_final: 0.7883 (mt0) REVERT: B 1235 LEU cc_start: 0.8953 (mt) cc_final: 0.8617 (mm) REVERT: B 1252 GLU cc_start: 0.6887 (mp0) cc_final: 0.6681 (mp0) REVERT: B 1256 ILE cc_start: 0.8899 (tp) cc_final: 0.8255 (tp) REVERT: B 1260 ASN cc_start: 0.8264 (m-40) cc_final: 0.7905 (m-40) REVERT: B 1290 HIS cc_start: 0.8325 (m90) cc_final: 0.7885 (m90) REVERT: B 1297 LEU cc_start: 0.8617 (mt) cc_final: 0.8397 (mm) REVERT: B 1342 THR cc_start: 0.7975 (m) cc_final: 0.7668 (p) REVERT: B 1351 ILE cc_start: 0.9028 (mt) cc_final: 0.8780 (mm) REVERT: B 1371 TRP cc_start: 0.8315 (p-90) cc_final: 0.7964 (p-90) REVERT: B 1372 VAL cc_start: 0.8863 (t) cc_final: 0.8213 (t) REVERT: B 1409 GLN cc_start: 0.8489 (mt0) cc_final: 0.8035 (mm-40) REVERT: B 1410 MET cc_start: 0.7695 (mtm) cc_final: 0.7387 (mtm) REVERT: B 1417 LEU cc_start: 0.7664 (mt) cc_final: 0.7400 (mt) REVERT: B 1441 VAL cc_start: 0.8630 (t) cc_final: 0.7865 (p) REVERT: B 1473 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8039 (mmtp) REVERT: B 1498 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8564 (mmmt) REVERT: B 1505 MET cc_start: 0.7006 (mtp) cc_final: 0.6275 (mtp) REVERT: B 1522 MET cc_start: 0.7826 (ttp) cc_final: 0.6940 (tpt) REVERT: B 1529 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7684 (mmm160) REVERT: B 1530 GLN cc_start: 0.8707 (mt0) cc_final: 0.8233 (mt0) REVERT: B 1543 ILE cc_start: 0.8254 (mt) cc_final: 0.7871 (tp) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.1572 time to fit residues: 132.2504 Evaluate side-chains 497 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 198 optimal weight: 10.0000 chunk 64 optimal weight: 0.0970 chunk 146 optimal weight: 0.0870 chunk 53 optimal weight: 0.2980 chunk 193 optimal weight: 0.0020 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 280 HIS A1260 ASN ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1302 GLN ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1302 GLN B1484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.214942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.165098 restraints weight = 96123.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.173100 restraints weight = 54026.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.178536 restraints weight = 35320.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.182765 restraints weight = 25533.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.185876 restraints weight = 19379.903| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4455 r_free = 0.4455 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4455 r_free = 0.4455 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23515 Z= 0.117 Angle : 0.608 10.227 31845 Z= 0.312 Chirality : 0.044 0.244 3693 Planarity : 0.004 0.052 4070 Dihedral : 4.716 25.158 3187 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -1.73 (0.15), residues: 2985 helix: -0.83 (0.14), residues: 1339 sheet: -1.20 (0.23), residues: 490 loop : -1.28 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 308 TYR 0.023 0.001 TYR B 169 PHE 0.045 0.002 PHE B 176 TRP 0.023 0.002 TRP B 828 HIS 0.010 0.001 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00258 (23515) covalent geometry : angle 0.60841 (31845) hydrogen bonds : bond 0.03437 ( 798) hydrogen bonds : angle 4.96978 ( 2205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.7279 (tt) cc_final: 0.7072 (tt) REVERT: A 23 HIS cc_start: 0.7670 (t70) cc_final: 0.7002 (t70) REVERT: A 75 CYS cc_start: 0.7266 (p) cc_final: 0.6874 (m) REVERT: A 80 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 88 LYS cc_start: 0.7540 (tmmt) cc_final: 0.7065 (tmmt) REVERT: A 117 MET cc_start: 0.7375 (ttp) cc_final: 0.7078 (ttp) REVERT: A 120 PHE cc_start: 0.8725 (t80) cc_final: 0.8194 (t80) REVERT: A 126 MET cc_start: 0.6229 (mmp) cc_final: 0.5828 (mmp) REVERT: A 160 PHE cc_start: 0.7796 (m-80) cc_final: 0.7296 (m-10) REVERT: A 180 LEU cc_start: 0.6758 (mt) cc_final: 0.6524 (pp) REVERT: A 185 PHE cc_start: 0.6339 (t80) cc_final: 0.6109 (t80) REVERT: A 288 MET cc_start: 0.8060 (mtm) cc_final: 0.7162 (mtm) REVERT: A 294 LEU cc_start: 0.9048 (tp) cc_final: 0.8702 (mt) REVERT: A 302 PRO cc_start: 0.6597 (Cg_endo) cc_final: 0.6372 (Cg_exo) REVERT: A 311 LYS cc_start: 0.8789 (tptp) cc_final: 0.8252 (ttmm) REVERT: A 339 GLU cc_start: 0.7980 (mp0) cc_final: 0.7672 (mp0) REVERT: A 573 MET cc_start: 0.8233 (mtm) cc_final: 0.7926 (mtm) REVERT: A 878 LEU cc_start: 0.8310 (tp) cc_final: 0.8096 (tp) REVERT: A 886 MET cc_start: 0.7045 (tmm) cc_final: 0.6542 (tmm) REVERT: A 889 MET cc_start: 0.3995 (tpt) cc_final: 0.3423 (tpt) REVERT: A 947 ARG cc_start: 0.7239 (mmp80) cc_final: 0.6499 (mmp80) REVERT: A 994 ARG cc_start: 0.7436 (mtt90) cc_final: 0.6450 (mmt180) REVERT: A 1003 ASN cc_start: 0.7352 (t0) cc_final: 0.7129 (t0) REVERT: A 1007 TYR cc_start: 0.6551 (m-80) cc_final: 0.6050 (m-80) REVERT: A 1024 PHE cc_start: 0.7906 (t80) cc_final: 0.7491 (t80) REVERT: A 1027 TYR cc_start: 0.7535 (t80) cc_final: 0.7311 (t80) REVERT: A 1029 LYS cc_start: 0.8317 (ptmt) cc_final: 0.7645 (ptmm) REVERT: A 1030 LEU cc_start: 0.7515 (tp) cc_final: 0.7273 (tp) REVERT: A 1031 ILE cc_start: 0.7249 (pt) cc_final: 0.7017 (pt) REVERT: A 1035 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 1048 VAL cc_start: 0.8865 (t) cc_final: 0.8433 (m) REVERT: A 1072 GLU cc_start: 0.7213 (tp30) cc_final: 0.6634 (tp30) REVERT: A 1103 TYR cc_start: 0.6410 (t80) cc_final: 0.5928 (t80) REVERT: A 1125 LEU cc_start: 0.8268 (mt) cc_final: 0.7901 (mp) REVERT: A 1158 THR cc_start: 0.7190 (m) cc_final: 0.6826 (p) REVERT: A 1171 LEU cc_start: 0.6992 (mt) cc_final: 0.6613 (mt) REVERT: A 1180 ASN cc_start: 0.8077 (m-40) cc_final: 0.7778 (t0) REVERT: A 1202 ILE cc_start: 0.8263 (tt) cc_final: 0.8041 (mm) REVERT: A 1224 ASN cc_start: 0.8003 (m-40) cc_final: 0.7658 (m110) REVERT: A 1261 GLN cc_start: 0.7664 (tp40) cc_final: 0.6435 (tm-30) REVERT: A 1265 ASP cc_start: 0.8088 (m-30) cc_final: 0.6327 (m-30) REVERT: A 1272 LYS cc_start: 0.8471 (mttp) cc_final: 0.7975 (mmmt) REVERT: A 1273 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8105 (mmmm) REVERT: A 1290 HIS cc_start: 0.6557 (m-70) cc_final: 0.5825 (m-70) REVERT: A 1295 LYS cc_start: 0.8891 (pttm) cc_final: 0.8330 (ptpt) REVERT: A 1297 LEU cc_start: 0.8730 (mt) cc_final: 0.8430 (mm) REVERT: A 1298 ASN cc_start: 0.7549 (t0) cc_final: 0.7126 (t0) REVERT: A 1344 LEU cc_start: 0.7931 (tp) cc_final: 0.6579 (tp) REVERT: A 1349 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7475 (mm-30) REVERT: A 1356 THR cc_start: 0.7508 (m) cc_final: 0.6978 (p) REVERT: A 1374 ILE cc_start: 0.8526 (mt) cc_final: 0.8286 (mm) REVERT: A 1407 LEU cc_start: 0.7918 (mt) cc_final: 0.7646 (mt) REVERT: A 1410 MET cc_start: 0.6643 (tpp) cc_final: 0.5389 (tpp) REVERT: A 1418 VAL cc_start: 0.7381 (t) cc_final: 0.6781 (p) REVERT: A 1428 LEU cc_start: 0.8624 (mt) cc_final: 0.8264 (mt) REVERT: A 1432 PHE cc_start: 0.7432 (m-80) cc_final: 0.6674 (m-80) REVERT: A 1477 ILE cc_start: 0.8629 (tp) cc_final: 0.8105 (pt) REVERT: A 1514 TRP cc_start: 0.7862 (m-90) cc_final: 0.7610 (m-90) REVERT: A 1522 MET cc_start: 0.8255 (ptt) cc_final: 0.7834 (ptt) REVERT: A 1524 VAL cc_start: 0.7902 (t) cc_final: 0.7518 (p) REVERT: A 1528 ASP cc_start: 0.7734 (m-30) cc_final: 0.7072 (m-30) REVERT: A 1529 ARG cc_start: 0.8055 (tpt90) cc_final: 0.7131 (mmm-85) REVERT: A 1530 GLN cc_start: 0.8272 (pp30) cc_final: 0.7109 (pp30) REVERT: A 1532 LYS cc_start: 0.8898 (tptp) cc_final: 0.8140 (tppt) REVERT: A 1546 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.7103 (ttm110) REVERT: B 31 ASN cc_start: 0.6540 (p0) cc_final: 0.6326 (p0) REVERT: B 32 LEU cc_start: 0.8381 (tp) cc_final: 0.8164 (tp) REVERT: B 45 MET cc_start: 0.6658 (ttm) cc_final: 0.6396 (ttm) REVERT: B 92 GLU cc_start: 0.8062 (tt0) cc_final: 0.7278 (mt-10) REVERT: B 94 PHE cc_start: 0.5821 (t80) cc_final: 0.4939 (t80) REVERT: B 102 ARG cc_start: 0.8004 (ppt170) cc_final: 0.7533 (ttp80) REVERT: B 117 MET cc_start: 0.7566 (ttp) cc_final: 0.7188 (ttp) REVERT: B 133 GLN cc_start: 0.6114 (tp-100) cc_final: 0.5862 (tp40) REVERT: B 141 MET cc_start: 0.7138 (mtt) cc_final: 0.5702 (tmm) REVERT: B 184 GLN cc_start: 0.8765 (mt0) cc_final: 0.8313 (mp10) REVERT: B 200 ASN cc_start: 0.7598 (p0) cc_final: 0.7249 (p0) REVERT: B 204 PHE cc_start: 0.7421 (t80) cc_final: 0.7125 (t80) REVERT: B 240 VAL cc_start: 0.7959 (t) cc_final: 0.7735 (m) REVERT: B 243 LYS cc_start: 0.8963 (tttm) cc_final: 0.8647 (ptpt) REVERT: B 288 MET cc_start: 0.8459 (mtt) cc_final: 0.7949 (mtt) REVERT: B 296 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7593 (mmm-85) REVERT: B 300 ILE cc_start: 0.7798 (mt) cc_final: 0.7589 (mm) REVERT: B 311 LYS cc_start: 0.8799 (pttt) cc_final: 0.8573 (pttt) REVERT: B 604 MET cc_start: 0.6479 (ppp) cc_final: 0.5982 (ppp) REVERT: B 861 ILE cc_start: 0.8138 (mp) cc_final: 0.7922 (mp) REVERT: B 862 ILE cc_start: 0.7573 (mm) cc_final: 0.7333 (mm) REVERT: B 1029 LYS cc_start: 0.8202 (mttt) cc_final: 0.7542 (tttm) REVERT: B 1069 ASP cc_start: 0.8047 (m-30) cc_final: 0.7679 (m-30) REVERT: B 1085 PHE cc_start: 0.7330 (t80) cc_final: 0.6703 (t80) REVERT: B 1090 ILE cc_start: 0.8586 (mt) cc_final: 0.8114 (tp) REVERT: B 1098 ASP cc_start: 0.6888 (p0) cc_final: 0.6639 (p0) REVERT: B 1106 ARG cc_start: 0.7209 (mmt90) cc_final: 0.6735 (mmm-85) REVERT: B 1120 ASP cc_start: 0.8414 (t0) cc_final: 0.8206 (p0) REVERT: B 1121 GLU cc_start: 0.7824 (tp30) cc_final: 0.7606 (tm-30) REVERT: B 1125 LEU cc_start: 0.8765 (mt) cc_final: 0.8200 (mt) REVERT: B 1126 LEU cc_start: 0.8532 (mt) cc_final: 0.7913 (mt) REVERT: B 1130 ILE cc_start: 0.6988 (mt) cc_final: 0.6614 (mt) REVERT: B 1152 SER cc_start: 0.8700 (m) cc_final: 0.8367 (p) REVERT: B 1178 TRP cc_start: 0.6488 (m100) cc_final: 0.6105 (m100) REVERT: B 1207 ASP cc_start: 0.7464 (t0) cc_final: 0.6801 (t0) REVERT: B 1211 PHE cc_start: 0.8038 (t80) cc_final: 0.7829 (t80) REVERT: B 1213 LYS cc_start: 0.8476 (tmmt) cc_final: 0.8022 (tmmt) REVERT: B 1228 GLN cc_start: 0.7728 (mt0) cc_final: 0.7449 (tt0) REVERT: B 1233 GLN cc_start: 0.8103 (mt0) cc_final: 0.7605 (tt0) REVERT: B 1235 LEU cc_start: 0.8920 (mt) cc_final: 0.8581 (mm) REVERT: B 1242 ILE cc_start: 0.8205 (pt) cc_final: 0.7366 (mp) REVERT: B 1256 ILE cc_start: 0.8785 (tp) cc_final: 0.8042 (tp) REVERT: B 1260 ASN cc_start: 0.8187 (m-40) cc_final: 0.7812 (m-40) REVERT: B 1297 LEU cc_start: 0.8654 (mt) cc_final: 0.8347 (mm) REVERT: B 1342 THR cc_start: 0.7888 (m) cc_final: 0.7550 (p) REVERT: B 1372 VAL cc_start: 0.8752 (t) cc_final: 0.8442 (t) REVERT: B 1376 ASN cc_start: 0.7988 (m110) cc_final: 0.7735 (m110) REVERT: B 1409 GLN cc_start: 0.8404 (mt0) cc_final: 0.7960 (mp10) REVERT: B 1410 MET cc_start: 0.7393 (mtm) cc_final: 0.7000 (mtm) REVERT: B 1417 LEU cc_start: 0.7605 (mt) cc_final: 0.7355 (mt) REVERT: B 1430 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7979 (mmmm) REVERT: B 1441 VAL cc_start: 0.8534 (t) cc_final: 0.8303 (p) REVERT: B 1473 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8114 (mmtm) REVERT: B 1498 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8582 (mmmt) REVERT: B 1505 MET cc_start: 0.6972 (mtp) cc_final: 0.6247 (mtp) REVERT: B 1515 LYS cc_start: 0.7889 (tppt) cc_final: 0.7670 (tppt) REVERT: B 1522 MET cc_start: 0.7624 (ttp) cc_final: 0.6637 (tpt) REVERT: B 1529 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7633 (mmm160) REVERT: B 1530 GLN cc_start: 0.8605 (mt0) cc_final: 0.8072 (mt0) REVERT: B 1531 PHE cc_start: 0.8074 (t80) cc_final: 0.7789 (t80) REVERT: B 1543 ILE cc_start: 0.8210 (mt) cc_final: 0.7849 (tp) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.1568 time to fit residues: 128.5538 Evaluate side-chains 485 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 216 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 0.2980 chunk 45 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 949 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1302 GLN B1484 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.209306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.157818 restraints weight = 103075.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.167186 restraints weight = 57212.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.171964 restraints weight = 36329.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.176173 restraints weight = 26205.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.178839 restraints weight = 19814.672| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4377 r_free = 0.4377 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4377 r_free = 0.4377 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23515 Z= 0.173 Angle : 0.666 13.854 31845 Z= 0.343 Chirality : 0.045 0.227 3693 Planarity : 0.005 0.075 4070 Dihedral : 4.805 26.013 3187 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -1.60 (0.15), residues: 2985 helix: -0.75 (0.14), residues: 1338 sheet: -1.14 (0.23), residues: 498 loop : -1.18 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 742 TYR 0.018 0.002 TYR B 297 PHE 0.036 0.002 PHE B 802 TRP 0.026 0.002 TRP B 997 HIS 0.019 0.002 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00353 (23515) covalent geometry : angle 0.66620 (31845) hydrogen bonds : bond 0.03667 ( 798) hydrogen bonds : angle 5.12394 ( 2205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.7370 (p) cc_final: 0.6842 (m) REVERT: A 80 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 88 LYS cc_start: 0.7615 (tmmt) cc_final: 0.6966 (tmmt) REVERT: A 117 MET cc_start: 0.7583 (ttp) cc_final: 0.7268 (ttp) REVERT: A 126 MET cc_start: 0.6417 (mmp) cc_final: 0.5989 (mmp) REVERT: A 134 VAL cc_start: 0.8197 (t) cc_final: 0.7716 (p) REVERT: A 160 PHE cc_start: 0.7665 (m-80) cc_final: 0.7186 (m-10) REVERT: A 165 HIS cc_start: 0.8036 (t70) cc_final: 0.7771 (t70) REVERT: A 169 TYR cc_start: 0.5831 (m-80) cc_final: 0.5391 (m-10) REVERT: A 192 VAL cc_start: 0.8245 (p) cc_final: 0.7693 (t) REVERT: A 241 ARG cc_start: 0.7796 (ptm-80) cc_final: 0.7231 (ptm-80) REVERT: A 280 HIS cc_start: 0.6896 (t-170) cc_final: 0.6417 (t-90) REVERT: A 288 MET cc_start: 0.8105 (mtm) cc_final: 0.7219 (mtm) REVERT: A 294 LEU cc_start: 0.9091 (tp) cc_final: 0.8752 (mt) REVERT: A 302 PRO cc_start: 0.6631 (Cg_endo) cc_final: 0.6321 (Cg_exo) REVERT: A 311 LYS cc_start: 0.8884 (tptp) cc_final: 0.8611 (tptp) REVERT: A 327 PHE cc_start: 0.7970 (t80) cc_final: 0.7709 (t80) REVERT: A 573 MET cc_start: 0.8219 (mtm) cc_final: 0.7963 (mmt) REVERT: A 681 MET cc_start: 0.7968 (mmp) cc_final: 0.7767 (mmt) REVERT: A 886 MET cc_start: 0.7060 (tmm) cc_final: 0.6560 (tmm) REVERT: A 889 MET cc_start: 0.4091 (tpt) cc_final: 0.3587 (tpt) REVERT: A 947 ARG cc_start: 0.7269 (mmp80) cc_final: 0.6031 (mmp80) REVERT: A 994 ARG cc_start: 0.7451 (mtt90) cc_final: 0.5240 (ptp90) REVERT: A 1007 TYR cc_start: 0.6696 (m-80) cc_final: 0.6150 (m-80) REVERT: A 1009 SER cc_start: 0.7483 (m) cc_final: 0.6743 (t) REVERT: A 1024 PHE cc_start: 0.8016 (t80) cc_final: 0.7270 (t80) REVERT: A 1029 LYS cc_start: 0.8396 (ptmt) cc_final: 0.7381 (ptmm) REVERT: A 1030 LEU cc_start: 0.7573 (tp) cc_final: 0.7285 (tp) REVERT: A 1048 VAL cc_start: 0.8801 (t) cc_final: 0.8390 (m) REVERT: A 1072 GLU cc_start: 0.7297 (tp30) cc_final: 0.6202 (tp30) REVERT: A 1158 THR cc_start: 0.7305 (m) cc_final: 0.6982 (p) REVERT: A 1180 ASN cc_start: 0.8140 (m-40) cc_final: 0.7876 (t0) REVERT: A 1205 ASN cc_start: 0.8038 (m-40) cc_final: 0.7498 (m-40) REVERT: A 1224 ASN cc_start: 0.8175 (m-40) cc_final: 0.7646 (m110) REVERT: A 1228 GLN cc_start: 0.8082 (mp10) cc_final: 0.7628 (mp10) REVERT: A 1231 LEU cc_start: 0.8500 (tt) cc_final: 0.8183 (tt) REVERT: A 1235 LEU cc_start: 0.8387 (mt) cc_final: 0.7844 (tp) REVERT: A 1245 LYS cc_start: 0.8730 (tmtt) cc_final: 0.8416 (tmmt) REVERT: A 1251 GLU cc_start: 0.7693 (tp30) cc_final: 0.7491 (tp30) REVERT: A 1261 GLN cc_start: 0.7859 (tp40) cc_final: 0.7040 (tm-30) REVERT: A 1262 THR cc_start: 0.8291 (p) cc_final: 0.7757 (t) REVERT: A 1265 ASP cc_start: 0.8315 (m-30) cc_final: 0.6449 (m-30) REVERT: A 1272 LYS cc_start: 0.8526 (mttp) cc_final: 0.8012 (mmmt) REVERT: A 1273 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8284 (mmmm) REVERT: A 1290 HIS cc_start: 0.7182 (m-70) cc_final: 0.6772 (m-70) REVERT: A 1295 LYS cc_start: 0.8942 (pttm) cc_final: 0.8711 (ptmm) REVERT: A 1297 LEU cc_start: 0.8830 (mt) cc_final: 0.8604 (mm) REVERT: A 1298 ASN cc_start: 0.7653 (t0) cc_final: 0.7264 (t0) REVERT: A 1327 LEU cc_start: 0.6630 (mt) cc_final: 0.6362 (mt) REVERT: A 1344 LEU cc_start: 0.8043 (tp) cc_final: 0.7555 (tp) REVERT: A 1349 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7858 (tp30) REVERT: A 1356 THR cc_start: 0.7845 (m) cc_final: 0.7246 (p) REVERT: A 1410 MET cc_start: 0.6734 (tpp) cc_final: 0.6286 (tpp) REVERT: A 1428 LEU cc_start: 0.8630 (mt) cc_final: 0.8216 (mt) REVERT: A 1432 PHE cc_start: 0.7509 (m-80) cc_final: 0.6700 (m-80) REVERT: A 1440 ILE cc_start: 0.6639 (tp) cc_final: 0.6257 (tt) REVERT: A 1452 LYS cc_start: 0.7691 (tttt) cc_final: 0.7468 (tmtt) REVERT: A 1475 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 1520 VAL cc_start: 0.8476 (m) cc_final: 0.8019 (m) REVERT: A 1522 MET cc_start: 0.8337 (ptt) cc_final: 0.7895 (ptt) REVERT: A 1524 VAL cc_start: 0.7930 (t) cc_final: 0.7580 (p) REVERT: A 1526 GLN cc_start: 0.7865 (pt0) cc_final: 0.7342 (pp30) REVERT: A 1528 ASP cc_start: 0.7755 (m-30) cc_final: 0.7009 (m-30) REVERT: A 1529 ARG cc_start: 0.8168 (tpt90) cc_final: 0.7884 (tpt170) REVERT: A 1530 GLN cc_start: 0.8503 (pp30) cc_final: 0.7999 (pp30) REVERT: A 1532 LYS cc_start: 0.9049 (tptp) cc_final: 0.8421 (tppt) REVERT: A 1533 LEU cc_start: 0.8708 (mt) cc_final: 0.8504 (mt) REVERT: A 1546 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.6652 (ttp-110) REVERT: B 31 ASN cc_start: 0.6676 (p0) cc_final: 0.6429 (p0) REVERT: B 98 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7899 (tp40) REVERT: B 102 ARG cc_start: 0.8075 (ppt170) cc_final: 0.7849 (ttp80) REVERT: B 117 MET cc_start: 0.7698 (ttp) cc_final: 0.7325 (ttp) REVERT: B 141 MET cc_start: 0.7085 (mtt) cc_final: 0.5999 (tmm) REVERT: B 184 GLN cc_start: 0.8791 (mt0) cc_final: 0.8448 (mp10) REVERT: B 200 ASN cc_start: 0.7726 (p0) cc_final: 0.7180 (p0) REVERT: B 201 GLU cc_start: 0.7925 (pt0) cc_final: 0.7703 (mt-10) REVERT: B 204 PHE cc_start: 0.7342 (t80) cc_final: 0.7097 (t80) REVERT: B 240 VAL cc_start: 0.8169 (t) cc_final: 0.7416 (m) REVERT: B 243 LYS cc_start: 0.8973 (tttm) cc_final: 0.8669 (ptpt) REVERT: B 288 MET cc_start: 0.8514 (mtt) cc_final: 0.8018 (mtt) REVERT: B 311 LYS cc_start: 0.8824 (pttt) cc_final: 0.8610 (pttt) REVERT: B 604 MET cc_start: 0.6650 (ppp) cc_final: 0.6114 (ppp) REVERT: B 800 MET cc_start: 0.4677 (mtm) cc_final: 0.4386 (mtm) REVERT: B 838 ILE cc_start: 0.7948 (mp) cc_final: 0.7736 (mp) REVERT: B 997 TRP cc_start: 0.8358 (m-90) cc_final: 0.8104 (m-90) REVERT: B 1004 TYR cc_start: 0.7399 (m-80) cc_final: 0.7160 (m-80) REVERT: B 1016 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7544 (mt-10) REVERT: B 1029 LYS cc_start: 0.8383 (mttt) cc_final: 0.7750 (tttm) REVERT: B 1035 GLU cc_start: 0.7063 (pp20) cc_final: 0.6737 (tm-30) REVERT: B 1069 ASP cc_start: 0.8087 (m-30) cc_final: 0.7751 (m-30) REVERT: B 1077 LEU cc_start: 0.8650 (tt) cc_final: 0.8350 (tt) REVERT: B 1090 ILE cc_start: 0.8708 (mt) cc_final: 0.8269 (tp) REVERT: B 1120 ASP cc_start: 0.8430 (t0) cc_final: 0.8220 (p0) REVERT: B 1121 GLU cc_start: 0.7994 (tp30) cc_final: 0.7705 (tm-30) REVERT: B 1125 LEU cc_start: 0.8811 (mt) cc_final: 0.8502 (mt) REVERT: B 1126 LEU cc_start: 0.8611 (mt) cc_final: 0.7950 (mt) REVERT: B 1130 ILE cc_start: 0.7282 (mt) cc_final: 0.6905 (mt) REVERT: B 1152 SER cc_start: 0.8808 (m) cc_final: 0.8498 (p) REVERT: B 1178 TRP cc_start: 0.6675 (m100) cc_final: 0.6299 (m100) REVERT: B 1207 ASP cc_start: 0.7731 (t0) cc_final: 0.7035 (t0) REVERT: B 1213 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8175 (tmmt) REVERT: B 1228 GLN cc_start: 0.7954 (mt0) cc_final: 0.7458 (tt0) REVERT: B 1233 GLN cc_start: 0.8152 (mt0) cc_final: 0.7790 (mt0) REVERT: B 1235 LEU cc_start: 0.8990 (mt) cc_final: 0.8634 (mm) REVERT: B 1239 PHE cc_start: 0.7982 (m-80) cc_final: 0.7770 (m-80) REVERT: B 1256 ILE cc_start: 0.8979 (tp) cc_final: 0.8478 (tp) REVERT: B 1260 ASN cc_start: 0.8376 (m-40) cc_final: 0.8009 (p0) REVERT: B 1295 LYS cc_start: 0.9124 (tmmt) cc_final: 0.8587 (ptmm) REVERT: B 1297 LEU cc_start: 0.8631 (mt) cc_final: 0.8301 (mm) REVERT: B 1313 VAL cc_start: 0.9010 (t) cc_final: 0.8630 (p) REVERT: B 1342 THR cc_start: 0.8089 (m) cc_final: 0.7829 (p) REVERT: B 1371 TRP cc_start: 0.8561 (p-90) cc_final: 0.8134 (p-90) REVERT: B 1372 VAL cc_start: 0.8819 (t) cc_final: 0.8322 (t) REVERT: B 1376 ASN cc_start: 0.8113 (m110) cc_final: 0.7874 (m110) REVERT: B 1407 LEU cc_start: 0.8471 (mt) cc_final: 0.8205 (mt) REVERT: B 1409 GLN cc_start: 0.8378 (mt0) cc_final: 0.7900 (mm-40) REVERT: B 1410 MET cc_start: 0.7330 (mtm) cc_final: 0.6899 (mtm) REVERT: B 1417 LEU cc_start: 0.7890 (mt) cc_final: 0.7582 (mt) REVERT: B 1429 VAL cc_start: 0.8683 (t) cc_final: 0.8180 (p) REVERT: B 1430 LYS cc_start: 0.8588 (mmmt) cc_final: 0.7719 (mmmm) REVERT: B 1441 VAL cc_start: 0.8518 (t) cc_final: 0.8168 (p) REVERT: B 1498 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8602 (mmmt) REVERT: B 1505 MET cc_start: 0.7002 (mtp) cc_final: 0.6221 (mtp) REVERT: B 1515 LYS cc_start: 0.7988 (tppt) cc_final: 0.7769 (tppt) REVERT: B 1522 MET cc_start: 0.7829 (ttp) cc_final: 0.7113 (tpt) REVERT: B 1529 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7646 (mmm160) REVERT: B 1530 GLN cc_start: 0.8628 (mt0) cc_final: 0.8136 (mt0) REVERT: B 1531 PHE cc_start: 0.8138 (t80) cc_final: 0.7806 (t80) REVERT: B 1543 ILE cc_start: 0.8249 (mt) cc_final: 0.7963 (tp) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.1629 time to fit residues: 133.3822 Evaluate side-chains 486 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 274 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1409 GLN ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 HIS ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1302 GLN B1484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.211054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.163863 restraints weight = 75800.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.170858 restraints weight = 45516.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.175559 restraints weight = 30860.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.179205 restraints weight = 22894.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.181948 restraints weight = 17843.427| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23515 Z= 0.124 Angle : 0.615 8.423 31845 Z= 0.314 Chirality : 0.045 0.199 3693 Planarity : 0.005 0.057 4070 Dihedral : 4.649 24.915 3187 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -1.39 (0.15), residues: 2985 helix: -0.55 (0.14), residues: 1337 sheet: -1.06 (0.23), residues: 483 loop : -1.11 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 308 TYR 0.030 0.002 TYR A1027 PHE 0.037 0.002 PHE A1024 TRP 0.046 0.002 TRP B1514 HIS 0.010 0.001 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00274 (23515) covalent geometry : angle 0.61469 (31845) hydrogen bonds : bond 0.03333 ( 798) hydrogen bonds : angle 5.00184 ( 2205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 CYS cc_start: 0.7396 (p) cc_final: 0.7005 (m) REVERT: A 80 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 88 LYS cc_start: 0.7634 (tmmt) cc_final: 0.7325 (tmmt) REVERT: A 117 MET cc_start: 0.7551 (ttp) cc_final: 0.7217 (ttp) REVERT: A 120 PHE cc_start: 0.8796 (t80) cc_final: 0.8266 (t80) REVERT: A 126 MET cc_start: 0.6277 (mmp) cc_final: 0.5880 (mmp) REVERT: A 160 PHE cc_start: 0.7674 (m-80) cc_final: 0.7135 (m-80) REVERT: A 165 HIS cc_start: 0.8096 (t70) cc_final: 0.7854 (t70) REVERT: A 169 TYR cc_start: 0.5884 (m-80) cc_final: 0.5491 (m-10) REVERT: A 192 VAL cc_start: 0.8184 (p) cc_final: 0.7684 (t) REVERT: A 241 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7265 (ptm-80) REVERT: A 288 MET cc_start: 0.8131 (mtm) cc_final: 0.7266 (mtm) REVERT: A 294 LEU cc_start: 0.9091 (tp) cc_final: 0.8759 (mt) REVERT: A 302 PRO cc_start: 0.6713 (Cg_endo) cc_final: 0.6477 (Cg_exo) REVERT: A 311 LYS cc_start: 0.8814 (tptp) cc_final: 0.8515 (tptp) REVERT: A 335 ARG cc_start: 0.7878 (tmt170) cc_final: 0.7635 (tmt170) REVERT: A 386 LEU cc_start: 0.7670 (tp) cc_final: 0.7467 (tp) REVERT: A 886 MET cc_start: 0.7108 (tmm) cc_final: 0.6664 (tmm) REVERT: A 889 MET cc_start: 0.3889 (tpt) cc_final: 0.3518 (tpt) REVERT: A 947 ARG cc_start: 0.7331 (mmp80) cc_final: 0.6602 (mmp80) REVERT: A 1007 TYR cc_start: 0.6725 (m-80) cc_final: 0.6166 (m-80) REVERT: A 1009 SER cc_start: 0.7385 (m) cc_final: 0.6638 (t) REVERT: A 1024 PHE cc_start: 0.8110 (t80) cc_final: 0.7516 (t80) REVERT: A 1025 VAL cc_start: 0.9007 (t) cc_final: 0.8521 (t) REVERT: A 1029 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7677 (pttt) REVERT: A 1030 LEU cc_start: 0.7530 (tp) cc_final: 0.7322 (tp) REVERT: A 1031 ILE cc_start: 0.7448 (pt) cc_final: 0.7229 (pt) REVERT: A 1048 VAL cc_start: 0.8814 (t) cc_final: 0.8399 (m) REVERT: A 1072 GLU cc_start: 0.7225 (tp30) cc_final: 0.6187 (tp30) REVERT: A 1093 ILE cc_start: 0.8183 (tt) cc_final: 0.7579 (mm) REVERT: A 1158 THR cc_start: 0.7289 (m) cc_final: 0.6988 (p) REVERT: A 1180 ASN cc_start: 0.8075 (m-40) cc_final: 0.7875 (t0) REVERT: A 1205 ASN cc_start: 0.8149 (m-40) cc_final: 0.7627 (m-40) REVERT: A 1224 ASN cc_start: 0.8254 (m-40) cc_final: 0.7758 (m110) REVERT: A 1231 LEU cc_start: 0.8457 (tt) cc_final: 0.8181 (tt) REVERT: A 1235 LEU cc_start: 0.8335 (mt) cc_final: 0.7846 (tp) REVERT: A 1251 GLU cc_start: 0.7679 (tp30) cc_final: 0.7450 (tp30) REVERT: A 1261 GLN cc_start: 0.7763 (tp40) cc_final: 0.6788 (tm-30) REVERT: A 1265 ASP cc_start: 0.8231 (m-30) cc_final: 0.6309 (m-30) REVERT: A 1272 LYS cc_start: 0.8416 (mttp) cc_final: 0.8051 (mmmt) REVERT: A 1273 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8173 (mmmm) REVERT: A 1290 HIS cc_start: 0.7088 (m-70) cc_final: 0.6680 (m-70) REVERT: A 1295 LYS cc_start: 0.8928 (pttm) cc_final: 0.8365 (ptpt) REVERT: A 1297 LEU cc_start: 0.8823 (mt) cc_final: 0.8561 (mm) REVERT: A 1298 ASN cc_start: 0.7627 (t0) cc_final: 0.7184 (t0) REVERT: A 1344 LEU cc_start: 0.8000 (tp) cc_final: 0.7375 (tp) REVERT: A 1349 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7887 (tp30) REVERT: A 1356 THR cc_start: 0.7817 (m) cc_final: 0.7329 (p) REVERT: A 1410 MET cc_start: 0.6561 (tpp) cc_final: 0.5668 (tpp) REVERT: A 1418 VAL cc_start: 0.7259 (t) cc_final: 0.6681 (p) REVERT: A 1428 LEU cc_start: 0.8618 (mt) cc_final: 0.8184 (mt) REVERT: A 1432 PHE cc_start: 0.7509 (m-80) cc_final: 0.6773 (m-80) REVERT: A 1440 ILE cc_start: 0.6737 (tp) cc_final: 0.6277 (tt) REVERT: A 1452 LYS cc_start: 0.7810 (tttt) cc_final: 0.7568 (tmtt) REVERT: A 1475 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7749 (mt-10) REVERT: A 1477 ILE cc_start: 0.8463 (tp) cc_final: 0.7949 (pt) REVERT: A 1520 VAL cc_start: 0.8449 (m) cc_final: 0.7855 (m) REVERT: A 1522 MET cc_start: 0.8336 (ptt) cc_final: 0.7858 (ptt) REVERT: A 1524 VAL cc_start: 0.7814 (t) cc_final: 0.7343 (p) REVERT: A 1526 GLN cc_start: 0.7730 (pt0) cc_final: 0.7288 (pp30) REVERT: A 1528 ASP cc_start: 0.7740 (m-30) cc_final: 0.7047 (m-30) REVERT: A 1529 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7174 (mmm-85) REVERT: A 1530 GLN cc_start: 0.8510 (pp30) cc_final: 0.8225 (pp30) REVERT: A 1532 LYS cc_start: 0.9006 (tptp) cc_final: 0.8333 (tppt) REVERT: A 1533 LEU cc_start: 0.8783 (mt) cc_final: 0.8374 (mt) REVERT: A 1546 ARG cc_start: 0.7678 (ttp-110) cc_final: 0.6883 (ttm110) REVERT: B 31 ASN cc_start: 0.6575 (p0) cc_final: 0.6361 (p0) REVERT: B 102 ARG cc_start: 0.8040 (ppt170) cc_final: 0.7626 (ttp80) REVERT: B 117 MET cc_start: 0.7677 (ttp) cc_final: 0.7320 (ttp) REVERT: B 133 GLN cc_start: 0.6086 (tp-100) cc_final: 0.5824 (tp40) REVERT: B 141 MET cc_start: 0.7047 (mtt) cc_final: 0.5677 (tmm) REVERT: B 184 GLN cc_start: 0.8794 (mt0) cc_final: 0.8422 (mp10) REVERT: B 200 ASN cc_start: 0.7627 (p0) cc_final: 0.6974 (p0) REVERT: B 201 GLU cc_start: 0.7963 (pt0) cc_final: 0.7622 (mt-10) REVERT: B 204 PHE cc_start: 0.7328 (t80) cc_final: 0.7117 (t80) REVERT: B 242 VAL cc_start: 0.8643 (t) cc_final: 0.8210 (p) REVERT: B 243 LYS cc_start: 0.9011 (tttm) cc_final: 0.8722 (ptpt) REVERT: B 288 MET cc_start: 0.8500 (mtt) cc_final: 0.7921 (mtm) REVERT: B 311 LYS cc_start: 0.8776 (pttt) cc_final: 0.8502 (pttt) REVERT: B 573 MET cc_start: 0.0406 (ttt) cc_final: -0.0503 (ptm) REVERT: B 604 MET cc_start: 0.6545 (ppp) cc_final: 0.6096 (ppp) REVERT: B 800 MET cc_start: 0.4830 (mtm) cc_final: 0.4472 (mtm) REVERT: B 838 ILE cc_start: 0.7810 (mp) cc_final: 0.7597 (mp) REVERT: B 997 TRP cc_start: 0.8390 (m-90) cc_final: 0.8103 (m-90) REVERT: B 1004 TYR cc_start: 0.7456 (m-80) cc_final: 0.7180 (m-80) REVERT: B 1016 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 1024 PHE cc_start: 0.8113 (t80) cc_final: 0.7234 (t80) REVERT: B 1029 LYS cc_start: 0.8393 (mttt) cc_final: 0.7719 (tttm) REVERT: B 1035 GLU cc_start: 0.7119 (pp20) cc_final: 0.6760 (tm-30) REVERT: B 1069 ASP cc_start: 0.8063 (m-30) cc_final: 0.7660 (m-30) REVERT: B 1090 ILE cc_start: 0.8629 (mt) cc_final: 0.8205 (tp) REVERT: B 1106 ARG cc_start: 0.7528 (mmt90) cc_final: 0.7034 (mmm160) REVERT: B 1121 GLU cc_start: 0.7963 (tp30) cc_final: 0.7674 (tm-30) REVERT: B 1122 LEU cc_start: 0.8738 (tt) cc_final: 0.8521 (tt) REVERT: B 1125 LEU cc_start: 0.8739 (mt) cc_final: 0.8422 (mt) REVERT: B 1126 LEU cc_start: 0.8647 (mt) cc_final: 0.7993 (mt) REVERT: B 1130 ILE cc_start: 0.7218 (mt) cc_final: 0.6840 (mt) REVERT: B 1152 SER cc_start: 0.8766 (m) cc_final: 0.8500 (p) REVERT: B 1178 TRP cc_start: 0.6722 (m100) cc_final: 0.6321 (m100) REVERT: B 1207 ASP cc_start: 0.7739 (t0) cc_final: 0.7002 (t0) REVERT: B 1213 LYS cc_start: 0.8604 (tmmt) cc_final: 0.8196 (tmmt) REVERT: B 1228 GLN cc_start: 0.7915 (mt0) cc_final: 0.7403 (tt0) REVERT: B 1233 GLN cc_start: 0.8141 (mt0) cc_final: 0.7789 (mt0) REVERT: B 1235 LEU cc_start: 0.8956 (mt) cc_final: 0.8629 (mm) REVERT: B 1256 ILE cc_start: 0.8952 (tp) cc_final: 0.8439 (tp) REVERT: B 1260 ASN cc_start: 0.8269 (m-40) cc_final: 0.7998 (p0) REVERT: B 1294 TYR cc_start: 0.7832 (m-10) cc_final: 0.7583 (m-10) REVERT: B 1297 LEU cc_start: 0.8636 (mt) cc_final: 0.8388 (mm) REVERT: B 1342 THR cc_start: 0.8005 (m) cc_final: 0.7741 (p) REVERT: B 1371 TRP cc_start: 0.8422 (p-90) cc_final: 0.8087 (p-90) REVERT: B 1372 VAL cc_start: 0.8774 (t) cc_final: 0.8213 (t) REVERT: B 1376 ASN cc_start: 0.8090 (m110) cc_final: 0.7841 (m110) REVERT: B 1386 LYS cc_start: 0.8132 (mptt) cc_final: 0.7856 (mmtm) REVERT: B 1407 LEU cc_start: 0.8452 (mt) cc_final: 0.8213 (mt) REVERT: B 1409 GLN cc_start: 0.8484 (mt0) cc_final: 0.7959 (mm-40) REVERT: B 1410 MET cc_start: 0.7384 (mtm) cc_final: 0.6937 (mtm) REVERT: B 1417 LEU cc_start: 0.7805 (mt) cc_final: 0.7544 (mt) REVERT: B 1429 VAL cc_start: 0.8747 (t) cc_final: 0.8203 (p) REVERT: B 1430 LYS cc_start: 0.8595 (mmmt) cc_final: 0.7700 (mmmm) REVERT: B 1441 VAL cc_start: 0.8437 (t) cc_final: 0.8112 (p) REVERT: B 1460 ILE cc_start: 0.7761 (mm) cc_final: 0.7435 (mp) REVERT: B 1492 LEU cc_start: 0.7901 (tt) cc_final: 0.7641 (tt) REVERT: B 1498 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8502 (mmmt) REVERT: B 1505 MET cc_start: 0.6965 (mtp) cc_final: 0.6226 (mtp) REVERT: B 1515 LYS cc_start: 0.7826 (tppt) cc_final: 0.7464 (tppt) REVERT: B 1522 MET cc_start: 0.7804 (ttp) cc_final: 0.7000 (tpt) REVERT: B 1529 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7646 (mmm160) REVERT: B 1530 GLN cc_start: 0.8543 (mt0) cc_final: 0.8064 (mt0) REVERT: B 1531 PHE cc_start: 0.8135 (t80) cc_final: 0.7740 (t80) REVERT: B 1543 ILE cc_start: 0.8215 (mt) cc_final: 0.7952 (tp) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.1632 time to fit residues: 129.2452 Evaluate side-chains 473 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 137 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 833 HIS B 962 HIS B1018 ASN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1484 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.208338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.157606 restraints weight = 92228.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.166960 restraints weight = 53201.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.171153 restraints weight = 33727.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.174944 restraints weight = 25070.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.177823 restraints weight = 19187.492| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4360 r_free = 0.4360 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4360 r_free = 0.4360 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23515 Z= 0.160 Angle : 0.652 9.681 31845 Z= 0.334 Chirality : 0.045 0.227 3693 Planarity : 0.005 0.057 4070 Dihedral : 4.707 24.097 3187 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.35 (0.15), residues: 2985 helix: -0.56 (0.14), residues: 1332 sheet: -1.01 (0.24), residues: 478 loop : -1.03 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 748 TYR 0.015 0.002 TYR A1436 PHE 0.026 0.002 PHE A 204 TRP 0.060 0.002 TRP B1514 HIS 0.011 0.001 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00332 (23515) covalent geometry : angle 0.65248 (31845) hydrogen bonds : bond 0.03448 ( 798) hydrogen bonds : angle 5.09821 ( 2205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 83 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7881 (ttpt) REVERT: A 88 LYS cc_start: 0.7703 (tmmt) cc_final: 0.7337 (tmmt) REVERT: A 117 MET cc_start: 0.7640 (ttp) cc_final: 0.7356 (ttp) REVERT: A 120 PHE cc_start: 0.8802 (t80) cc_final: 0.8238 (t80) REVERT: A 126 MET cc_start: 0.6441 (mmp) cc_final: 0.6008 (mmp) REVERT: A 134 VAL cc_start: 0.8287 (t) cc_final: 0.7865 (p) REVERT: A 139 LEU cc_start: 0.7992 (tp) cc_final: 0.7664 (tp) REVERT: A 160 PHE cc_start: 0.7653 (m-80) cc_final: 0.7211 (m-80) REVERT: A 165 HIS cc_start: 0.8223 (t70) cc_final: 0.8003 (t70) REVERT: A 192 VAL cc_start: 0.8310 (p) cc_final: 0.7783 (t) REVERT: A 209 ASN cc_start: 0.8334 (m110) cc_final: 0.7868 (m110) REVERT: A 241 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.7429 (ptm-80) REVERT: A 271 GLU cc_start: 0.7749 (tt0) cc_final: 0.7542 (tt0) REVERT: A 288 MET cc_start: 0.8139 (mtm) cc_final: 0.7272 (mtm) REVERT: A 294 LEU cc_start: 0.9081 (tp) cc_final: 0.8723 (mt) REVERT: A 311 LYS cc_start: 0.8819 (tptp) cc_final: 0.8529 (tptp) REVERT: A 347 MET cc_start: 0.7160 (tpt) cc_final: 0.6909 (tpt) REVERT: A 386 LEU cc_start: 0.7721 (tp) cc_final: 0.7513 (tp) REVERT: A 573 MET cc_start: 0.8059 (mtm) cc_final: 0.6814 (pmm) REVERT: A 828 TRP cc_start: 0.6924 (t-100) cc_final: 0.6717 (t-100) REVERT: A 886 MET cc_start: 0.7121 (tmm) cc_final: 0.6696 (tmm) REVERT: A 889 MET cc_start: 0.3855 (tpt) cc_final: 0.3514 (tpt) REVERT: A 947 ARG cc_start: 0.7204 (mmp80) cc_final: 0.6544 (mmp80) REVERT: A 1007 TYR cc_start: 0.6825 (m-80) cc_final: 0.6347 (m-80) REVERT: A 1009 SER cc_start: 0.7452 (m) cc_final: 0.6696 (t) REVERT: A 1024 PHE cc_start: 0.7684 (t80) cc_final: 0.7444 (t80) REVERT: A 1048 VAL cc_start: 0.8767 (t) cc_final: 0.8461 (m) REVERT: A 1072 GLU cc_start: 0.7267 (tp30) cc_final: 0.6282 (tp30) REVERT: A 1093 ILE cc_start: 0.8274 (tt) cc_final: 0.7689 (mm) REVERT: A 1099 LEU cc_start: 0.9016 (mp) cc_final: 0.8247 (tp) REVERT: A 1158 THR cc_start: 0.7315 (m) cc_final: 0.6998 (p) REVERT: A 1205 ASN cc_start: 0.8207 (m-40) cc_final: 0.7361 (m-40) REVERT: A 1224 ASN cc_start: 0.8186 (m-40) cc_final: 0.7570 (m110) REVERT: A 1228 GLN cc_start: 0.8094 (mp10) cc_final: 0.7572 (mp10) REVERT: A 1231 LEU cc_start: 0.8477 (tt) cc_final: 0.8182 (tt) REVERT: A 1235 LEU cc_start: 0.8374 (mt) cc_final: 0.7604 (tt) REVERT: A 1238 THR cc_start: 0.7645 (t) cc_final: 0.7405 (t) REVERT: A 1251 GLU cc_start: 0.7723 (tp30) cc_final: 0.7514 (tp30) REVERT: A 1261 GLN cc_start: 0.7797 (tp40) cc_final: 0.6857 (tm-30) REVERT: A 1265 ASP cc_start: 0.8310 (m-30) cc_final: 0.6375 (m-30) REVERT: A 1272 LYS cc_start: 0.8416 (mttp) cc_final: 0.8078 (mmmt) REVERT: A 1274 PHE cc_start: 0.7873 (m-80) cc_final: 0.7608 (m-10) REVERT: A 1290 HIS cc_start: 0.7297 (m-70) cc_final: 0.6783 (m-70) REVERT: A 1295 LYS cc_start: 0.8935 (pttm) cc_final: 0.8594 (ptmm) REVERT: A 1297 LEU cc_start: 0.8845 (mt) cc_final: 0.8593 (mm) REVERT: A 1298 ASN cc_start: 0.7607 (t0) cc_final: 0.7255 (t0) REVERT: A 1327 LEU cc_start: 0.6641 (mt) cc_final: 0.6379 (mt) REVERT: A 1356 THR cc_start: 0.7890 (m) cc_final: 0.7361 (p) REVERT: A 1410 MET cc_start: 0.6781 (tpp) cc_final: 0.5891 (tpp) REVERT: A 1418 VAL cc_start: 0.7210 (t) cc_final: 0.6696 (p) REVERT: A 1426 GLU cc_start: 0.7490 (mp0) cc_final: 0.7142 (mp0) REVERT: A 1428 LEU cc_start: 0.8612 (mt) cc_final: 0.8116 (mt) REVERT: A 1432 PHE cc_start: 0.7538 (m-80) cc_final: 0.6770 (m-80) REVERT: A 1440 ILE cc_start: 0.6674 (tp) cc_final: 0.6214 (tt) REVERT: A 1452 LYS cc_start: 0.7850 (tttt) cc_final: 0.7622 (tmtt) REVERT: A 1475 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 1477 ILE cc_start: 0.8440 (tp) cc_final: 0.7953 (pt) REVERT: A 1520 VAL cc_start: 0.8484 (m) cc_final: 0.8007 (m) REVERT: A 1522 MET cc_start: 0.8420 (ptt) cc_final: 0.7977 (ptt) REVERT: A 1524 VAL cc_start: 0.7822 (t) cc_final: 0.7390 (p) REVERT: A 1526 GLN cc_start: 0.7828 (pt0) cc_final: 0.7416 (pp30) REVERT: A 1528 ASP cc_start: 0.7774 (m-30) cc_final: 0.7066 (m-30) REVERT: A 1529 ARG cc_start: 0.8321 (tpt90) cc_final: 0.7336 (mmm-85) REVERT: A 1530 GLN cc_start: 0.8410 (pp30) cc_final: 0.7905 (pp30) REVERT: A 1532 LYS cc_start: 0.9007 (tptp) cc_final: 0.8325 (tppt) REVERT: A 1533 LEU cc_start: 0.8771 (mt) cc_final: 0.8318 (mt) REVERT: A 1534 HIS cc_start: 0.8022 (m90) cc_final: 0.7770 (m90) REVERT: A 1546 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.6985 (ttm110) REVERT: B 31 ASN cc_start: 0.6669 (p0) cc_final: 0.6420 (p0) REVERT: B 102 ARG cc_start: 0.8127 (ppt170) cc_final: 0.7874 (ttp80) REVERT: B 117 MET cc_start: 0.7677 (ttp) cc_final: 0.7323 (ttp) REVERT: B 133 GLN cc_start: 0.6201 (tp-100) cc_final: 0.5984 (tp40) REVERT: B 141 MET cc_start: 0.7060 (mtt) cc_final: 0.5725 (tmm) REVERT: B 200 ASN cc_start: 0.7687 (p0) cc_final: 0.7188 (p0) REVERT: B 201 GLU cc_start: 0.8008 (pt0) cc_final: 0.7711 (tt0) REVERT: B 271 GLU cc_start: 0.6798 (pt0) cc_final: 0.6587 (pt0) REVERT: B 288 MET cc_start: 0.8468 (mtt) cc_final: 0.7935 (mtm) REVERT: B 311 LYS cc_start: 0.8791 (pttt) cc_final: 0.8506 (pttt) REVERT: B 312 CYS cc_start: 0.8136 (p) cc_final: 0.7936 (p) REVERT: B 604 MET cc_start: 0.6596 (ppp) cc_final: 0.6157 (ppp) REVERT: B 667 LEU cc_start: 0.6149 (pp) cc_final: 0.5830 (pp) REVERT: B 800 MET cc_start: 0.5356 (mtm) cc_final: 0.4975 (mtm) REVERT: B 838 ILE cc_start: 0.7841 (mp) cc_final: 0.7626 (mp) REVERT: B 875 SER cc_start: 0.8604 (m) cc_final: 0.8197 (p) REVERT: B 933 VAL cc_start: 0.8409 (p) cc_final: 0.8083 (m) REVERT: B 997 TRP cc_start: 0.8394 (m-90) cc_final: 0.8040 (m-90) REVERT: B 1004 TYR cc_start: 0.7525 (m-80) cc_final: 0.7269 (m-80) REVERT: B 1016 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 1029 LYS cc_start: 0.8611 (mttt) cc_final: 0.7869 (tttm) REVERT: B 1069 ASP cc_start: 0.8034 (m-30) cc_final: 0.7712 (m-30) REVERT: B 1090 ILE cc_start: 0.8675 (mt) cc_final: 0.8271 (tp) REVERT: B 1106 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7036 (mmm160) REVERT: B 1113 LYS cc_start: 0.8423 (tppt) cc_final: 0.7897 (ttmt) REVERT: B 1122 LEU cc_start: 0.8632 (tt) cc_final: 0.8379 (tt) REVERT: B 1125 LEU cc_start: 0.8763 (mt) cc_final: 0.8470 (mt) REVERT: B 1126 LEU cc_start: 0.8556 (mt) cc_final: 0.7933 (mt) REVERT: B 1130 ILE cc_start: 0.7469 (mt) cc_final: 0.7144 (mt) REVERT: B 1152 SER cc_start: 0.8817 (m) cc_final: 0.8568 (p) REVERT: B 1178 TRP cc_start: 0.6734 (m100) cc_final: 0.6471 (m100) REVERT: B 1191 ASP cc_start: 0.7641 (m-30) cc_final: 0.7433 (m-30) REVERT: B 1207 ASP cc_start: 0.7800 (t0) cc_final: 0.7097 (t0) REVERT: B 1213 LYS cc_start: 0.8652 (tmmt) cc_final: 0.8259 (tmmt) REVERT: B 1228 GLN cc_start: 0.8036 (mt0) cc_final: 0.7531 (tt0) REVERT: B 1233 GLN cc_start: 0.8162 (mt0) cc_final: 0.7822 (mt0) REVERT: B 1235 LEU cc_start: 0.8995 (mt) cc_final: 0.8672 (mm) REVERT: B 1245 LYS cc_start: 0.8955 (pptt) cc_final: 0.8491 (pptt) REVERT: B 1256 ILE cc_start: 0.9002 (tp) cc_final: 0.8528 (tp) REVERT: B 1260 ASN cc_start: 0.8391 (m-40) cc_final: 0.8039 (p0) REVERT: B 1269 PHE cc_start: 0.7637 (m-80) cc_final: 0.7413 (m-10) REVERT: B 1295 LYS cc_start: 0.8974 (pptt) cc_final: 0.8759 (ptmm) REVERT: B 1297 LEU cc_start: 0.8627 (mt) cc_final: 0.8384 (mm) REVERT: B 1306 PHE cc_start: 0.7855 (t80) cc_final: 0.7300 (t80) REVERT: B 1364 TYR cc_start: 0.7785 (m-10) cc_final: 0.7217 (m-10) REVERT: B 1371 TRP cc_start: 0.8530 (p-90) cc_final: 0.8194 (p-90) REVERT: B 1372 VAL cc_start: 0.8656 (t) cc_final: 0.8423 (t) REVERT: B 1386 LYS cc_start: 0.8098 (mptt) cc_final: 0.7819 (mmmt) REVERT: B 1409 GLN cc_start: 0.8476 (mt0) cc_final: 0.7984 (mm-40) REVERT: B 1410 MET cc_start: 0.7393 (mtm) cc_final: 0.6986 (mtm) REVERT: B 1417 LEU cc_start: 0.7967 (mt) cc_final: 0.7686 (mt) REVERT: B 1429 VAL cc_start: 0.8855 (t) cc_final: 0.8624 (p) REVERT: B 1430 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8105 (mmmt) REVERT: B 1441 VAL cc_start: 0.8416 (t) cc_final: 0.8087 (p) REVERT: B 1498 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8533 (mmmt) REVERT: B 1505 MET cc_start: 0.7052 (mtp) cc_final: 0.6273 (mtp) REVERT: B 1522 MET cc_start: 0.8042 (ttp) cc_final: 0.7167 (tpt) REVERT: B 1529 ARG cc_start: 0.8504 (tpt-90) cc_final: 0.7765 (mmm-85) REVERT: B 1531 PHE cc_start: 0.8119 (t80) cc_final: 0.7741 (t80) REVERT: B 1543 ILE cc_start: 0.8300 (mt) cc_final: 0.7997 (tp) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1561 time to fit residues: 125.1367 Evaluate side-chains 489 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 HIS ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1409 GLN ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 833 HIS ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 ASN B1096 HIS ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1288 ASN B1302 GLN B1484 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.206053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.156847 restraints weight = 84500.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.165312 restraints weight = 50206.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.169665 restraints weight = 32817.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.173129 restraints weight = 24402.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.175938 restraints weight = 18880.781| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4337 r_free = 0.4337 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4337 r_free = 0.4337 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23515 Z= 0.188 Angle : 0.683 10.633 31845 Z= 0.354 Chirality : 0.046 0.223 3693 Planarity : 0.005 0.088 4070 Dihedral : 4.875 23.924 3187 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -1.39 (0.15), residues: 2985 helix: -0.66 (0.14), residues: 1335 sheet: -0.99 (0.24), residues: 467 loop : -0.97 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG B1159 TYR 0.046 0.002 TYR B 297 PHE 0.029 0.002 PHE A1024 TRP 0.046 0.003 TRP B1514 HIS 0.009 0.001 HIS A 999 Details of bonding type rmsd covalent geometry : bond 0.00379 (23515) covalent geometry : angle 0.68285 (31845) hydrogen bonds : bond 0.03667 ( 798) hydrogen bonds : angle 5.24038 ( 2205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.5455 (m-10) cc_final: 0.5043 (m-10) REVERT: A 80 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8045 (mm-30) REVERT: A 88 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7510 (tmmt) REVERT: A 102 ARG cc_start: 0.8814 (mtt-85) cc_final: 0.7234 (mmm-85) REVERT: A 120 PHE cc_start: 0.8744 (t80) cc_final: 0.8158 (t80) REVERT: A 126 MET cc_start: 0.6405 (mmp) cc_final: 0.5451 (mmp) REVERT: A 134 VAL cc_start: 0.8379 (t) cc_final: 0.7917 (p) REVERT: A 160 PHE cc_start: 0.7796 (m-80) cc_final: 0.7277 (m-80) REVERT: A 168 GLU cc_start: 0.7554 (tp30) cc_final: 0.7234 (tp30) REVERT: A 169 TYR cc_start: 0.6111 (m-10) cc_final: 0.5127 (m-10) REVERT: A 171 PHE cc_start: 0.8007 (m-10) cc_final: 0.7779 (m-80) REVERT: A 177 LEU cc_start: 0.8309 (mp) cc_final: 0.8046 (mp) REVERT: A 186 ILE cc_start: 0.8743 (mm) cc_final: 0.8439 (pt) REVERT: A 192 VAL cc_start: 0.8342 (p) cc_final: 0.7750 (t) REVERT: A 205 THR cc_start: 0.8808 (m) cc_final: 0.7213 (m) REVERT: A 206 ARG cc_start: 0.8349 (mmp80) cc_final: 0.8068 (mmp80) REVERT: A 209 ASN cc_start: 0.8210 (m110) cc_final: 0.7928 (m110) REVERT: A 241 ARG cc_start: 0.7908 (ptm-80) cc_final: 0.7485 (ptm-80) REVERT: A 271 GLU cc_start: 0.7751 (tt0) cc_final: 0.7275 (tt0) REVERT: A 288 MET cc_start: 0.8195 (mtm) cc_final: 0.7324 (mtm) REVERT: A 294 LEU cc_start: 0.9096 (tp) cc_final: 0.8723 (mt) REVERT: A 311 LYS cc_start: 0.8843 (tptp) cc_final: 0.8547 (tptp) REVERT: A 335 ARG cc_start: 0.7802 (tmt170) cc_final: 0.7577 (tmt170) REVERT: A 573 MET cc_start: 0.8276 (mtm) cc_final: 0.7637 (mtm) REVERT: A 681 MET cc_start: 0.8191 (mmt) cc_final: 0.7747 (tmm) REVERT: A 886 MET cc_start: 0.7117 (tmm) cc_final: 0.6699 (tmm) REVERT: A 889 MET cc_start: 0.3857 (tpt) cc_final: 0.3541 (tpt) REVERT: A 947 ARG cc_start: 0.7039 (mmp80) cc_final: 0.6194 (mmp-170) REVERT: A 994 ARG cc_start: 0.7730 (mpt180) cc_final: 0.7240 (mtt90) REVERT: A 1007 TYR cc_start: 0.6869 (m-80) cc_final: 0.6458 (m-80) REVERT: A 1009 SER cc_start: 0.7306 (m) cc_final: 0.6571 (t) REVERT: A 1024 PHE cc_start: 0.8017 (t80) cc_final: 0.7547 (t80) REVERT: A 1030 LEU cc_start: 0.7681 (tp) cc_final: 0.7407 (tp) REVERT: A 1031 ILE cc_start: 0.7568 (pt) cc_final: 0.7325 (pt) REVERT: A 1048 VAL cc_start: 0.8768 (t) cc_final: 0.8453 (m) REVERT: A 1072 GLU cc_start: 0.7194 (tp30) cc_final: 0.6258 (tp30) REVERT: A 1093 ILE cc_start: 0.8359 (tt) cc_final: 0.7730 (mm) REVERT: A 1099 LEU cc_start: 0.9045 (mp) cc_final: 0.8244 (tp) REVERT: A 1158 THR cc_start: 0.7397 (m) cc_final: 0.7146 (p) REVERT: A 1179 LYS cc_start: 0.8291 (ttmm) cc_final: 0.8057 (tptp) REVERT: A 1224 ASN cc_start: 0.8246 (m-40) cc_final: 0.7826 (m110) REVERT: A 1228 GLN cc_start: 0.8106 (mp10) cc_final: 0.7615 (mp10) REVERT: A 1235 LEU cc_start: 0.8424 (mt) cc_final: 0.8017 (tp) REVERT: A 1238 THR cc_start: 0.7678 (t) cc_final: 0.7222 (p) REVERT: A 1251 GLU cc_start: 0.7819 (tp30) cc_final: 0.7616 (tp30) REVERT: A 1261 GLN cc_start: 0.7851 (tp40) cc_final: 0.6964 (tm-30) REVERT: A 1262 THR cc_start: 0.8336 (p) cc_final: 0.8073 (p) REVERT: A 1265 ASP cc_start: 0.8287 (m-30) cc_final: 0.6433 (m-30) REVERT: A 1273 LYS cc_start: 0.8007 (tptm) cc_final: 0.7489 (tptp) REVERT: A 1274 PHE cc_start: 0.7768 (m-80) cc_final: 0.7418 (m-80) REVERT: A 1290 HIS cc_start: 0.7358 (m-70) cc_final: 0.6781 (m-70) REVERT: A 1295 LYS cc_start: 0.8929 (pttm) cc_final: 0.8559 (ptmm) REVERT: A 1297 LEU cc_start: 0.8925 (mt) cc_final: 0.8497 (mm) REVERT: A 1298 ASN cc_start: 0.7650 (t0) cc_final: 0.7293 (t0) REVERT: A 1302 GLN cc_start: 0.7358 (tp-100) cc_final: 0.7015 (tp-100) REVERT: A 1327 LEU cc_start: 0.6699 (mt) cc_final: 0.6375 (mt) REVERT: A 1349 GLU cc_start: 0.8043 (tp30) cc_final: 0.7548 (tp30) REVERT: A 1356 THR cc_start: 0.7899 (m) cc_final: 0.7254 (p) REVERT: A 1410 MET cc_start: 0.6785 (tpp) cc_final: 0.5916 (tpp) REVERT: A 1414 LYS cc_start: 0.7267 (pttt) cc_final: 0.6823 (pttm) REVERT: A 1418 VAL cc_start: 0.7135 (t) cc_final: 0.6671 (p) REVERT: A 1426 GLU cc_start: 0.7516 (mp0) cc_final: 0.7141 (mp0) REVERT: A 1432 PHE cc_start: 0.7518 (m-80) cc_final: 0.6687 (m-80) REVERT: A 1452 LYS cc_start: 0.8010 (tttt) cc_final: 0.7705 (tmtt) REVERT: A 1475 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7640 (mt-10) REVERT: A 1477 ILE cc_start: 0.8377 (tp) cc_final: 0.7918 (pt) REVERT: A 1520 VAL cc_start: 0.8453 (m) cc_final: 0.7994 (m) REVERT: A 1522 MET cc_start: 0.8475 (ptt) cc_final: 0.8060 (ptt) REVERT: A 1524 VAL cc_start: 0.7920 (t) cc_final: 0.7497 (p) REVERT: A 1526 GLN cc_start: 0.7957 (pt0) cc_final: 0.7490 (pp30) REVERT: A 1528 ASP cc_start: 0.7785 (m-30) cc_final: 0.7114 (m-30) REVERT: A 1530 GLN cc_start: 0.8437 (pp30) cc_final: 0.7794 (pp30) REVERT: A 1532 LYS cc_start: 0.8991 (tptp) cc_final: 0.8301 (tppt) REVERT: A 1533 LEU cc_start: 0.8790 (mt) cc_final: 0.8472 (mt) REVERT: A 1534 HIS cc_start: 0.8034 (m90) cc_final: 0.7691 (m90) REVERT: B 102 ARG cc_start: 0.8165 (ppt170) cc_final: 0.7897 (ttp80) REVERT: B 117 MET cc_start: 0.7721 (ttp) cc_final: 0.7404 (ttp) REVERT: B 141 MET cc_start: 0.7212 (mtt) cc_final: 0.6180 (tmm) REVERT: B 184 GLN cc_start: 0.8757 (mt0) cc_final: 0.8490 (mp10) REVERT: B 189 MET cc_start: 0.6980 (mmm) cc_final: 0.6486 (mpp) REVERT: B 200 ASN cc_start: 0.7734 (p0) cc_final: 0.7112 (p0) REVERT: B 201 GLU cc_start: 0.8053 (pt0) cc_final: 0.7796 (mt-10) REVERT: B 243 LYS cc_start: 0.8853 (ptpt) cc_final: 0.8561 (ptpt) REVERT: B 268 HIS cc_start: 0.8266 (t-90) cc_final: 0.7710 (t-90) REVERT: B 288 MET cc_start: 0.8490 (mtt) cc_final: 0.7934 (mtm) REVERT: B 296 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7753 (mmm-85) REVERT: B 301 LEU cc_start: 0.7784 (tp) cc_final: 0.7403 (tp) REVERT: B 311 LYS cc_start: 0.8870 (pttt) cc_final: 0.8559 (pttt) REVERT: B 604 MET cc_start: 0.6612 (ppp) cc_final: 0.6185 (ppp) REVERT: B 667 LEU cc_start: 0.6247 (pp) cc_final: 0.5932 (pp) REVERT: B 718 LEU cc_start: 0.6602 (mp) cc_final: 0.6356 (mp) REVERT: B 742 ARG cc_start: 0.8158 (tpp-160) cc_final: 0.7828 (mmp80) REVERT: B 748 ARG cc_start: 0.6654 (tmm160) cc_final: 0.6217 (tmm160) REVERT: B 800 MET cc_start: 0.5275 (mtm) cc_final: 0.4913 (mtm) REVERT: B 866 MET cc_start: 0.7758 (mmt) cc_final: 0.7504 (mmt) REVERT: B 875 SER cc_start: 0.8706 (m) cc_final: 0.8291 (p) REVERT: B 933 VAL cc_start: 0.8428 (p) cc_final: 0.8187 (m) REVERT: B 997 TRP cc_start: 0.8395 (m-90) cc_final: 0.7966 (m-90) REVERT: B 1016 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7571 (mt-10) REVERT: B 1024 PHE cc_start: 0.8258 (t80) cc_final: 0.7681 (t80) REVERT: B 1029 LYS cc_start: 0.8622 (mttt) cc_final: 0.7881 (tttm) REVERT: B 1069 ASP cc_start: 0.8029 (m-30) cc_final: 0.7690 (m-30) REVERT: B 1090 ILE cc_start: 0.8733 (mt) cc_final: 0.8315 (tp) REVERT: B 1113 LYS cc_start: 0.8475 (tppt) cc_final: 0.8013 (ttmt) REVERT: B 1126 LEU cc_start: 0.8586 (mt) cc_final: 0.7875 (mt) REVERT: B 1130 ILE cc_start: 0.7578 (mt) cc_final: 0.7268 (mt) REVERT: B 1152 SER cc_start: 0.8820 (m) cc_final: 0.8568 (p) REVERT: B 1159 ARG cc_start: 0.5552 (mtt180) cc_final: 0.3924 (mtt90) REVERT: B 1191 ASP cc_start: 0.7572 (m-30) cc_final: 0.7334 (m-30) REVERT: B 1207 ASP cc_start: 0.7950 (t0) cc_final: 0.7242 (t0) REVERT: B 1213 LYS cc_start: 0.8662 (tmmt) cc_final: 0.8261 (tmmt) REVERT: B 1220 LEU cc_start: 0.7727 (tp) cc_final: 0.7503 (tp) REVERT: B 1228 GLN cc_start: 0.8060 (mt0) cc_final: 0.7860 (mt0) REVERT: B 1233 GLN cc_start: 0.8143 (mt0) cc_final: 0.7834 (mt0) REVERT: B 1235 LEU cc_start: 0.9024 (mt) cc_final: 0.8717 (mm) REVERT: B 1239 PHE cc_start: 0.8029 (m-80) cc_final: 0.7755 (m-80) REVERT: B 1245 LYS cc_start: 0.8945 (pptt) cc_final: 0.8413 (pptt) REVERT: B 1252 GLU cc_start: 0.7048 (mp0) cc_final: 0.6668 (mp0) REVERT: B 1371 TRP cc_start: 0.8549 (p-90) cc_final: 0.8170 (p-90) REVERT: B 1372 VAL cc_start: 0.8846 (t) cc_final: 0.8022 (t) REVERT: B 1376 ASN cc_start: 0.8539 (m-40) cc_final: 0.8258 (p0) REVERT: B 1386 LYS cc_start: 0.8126 (mptt) cc_final: 0.7878 (mmtm) REVERT: B 1409 GLN cc_start: 0.8493 (mt0) cc_final: 0.8214 (mt0) REVERT: B 1410 MET cc_start: 0.7451 (mtm) cc_final: 0.7064 (mtm) REVERT: B 1417 LEU cc_start: 0.7969 (mt) cc_final: 0.7675 (mt) REVERT: B 1429 VAL cc_start: 0.8876 (t) cc_final: 0.8622 (m) REVERT: B 1430 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8106 (mmmt) REVERT: B 1441 VAL cc_start: 0.8420 (t) cc_final: 0.8087 (p) REVERT: B 1498 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8522 (mmmt) REVERT: B 1505 MET cc_start: 0.7033 (mtp) cc_final: 0.6257 (mtp) REVERT: B 1522 MET cc_start: 0.8072 (ttp) cc_final: 0.7284 (tpt) REVERT: B 1529 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.8011 (mmm160) REVERT: B 1531 PHE cc_start: 0.8175 (t80) cc_final: 0.7643 (t80) REVERT: B 1543 ILE cc_start: 0.8308 (mt) cc_final: 0.8090 (tp) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.1548 time to fit residues: 123.7921 Evaluate side-chains 490 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 225 optimal weight: 7.9990 chunk 264 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 131 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 ASN ** B1096 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1302 GLN B1484 GLN B1525 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.206084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.157727 restraints weight = 85255.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.165127 restraints weight = 49321.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.170271 restraints weight = 32769.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.174023 restraints weight = 23754.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.176706 restraints weight = 18297.104| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23515 Z= 0.169 Angle : 0.676 10.502 31845 Z= 0.347 Chirality : 0.046 0.233 3693 Planarity : 0.006 0.251 4070 Dihedral : 4.917 35.073 3187 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.15), residues: 2985 helix: -0.61 (0.14), residues: 1324 sheet: -0.91 (0.23), residues: 481 loop : -1.02 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A1285 TYR 0.033 0.002 TYR A1027 PHE 0.045 0.002 PHE B 171 TRP 0.070 0.003 TRP B1514 HIS 0.011 0.002 HIS A1408 Details of bonding type rmsd covalent geometry : bond 0.00354 (23515) covalent geometry : angle 0.67591 (31845) hydrogen bonds : bond 0.03652 ( 798) hydrogen bonds : angle 5.16464 ( 2205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.5503 (m-10) cc_final: 0.5148 (m-10) REVERT: A 88 LYS cc_start: 0.7806 (tmmt) cc_final: 0.7558 (tmmt) REVERT: A 96 LEU cc_start: 0.7390 (mp) cc_final: 0.7132 (mt) REVERT: A 102 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.7293 (mmm-85) REVERT: A 120 PHE cc_start: 0.8751 (t80) cc_final: 0.8185 (t80) REVERT: A 126 MET cc_start: 0.6351 (mmp) cc_final: 0.5465 (mmp) REVERT: A 134 VAL cc_start: 0.8383 (t) cc_final: 0.7906 (p) REVERT: A 160 PHE cc_start: 0.7769 (m-80) cc_final: 0.7266 (m-80) REVERT: A 169 TYR cc_start: 0.6161 (m-10) cc_final: 0.5570 (m-10) REVERT: A 206 ARG cc_start: 0.8303 (mmp80) cc_final: 0.8005 (mmp80) REVERT: A 209 ASN cc_start: 0.8131 (m110) cc_final: 0.7841 (m110) REVERT: A 234 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8491 (mmmt) REVERT: A 241 ARG cc_start: 0.7870 (ptm-80) cc_final: 0.7500 (ptm-80) REVERT: A 271 GLU cc_start: 0.7698 (tt0) cc_final: 0.7452 (tt0) REVERT: A 280 HIS cc_start: 0.7123 (t-90) cc_final: 0.6837 (t-90) REVERT: A 288 MET cc_start: 0.8224 (mtm) cc_final: 0.7307 (mtm) REVERT: A 294 LEU cc_start: 0.9051 (tp) cc_final: 0.8672 (mt) REVERT: A 311 LYS cc_start: 0.8829 (tptp) cc_final: 0.8496 (tptp) REVERT: A 327 PHE cc_start: 0.7811 (t80) cc_final: 0.7610 (t80) REVERT: A 330 LYS cc_start: 0.7778 (tppt) cc_final: 0.7252 (mmmm) REVERT: A 335 ARG cc_start: 0.7772 (tmt170) cc_final: 0.7533 (tmt170) REVERT: A 385 VAL cc_start: 0.8682 (m) cc_final: 0.8198 (m) REVERT: A 573 MET cc_start: 0.8175 (mtm) cc_final: 0.7568 (mtm) REVERT: A 794 ASP cc_start: 0.8126 (t0) cc_final: 0.7922 (m-30) REVERT: A 828 TRP cc_start: 0.7075 (t-100) cc_final: 0.6753 (t-100) REVERT: A 886 MET cc_start: 0.7091 (tmm) cc_final: 0.6713 (tmm) REVERT: A 889 MET cc_start: 0.3823 (tpt) cc_final: 0.3454 (tpt) REVERT: A 947 ARG cc_start: 0.7071 (mmp80) cc_final: 0.6242 (mmp-170) REVERT: A 994 ARG cc_start: 0.7723 (mpt180) cc_final: 0.7203 (mtt90) REVERT: A 1007 TYR cc_start: 0.6721 (m-80) cc_final: 0.6375 (m-80) REVERT: A 1009 SER cc_start: 0.7147 (m) cc_final: 0.6436 (t) REVERT: A 1020 LEU cc_start: 0.8177 (tt) cc_final: 0.7828 (mt) REVERT: A 1024 PHE cc_start: 0.8044 (t80) cc_final: 0.7422 (t80) REVERT: A 1030 LEU cc_start: 0.7731 (tp) cc_final: 0.7493 (tp) REVERT: A 1048 VAL cc_start: 0.8725 (t) cc_final: 0.8341 (m) REVERT: A 1061 LEU cc_start: 0.8479 (tt) cc_final: 0.8242 (tt) REVERT: A 1072 GLU cc_start: 0.7028 (tp30) cc_final: 0.6235 (tp30) REVERT: A 1093 ILE cc_start: 0.8339 (tt) cc_final: 0.7743 (mm) REVERT: A 1099 LEU cc_start: 0.9040 (mp) cc_final: 0.8235 (tp) REVERT: A 1158 THR cc_start: 0.7389 (m) cc_final: 0.7138 (p) REVERT: A 1179 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7990 (tppp) REVERT: A 1224 ASN cc_start: 0.8335 (m-40) cc_final: 0.7845 (m110) REVERT: A 1228 GLN cc_start: 0.8092 (mp10) cc_final: 0.7717 (mp10) REVERT: A 1235 LEU cc_start: 0.8445 (mt) cc_final: 0.8055 (tp) REVERT: A 1238 THR cc_start: 0.7675 (t) cc_final: 0.7270 (p) REVERT: A 1247 LEU cc_start: 0.8641 (mt) cc_final: 0.8247 (tp) REVERT: A 1261 GLN cc_start: 0.7799 (tp40) cc_final: 0.6927 (tm-30) REVERT: A 1262 THR cc_start: 0.8307 (p) cc_final: 0.8011 (p) REVERT: A 1265 ASP cc_start: 0.8167 (m-30) cc_final: 0.6377 (m-30) REVERT: A 1272 LYS cc_start: 0.8433 (mttp) cc_final: 0.7954 (mmmt) REVERT: A 1273 LYS cc_start: 0.7877 (tptm) cc_final: 0.7355 (tptp) REVERT: A 1289 LEU cc_start: 0.8528 (tt) cc_final: 0.8287 (tt) REVERT: A 1290 HIS cc_start: 0.7204 (m-70) cc_final: 0.6915 (m-70) REVERT: A 1295 LYS cc_start: 0.8887 (pttm) cc_final: 0.8533 (ptmm) REVERT: A 1297 LEU cc_start: 0.8926 (mt) cc_final: 0.8622 (mm) REVERT: A 1316 ASP cc_start: 0.7796 (m-30) cc_final: 0.7579 (m-30) REVERT: A 1327 LEU cc_start: 0.6713 (mt) cc_final: 0.6410 (mt) REVERT: A 1349 GLU cc_start: 0.8069 (tp30) cc_final: 0.7591 (tp30) REVERT: A 1356 THR cc_start: 0.8033 (m) cc_final: 0.7432 (p) REVERT: A 1410 MET cc_start: 0.6794 (tpp) cc_final: 0.5889 (tpp) REVERT: A 1414 LYS cc_start: 0.7328 (pttt) cc_final: 0.6845 (pttm) REVERT: A 1418 VAL cc_start: 0.7110 (t) cc_final: 0.6621 (p) REVERT: A 1426 GLU cc_start: 0.7519 (mp0) cc_final: 0.7135 (mp0) REVERT: A 1452 LYS cc_start: 0.8134 (tttt) cc_final: 0.7804 (tmtt) REVERT: A 1475 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 1477 ILE cc_start: 0.8313 (tp) cc_final: 0.7875 (pt) REVERT: A 1520 VAL cc_start: 0.8510 (m) cc_final: 0.7984 (m) REVERT: A 1522 MET cc_start: 0.8520 (ptt) cc_final: 0.8014 (ptt) REVERT: A 1524 VAL cc_start: 0.8019 (t) cc_final: 0.7472 (p) REVERT: A 1526 GLN cc_start: 0.8018 (pt0) cc_final: 0.7490 (pp30) REVERT: A 1528 ASP cc_start: 0.7641 (m-30) cc_final: 0.7011 (m-30) REVERT: A 1529 ARG cc_start: 0.8474 (tpt90) cc_final: 0.7418 (mmm-85) REVERT: A 1530 GLN cc_start: 0.8346 (pp30) cc_final: 0.7572 (pp30) REVERT: A 1532 LYS cc_start: 0.8977 (tptp) cc_final: 0.8281 (tppt) REVERT: A 1533 LEU cc_start: 0.8768 (mt) cc_final: 0.8451 (mt) REVERT: A 1534 HIS cc_start: 0.8062 (m90) cc_final: 0.7529 (m90) REVERT: B 31 ASN cc_start: 0.7596 (p0) cc_final: 0.7286 (p0) REVERT: B 92 GLU cc_start: 0.8216 (tt0) cc_final: 0.7496 (mt-10) REVERT: B 102 ARG cc_start: 0.8195 (ppt170) cc_final: 0.7900 (ttp80) REVERT: B 117 MET cc_start: 0.7638 (ttp) cc_final: 0.7369 (ttp) REVERT: B 141 MET cc_start: 0.7298 (mtt) cc_final: 0.6289 (tmm) REVERT: B 184 GLN cc_start: 0.8745 (mt0) cc_final: 0.8494 (mp10) REVERT: B 189 MET cc_start: 0.7156 (mmm) cc_final: 0.5976 (mmm) REVERT: B 200 ASN cc_start: 0.7733 (p0) cc_final: 0.7405 (p0) REVERT: B 201 GLU cc_start: 0.8075 (pt0) cc_final: 0.7857 (mt-10) REVERT: B 243 LYS cc_start: 0.8901 (ptpt) cc_final: 0.8626 (ptpt) REVERT: B 271 GLU cc_start: 0.7048 (tp30) cc_final: 0.5897 (pt0) REVERT: B 288 MET cc_start: 0.8439 (mtt) cc_final: 0.7874 (mtm) REVERT: B 296 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7891 (mmm-85) REVERT: B 301 LEU cc_start: 0.7806 (tp) cc_final: 0.7446 (tp) REVERT: B 311 LYS cc_start: 0.8881 (pttt) cc_final: 0.8617 (pttp) REVERT: B 604 MET cc_start: 0.6618 (ppp) cc_final: 0.6174 (ppp) REVERT: B 667 LEU cc_start: 0.6213 (pp) cc_final: 0.5894 (pp) REVERT: B 800 MET cc_start: 0.5210 (mtm) cc_final: 0.4870 (mtm) REVERT: B 838 ILE cc_start: 0.8256 (mp) cc_final: 0.7937 (mp) REVERT: B 866 MET cc_start: 0.7730 (mmt) cc_final: 0.7458 (mmt) REVERT: B 875 SER cc_start: 0.8777 (m) cc_final: 0.8361 (p) REVERT: B 878 LEU cc_start: 0.8774 (tp) cc_final: 0.8527 (tp) REVERT: B 933 VAL cc_start: 0.8531 (p) cc_final: 0.8218 (m) REVERT: B 959 ILE cc_start: 0.7693 (mt) cc_final: 0.7432 (mt) REVERT: B 997 TRP cc_start: 0.8211 (m-90) cc_final: 0.7977 (m-90) REVERT: B 1004 TYR cc_start: 0.7371 (m-80) cc_final: 0.7157 (m-80) REVERT: B 1016 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 1024 PHE cc_start: 0.8102 (t80) cc_final: 0.7512 (t80) REVERT: B 1029 LYS cc_start: 0.8700 (mttt) cc_final: 0.7935 (tttm) REVERT: B 1069 ASP cc_start: 0.7986 (m-30) cc_final: 0.7710 (m-30) REVERT: B 1090 ILE cc_start: 0.8657 (mt) cc_final: 0.8242 (tp) REVERT: B 1098 ASP cc_start: 0.7001 (p0) cc_final: 0.6579 (p0) REVERT: B 1113 LYS cc_start: 0.8445 (tppt) cc_final: 0.7943 (ttpt) REVERT: B 1121 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7607 (tm-30) REVERT: B 1126 LEU cc_start: 0.8605 (mt) cc_final: 0.8055 (mt) REVERT: B 1130 ILE cc_start: 0.7582 (mt) cc_final: 0.7269 (mt) REVERT: B 1152 SER cc_start: 0.8814 (m) cc_final: 0.8568 (p) REVERT: B 1207 ASP cc_start: 0.7970 (t0) cc_final: 0.7242 (t0) REVERT: B 1213 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8309 (tmmt) REVERT: B 1220 LEU cc_start: 0.7727 (tp) cc_final: 0.7511 (tp) REVERT: B 1228 GLN cc_start: 0.8077 (mt0) cc_final: 0.7863 (mt0) REVERT: B 1233 GLN cc_start: 0.8098 (mt0) cc_final: 0.7763 (mt0) REVERT: B 1235 LEU cc_start: 0.8957 (mt) cc_final: 0.8672 (mm) REVERT: B 1245 LYS cc_start: 0.8955 (pptt) cc_final: 0.8389 (pptt) REVERT: B 1252 GLU cc_start: 0.6960 (mp0) cc_final: 0.6644 (mp0) REVERT: B 1295 LYS cc_start: 0.8845 (tttm) cc_final: 0.8616 (ptmm) REVERT: B 1371 TRP cc_start: 0.8498 (p-90) cc_final: 0.8138 (p-90) REVERT: B 1372 VAL cc_start: 0.8902 (t) cc_final: 0.8034 (t) REVERT: B 1376 ASN cc_start: 0.8513 (m-40) cc_final: 0.8219 (p0) REVERT: B 1409 GLN cc_start: 0.8462 (mt0) cc_final: 0.8255 (mt0) REVERT: B 1410 MET cc_start: 0.7500 (mtm) cc_final: 0.7151 (mtm) REVERT: B 1417 LEU cc_start: 0.7954 (mt) cc_final: 0.7674 (mt) REVERT: B 1429 VAL cc_start: 0.8908 (t) cc_final: 0.8651 (m) REVERT: B 1430 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8144 (mmmt) REVERT: B 1473 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8290 (mmtt) REVERT: B 1498 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8460 (mmmt) REVERT: B 1505 MET cc_start: 0.7066 (mtp) cc_final: 0.6286 (mtp) REVERT: B 1522 MET cc_start: 0.8059 (ttp) cc_final: 0.7319 (tpt) REVERT: B 1529 ARG cc_start: 0.8342 (tpt-90) cc_final: 0.7881 (mmm160) REVERT: B 1531 PHE cc_start: 0.7980 (t80) cc_final: 0.7488 (t80) REVERT: B 1541 TYR cc_start: 0.7522 (t80) cc_final: 0.7309 (t80) REVERT: B 1543 ILE cc_start: 0.8328 (mt) cc_final: 0.8118 (tp) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.1610 time to fit residues: 129.1461 Evaluate side-chains 479 residues out of total 2537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 244 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 298 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 245 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 ASN B1096 HIS ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 ASN B1484 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.209215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.158684 restraints weight = 96950.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.167738 restraints weight = 53965.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.172589 restraints weight = 34884.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.176602 restraints weight = 25130.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.179359 restraints weight = 19056.940| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23515 Z= 0.156 Angle : 0.669 10.393 31845 Z= 0.343 Chirality : 0.046 0.240 3693 Planarity : 0.005 0.069 4070 Dihedral : 4.818 23.170 3187 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.15), residues: 2985 helix: -0.56 (0.14), residues: 1324 sheet: -1.03 (0.24), residues: 443 loop : -0.98 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 818 TYR 0.020 0.001 TYR A1294 PHE 0.025 0.002 PHE A 204 TRP 0.031 0.002 TRP B1514 HIS 0.009 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00335 (23515) covalent geometry : angle 0.66857 (31845) hydrogen bonds : bond 0.03502 ( 798) hydrogen bonds : angle 5.14561 ( 2205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5242.45 seconds wall clock time: 90 minutes 46.71 seconds (5446.71 seconds total)