Starting phenix.real_space_refine on Thu Feb 13 18:46:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c0v_7325/02_2025/6c0v_7325_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c0v_7325/02_2025/6c0v_7325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c0v_7325/02_2025/6c0v_7325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c0v_7325/02_2025/6c0v_7325.map" model { file = "/net/cci-nas-00/data/ceres_data/6c0v_7325/02_2025/6c0v_7325_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c0v_7325/02_2025/6c0v_7325_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5750 2.51 5 N 1535 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 8912 Classifications: {'peptide': 1154} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 26, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.92, per 1000 atoms: 0.66 Number of scatterers: 8976 At special positions: 0 Unit cell: (79.8, 107.52, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 6 15.00 Mg 2 11.99 O 1650 8.00 N 1535 7.00 C 5750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 70.4% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 44 through 68 removed outlier: 3.538A pdb=" N ALA A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 69 through 79 removed outlier: 3.805A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 157 removed outlier: 3.992A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.627A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.862A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 3.654A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 221 through 260 removed outlier: 4.484A pdb=" N LEU A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 319 removed outlier: 3.575A pdb=" N GLU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 362 removed outlier: 3.847A pdb=" N VAL A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.648A pdb=" N ALA A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 3.521A pdb=" N ILE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.681A pdb=" N THR A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 532 through 548 removed outlier: 3.520A pdb=" N GLN A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.563A pdb=" N ALA A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.516A pdb=" N ASN A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.881A pdb=" N LYS A 702 " --> pdb=" O TRP A 698 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 723 removed outlier: 4.276A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 720 " --> pdb=" O PHE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.882A pdb=" N ALA A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A 730 " --> pdb=" O PRO A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 797 removed outlier: 3.623A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.757A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 830 removed outlier: 3.560A pdb=" N ALA A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 853 removed outlier: 4.226A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 864 through 903 removed outlier: 3.816A pdb=" N ILE A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 884 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 Processing helix chain 'A' and resid 913 through 924 removed outlier: 3.611A pdb=" N GLU A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 966 removed outlier: 3.648A pdb=" N ALA A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 962 " --> pdb=" O ARG A 958 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 removed outlier: 3.918A pdb=" N LEU A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 993 removed outlier: 4.546A pdb=" N ALA A 987 " --> pdb=" O PHE A 983 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1014 removed outlier: 3.769A pdb=" N ILE A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 4.177A pdb=" N VAL A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.756A pdb=" N LEU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A1112 " --> pdb=" O TRP A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1153 removed outlier: 3.536A pdb=" N GLU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1163 through 1167 removed outlier: 3.922A pdb=" N THR A1167 " --> pdb=" O LYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 Processing helix chain 'A' and resid 1207 through 1221 removed outlier: 3.724A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1240 removed outlier: 3.648A pdb=" N ILE A1237 " --> pdb=" O ARG A1233 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1273 removed outlier: 3.606A pdb=" N VAL A1273 " --> pdb=" O SER A1269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 414 through 418 removed outlier: 3.617A pdb=" N SER A 452 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.645A pdb=" N PHE A 399 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 410 " --> pdb=" O PHE A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.670A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 597 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 598 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1053 through 1060 removed outlier: 6.897A pdb=" N GLN A1054 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A1041 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE A1037 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A1095 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU A1039 " --> pdb=" O LYS A1093 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A1093 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A1091 " --> pdb=" O VAL A1041 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 3.619A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A1197 " --> pdb=" O ILE A1228 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A1230 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A1199 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1242 " --> pdb=" O THR A1065 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2871 1.34 - 1.46: 968 1.46 - 1.58: 5230 1.58 - 1.69: 10 1.69 - 1.81: 59 Bond restraints: 9138 Sorted by residual: bond pdb=" C4 ATP A1301 " pdb=" C5 ATP A1301 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.55e+01 bond pdb=" C4 ATP A1302 " pdb=" C5 ATP A1302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C5 ATP A1302 " pdb=" C6 ATP A1302 " ideal model delta sigma weight residual 1.409 1.485 -0.076 1.00e-02 1.00e+04 5.76e+01 bond pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C8 ATP A1302 " pdb=" N7 ATP A1302 " ideal model delta sigma weight residual 1.310 1.359 -0.049 1.00e-02 1.00e+04 2.36e+01 ... (remaining 9133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 12243 3.35 - 6.69: 112 6.69 - 10.04: 6 10.04 - 13.39: 0 13.39 - 16.73: 4 Bond angle restraints: 12365 Sorted by residual: angle pdb=" PB ATP A1302 " pdb=" O3B ATP A1302 " pdb=" PG ATP A1302 " ideal model delta sigma weight residual 139.87 123.14 16.73 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PA ATP A1302 " pdb=" O3A ATP A1302 " pdb=" PB ATP A1302 " ideal model delta sigma weight residual 136.83 120.48 16.35 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 123.74 16.13 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 122.78 14.05 1.00e+00 1.00e+00 1.97e+02 angle pdb=" C5 ATP A1301 " pdb=" C4 ATP A1301 " pdb=" N3 ATP A1301 " ideal model delta sigma weight residual 126.80 118.36 8.44 1.00e+00 1.00e+00 7.13e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 4961 15.91 - 31.83: 383 31.83 - 47.74: 89 47.74 - 63.65: 32 63.65 - 79.57: 12 Dihedral angle restraints: 5477 sinusoidal: 2168 harmonic: 3309 Sorted by residual: dihedral pdb=" CA HIS A 518 " pdb=" C HIS A 518 " pdb=" N LYS A 519 " pdb=" CA LYS A 519 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A 587 " pdb=" C HIS A 587 " pdb=" N ARG A 588 " pdb=" CA ARG A 588 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C LYS A 619 " pdb=" N LYS A 619 " pdb=" CA LYS A 619 " pdb=" CB LYS A 619 " ideal model delta harmonic sigma weight residual -122.60 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1019 0.059 - 0.119: 318 0.119 - 0.178: 74 0.178 - 0.237: 15 0.237 - 0.296: 2 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA LYS A 619 " pdb=" N LYS A 619 " pdb=" C LYS A 619 " pdb=" CB LYS A 619 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN A1248 " pdb=" N ASN A1248 " pdb=" C ASN A1248 " pdb=" CB ASN A1248 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1425 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 66 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 835 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C VAL A 835 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 835 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 836 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 926 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 927 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.020 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 11 2.55 - 3.14: 6362 3.14 - 3.72: 12761 3.72 - 4.31: 17661 4.31 - 4.90: 29113 Nonbonded interactions: 65908 Sorted by model distance: nonbonded pdb=" OG SER A 434 " pdb="MG MG A1304 " model vdw 1.961 2.170 nonbonded pdb=" O2B ATP A1302 " pdb="MG MG A1303 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP A1301 " pdb="MG MG A1304 " model vdw 2.022 2.170 nonbonded pdb=" OE1 GLN A1118 " pdb="MG MG A1303 " model vdw 2.128 2.170 nonbonded pdb=" O2B ATP A1301 " pdb="MG MG A1304 " model vdw 2.133 2.170 ... (remaining 65903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 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 0.081 9138 Z= 0.504 Angle : 1.141 16.734 12365 Z= 0.832 Chirality : 0.061 0.296 1428 Planarity : 0.003 0.057 1555 Dihedral : 13.350 79.566 3353 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.20), residues: 1148 helix: -1.08 (0.16), residues: 687 sheet: -1.40 (0.59), residues: 71 loop : -1.90 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 803 HIS 0.003 0.001 HIS A1007 PHE 0.013 0.001 PHE A 40 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PRO cc_start: 0.6566 (Cg_exo) cc_final: 0.6227 (Cg_endo) REVERT: A 105 MET cc_start: 0.6875 (ttm) cc_final: 0.5504 (mmm) REVERT: A 157 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7286 (ttt-90) REVERT: A 184 GLU cc_start: 0.8860 (tp30) cc_final: 0.8640 (tp30) REVERT: A 197 MET cc_start: 0.7677 (mmm) cc_final: 0.7402 (mmm) REVERT: A 275 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7938 (mm-30) REVERT: A 299 ILE cc_start: 0.7955 (mt) cc_final: 0.7655 (mt) REVERT: A 326 TYR cc_start: 0.8409 (m-80) cc_final: 0.7736 (m-80) REVERT: A 353 GLU cc_start: 0.8139 (tt0) cc_final: 0.7868 (tt0) REVERT: A 372 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8013 (ttpt) REVERT: A 376 ASP cc_start: 0.7021 (t0) cc_final: 0.6600 (t0) REVERT: A 392 LEU cc_start: 0.8101 (mt) cc_final: 0.7839 (mm) REVERT: A 450 MET cc_start: 0.6573 (mtt) cc_final: 0.6206 (ptp) REVERT: A 555 ASP cc_start: 0.6528 (t0) cc_final: 0.6240 (t0) REVERT: A 564 GLU cc_start: 0.7958 (tt0) cc_final: 0.7372 (tp30) REVERT: A 566 GLU cc_start: 0.8232 (tt0) cc_final: 0.7994 (tp30) REVERT: A 575 LYS cc_start: 0.8239 (tttt) cc_final: 0.7971 (ttpt) REVERT: A 577 ARG cc_start: 0.6935 (ptt180) cc_final: 0.6582 (ptt180) REVERT: A 603 ASP cc_start: 0.8126 (t0) cc_final: 0.7911 (t0) REVERT: A 609 LYS cc_start: 0.8570 (ptpt) cc_final: 0.8345 (pttm) REVERT: A 703 LEU cc_start: 0.8353 (tp) cc_final: 0.7925 (tt) REVERT: A 771 PHE cc_start: 0.7010 (t80) cc_final: 0.6679 (t80) REVERT: A 787 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6877 (ttt90) REVERT: A 811 THR cc_start: 0.6584 (m) cc_final: 0.6325 (p) REVERT: A 820 ASN cc_start: 0.7352 (t0) cc_final: 0.7058 (t0) REVERT: A 857 LEU cc_start: 0.9118 (mt) cc_final: 0.8902 (mm) REVERT: A 858 THR cc_start: 0.7918 (p) cc_final: 0.7715 (p) REVERT: A 884 LEU cc_start: 0.7402 (tp) cc_final: 0.7195 (tp) REVERT: A 909 SER cc_start: 0.8591 (t) cc_final: 0.8348 (m) REVERT: A 925 GLN cc_start: 0.7411 (tt0) cc_final: 0.7113 (mm-40) REVERT: A 942 PHE cc_start: 0.8144 (t80) cc_final: 0.7835 (t80) REVERT: A 959 PHE cc_start: 0.8226 (t80) cc_final: 0.7564 (t80) REVERT: A 971 PHE cc_start: 0.8187 (p90) cc_final: 0.7860 (p90) REVERT: A 986 MET cc_start: 0.8212 (mtp) cc_final: 0.7832 (ttp) REVERT: A 988 VAL cc_start: 0.8046 (t) cc_final: 0.7788 (m) REVERT: A 990 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7581 (tp-100) REVERT: A 997 ASP cc_start: 0.8172 (m-30) cc_final: 0.7946 (m-30) REVERT: A 1021 TYR cc_start: 0.8112 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1115 ILE cc_start: 0.8945 (pp) cc_final: 0.8459 (pp) REVERT: A 1141 SER cc_start: 0.7746 (t) cc_final: 0.7534 (p) REVERT: A 1159 GLU cc_start: 0.8704 (tp30) cc_final: 0.8370 (mm-30) REVERT: A 1263 GLN cc_start: 0.7773 (mm110) cc_final: 0.7184 (tt0) REVERT: A 1267 TYR cc_start: 0.8333 (t80) cc_final: 0.7950 (t80) REVERT: A 1270 MET cc_start: 0.8927 (tpt) cc_final: 0.8688 (mmm) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2256 time to fit residues: 110.9957 Evaluate side-chains 234 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 172 ASN A 441 GLN A 530 GLN A 535 GLN A 570 GLN A 611 ASN A 725 GLN A 839 ASN A1043 ASN A1105 ASN A1248 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.099537 restraints weight = 18213.625| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.24 r_work: 0.3136 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9138 Z= 0.218 Angle : 0.570 7.354 12365 Z= 0.309 Chirality : 0.040 0.223 1428 Planarity : 0.004 0.039 1555 Dihedral : 7.979 86.225 1306 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.95 % Allowed : 11.54 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1148 helix: 0.91 (0.18), residues: 730 sheet: -0.33 (0.65), residues: 70 loop : -1.81 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 708 HIS 0.003 0.001 HIS A 61 PHE 0.018 0.001 PHE A 208 TYR 0.015 0.001 TYR A 130 ARG 0.005 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.6777 (ttm) cc_final: 0.6157 (ppp) REVERT: A 118 TYR cc_start: 0.8410 (m-80) cc_final: 0.8052 (m-80) REVERT: A 157 ARG cc_start: 0.9059 (ttt180) cc_final: 0.8790 (ttt-90) REVERT: A 299 ILE cc_start: 0.8995 (mt) cc_final: 0.8763 (mt) REVERT: A 372 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8455 (ttpt) REVERT: A 450 MET cc_start: 0.8140 (mtt) cc_final: 0.7867 (ptp) REVERT: A 499 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8759 (mt-10) REVERT: A 701 MET cc_start: 0.8327 (mmt) cc_final: 0.8063 (mmm) REVERT: A 703 LEU cc_start: 0.8732 (tp) cc_final: 0.8409 (tt) REVERT: A 858 THR cc_start: 0.8617 (p) cc_final: 0.8417 (m) REVERT: A 882 GLN cc_start: 0.8788 (tt0) cc_final: 0.8278 (tt0) REVERT: A 909 SER cc_start: 0.9395 (t) cc_final: 0.9172 (m) REVERT: A 959 PHE cc_start: 0.8841 (t80) cc_final: 0.8070 (t80) REVERT: A 967 LYS cc_start: 0.8591 (mttm) cc_final: 0.8353 (ttmm) REVERT: A 986 MET cc_start: 0.8460 (mtp) cc_final: 0.8115 (ttp) REVERT: A 997 ASP cc_start: 0.9189 (m-30) cc_final: 0.8970 (m-30) REVERT: A 1011 ILE cc_start: 0.9038 (tp) cc_final: 0.8814 (tp) REVERT: A 1166 SER cc_start: 0.8773 (m) cc_final: 0.8397 (p) REVERT: A 1252 LYS cc_start: 0.8781 (tptm) cc_final: 0.8487 (tppt) REVERT: A 1261 LEU cc_start: 0.9001 (mt) cc_final: 0.8564 (mt) outliers start: 37 outliers final: 24 residues processed: 273 average time/residue: 0.2097 time to fit residues: 80.5346 Evaluate side-chains 223 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 HIS A 494 ASN A 611 ASN ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094590 restraints weight = 18953.831| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.41 r_work: 0.3055 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9138 Z= 0.229 Angle : 0.556 8.607 12365 Z= 0.297 Chirality : 0.040 0.165 1428 Planarity : 0.003 0.032 1555 Dihedral : 7.025 78.535 1306 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.95 % Allowed : 15.17 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1148 helix: 1.40 (0.19), residues: 732 sheet: 0.18 (0.67), residues: 70 loop : -1.63 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 708 HIS 0.010 0.001 HIS A 612 PHE 0.015 0.001 PHE A 771 TYR 0.016 0.001 TYR A 962 ARG 0.005 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.6209 (ttm) cc_final: 0.5725 (ppp) REVERT: A 118 TYR cc_start: 0.8517 (m-80) cc_final: 0.8253 (m-80) REVERT: A 157 ARG cc_start: 0.9112 (ttt180) cc_final: 0.8822 (ttm-80) REVERT: A 450 MET cc_start: 0.8381 (mtt) cc_final: 0.8079 (ptp) REVERT: A 499 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 701 MET cc_start: 0.8322 (mmt) cc_final: 0.8004 (mmm) REVERT: A 703 LEU cc_start: 0.8749 (tp) cc_final: 0.8483 (tt) REVERT: A 704 ASN cc_start: 0.8727 (t0) cc_final: 0.8459 (t0) REVERT: A 707 GLU cc_start: 0.9023 (mp0) cc_final: 0.8545 (mp0) REVERT: A 882 GLN cc_start: 0.8832 (tt0) cc_final: 0.8436 (tt0) REVERT: A 909 SER cc_start: 0.9375 (t) cc_final: 0.9175 (m) REVERT: A 946 GLN cc_start: 0.9154 (mm110) cc_final: 0.8703 (mm-40) REVERT: A 959 PHE cc_start: 0.8816 (t80) cc_final: 0.8106 (t80) REVERT: A 967 LYS cc_start: 0.8561 (mttm) cc_final: 0.8334 (ttmm) REVERT: A 986 MET cc_start: 0.8525 (mtp) cc_final: 0.8184 (ttp) REVERT: A 997 ASP cc_start: 0.9218 (m-30) cc_final: 0.8943 (m-30) REVERT: A 1084 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: A 1115 ILE cc_start: 0.9303 (pp) cc_final: 0.9103 (pp) REVERT: A 1166 SER cc_start: 0.8874 (m) cc_final: 0.8502 (p) REVERT: A 1252 LYS cc_start: 0.8806 (tptm) cc_final: 0.8518 (tppt) outliers start: 37 outliers final: 26 residues processed: 235 average time/residue: 0.2002 time to fit residues: 66.7401 Evaluate side-chains 227 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096280 restraints weight = 18811.283| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.40 r_work: 0.3081 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9138 Z= 0.172 Angle : 0.504 6.672 12365 Z= 0.269 Chirality : 0.038 0.143 1428 Planarity : 0.003 0.031 1555 Dihedral : 6.656 80.519 1306 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.53 % Allowed : 17.31 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1148 helix: 1.62 (0.19), residues: 740 sheet: 0.40 (0.66), residues: 70 loop : -1.56 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.004 0.001 HIS A1257 PHE 0.009 0.001 PHE A 771 TYR 0.015 0.001 TYR A 962 ARG 0.004 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.6046 (ttm) cc_final: 0.5525 (ppp) REVERT: A 118 TYR cc_start: 0.8463 (m-80) cc_final: 0.8244 (m-80) REVERT: A 157 ARG cc_start: 0.9039 (ttt180) cc_final: 0.8780 (ttm-80) REVERT: A 326 TYR cc_start: 0.7883 (m-10) cc_final: 0.7679 (m-80) REVERT: A 450 MET cc_start: 0.8473 (mtt) cc_final: 0.8214 (ptp) REVERT: A 499 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8387 (mt-10) REVERT: A 707 GLU cc_start: 0.9132 (mp0) cc_final: 0.8597 (mp0) REVERT: A 946 GLN cc_start: 0.9174 (mm110) cc_final: 0.8735 (mm-40) REVERT: A 948 MET cc_start: 0.8881 (mmm) cc_final: 0.8671 (mmm) REVERT: A 959 PHE cc_start: 0.8775 (t80) cc_final: 0.8071 (t80) REVERT: A 967 LYS cc_start: 0.8607 (mttm) cc_final: 0.8385 (ttmm) REVERT: A 986 MET cc_start: 0.8479 (mtp) cc_final: 0.8000 (ttp) REVERT: A 997 ASP cc_start: 0.9216 (m-30) cc_final: 0.8955 (m-30) REVERT: A 1084 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8417 (mt-10) REVERT: A 1159 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8437 (mm-30) REVERT: A 1166 SER cc_start: 0.8891 (m) cc_final: 0.8544 (p) REVERT: A 1216 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8485 (mm-30) outliers start: 33 outliers final: 24 residues processed: 240 average time/residue: 0.1815 time to fit residues: 63.5458 Evaluate side-chains 222 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 HIS A 773 GLN A 839 ASN A1238 GLN A1239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096483 restraints weight = 18800.903| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.38 r_work: 0.3080 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9138 Z= 0.171 Angle : 0.509 6.992 12365 Z= 0.265 Chirality : 0.038 0.151 1428 Planarity : 0.003 0.030 1555 Dihedral : 6.503 85.417 1306 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.74 % Allowed : 19.23 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1148 helix: 1.73 (0.19), residues: 742 sheet: 0.60 (0.65), residues: 75 loop : -1.41 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 708 HIS 0.007 0.001 HIS A1257 PHE 0.012 0.001 PHE A 983 TYR 0.014 0.001 TYR A 962 ARG 0.004 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5928 (ttm) cc_final: 0.5505 (ppp) REVERT: A 157 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8814 (ttm-80) REVERT: A 208 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8190 (t80) REVERT: A 450 MET cc_start: 0.8475 (mtt) cc_final: 0.8257 (ptp) REVERT: A 519 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7761 (mttp) REVERT: A 701 MET cc_start: 0.8260 (mmt) cc_final: 0.7935 (mmm) REVERT: A 707 GLU cc_start: 0.9018 (mp0) cc_final: 0.8738 (mp0) REVERT: A 882 GLN cc_start: 0.8814 (tt0) cc_final: 0.8442 (tt0) REVERT: A 946 GLN cc_start: 0.9219 (mm110) cc_final: 0.8755 (mm-40) REVERT: A 959 PHE cc_start: 0.8767 (t80) cc_final: 0.8107 (t80) REVERT: A 986 MET cc_start: 0.8517 (mtp) cc_final: 0.8059 (ttp) REVERT: A 997 ASP cc_start: 0.9231 (m-30) cc_final: 0.8959 (m-30) REVERT: A 1084 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: A 1166 SER cc_start: 0.8872 (m) cc_final: 0.8529 (p) REVERT: A 1216 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8488 (mm-30) REVERT: A 1252 LYS cc_start: 0.8751 (tptm) cc_final: 0.8484 (tppt) outliers start: 35 outliers final: 31 residues processed: 223 average time/residue: 0.1991 time to fit residues: 63.6323 Evaluate side-chains 231 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.0020 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096928 restraints weight = 18739.018| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.40 r_work: 0.3089 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9138 Z= 0.164 Angle : 0.505 7.223 12365 Z= 0.264 Chirality : 0.038 0.144 1428 Planarity : 0.003 0.030 1555 Dihedral : 6.394 88.770 1306 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.31 % Allowed : 20.73 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1148 helix: 1.81 (0.19), residues: 746 sheet: 0.44 (0.64), residues: 78 loop : -1.37 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 708 HIS 0.005 0.001 HIS A1257 PHE 0.011 0.001 PHE A 394 TYR 0.012 0.001 TYR A 962 ARG 0.004 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5921 (ttm) cc_final: 0.5428 (ppp) REVERT: A 157 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8803 (ttm-80) REVERT: A 208 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (t80) REVERT: A 450 MET cc_start: 0.8428 (mtt) cc_final: 0.8170 (ptp) REVERT: A 519 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7738 (mttp) REVERT: A 522 THR cc_start: 0.9268 (m) cc_final: 0.9051 (p) REVERT: A 582 THR cc_start: 0.8991 (m) cc_final: 0.8722 (p) REVERT: A 701 MET cc_start: 0.8208 (mmt) cc_final: 0.7912 (mmm) REVERT: A 707 GLU cc_start: 0.9031 (mp0) cc_final: 0.8725 (mp0) REVERT: A 880 SER cc_start: 0.9464 (t) cc_final: 0.9200 (m) REVERT: A 946 GLN cc_start: 0.9233 (mm110) cc_final: 0.8830 (mm-40) REVERT: A 948 MET cc_start: 0.8898 (mmm) cc_final: 0.8689 (mmm) REVERT: A 959 PHE cc_start: 0.8694 (t80) cc_final: 0.8080 (t80) REVERT: A 986 MET cc_start: 0.8527 (mtp) cc_final: 0.8074 (ttp) REVERT: A 997 ASP cc_start: 0.9228 (m-30) cc_final: 0.8940 (m-30) REVERT: A 1084 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: A 1216 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 1252 LYS cc_start: 0.8760 (tptm) cc_final: 0.8470 (tppt) REVERT: A 1260 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8923 (tp) outliers start: 31 outliers final: 26 residues processed: 215 average time/residue: 0.1891 time to fit residues: 58.2698 Evaluate side-chains 223 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096361 restraints weight = 19139.205| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.42 r_work: 0.3074 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9138 Z= 0.181 Angle : 0.515 7.112 12365 Z= 0.271 Chirality : 0.038 0.156 1428 Planarity : 0.003 0.030 1555 Dihedral : 6.294 86.139 1306 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.02 % Allowed : 19.23 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1148 helix: 1.81 (0.19), residues: 746 sheet: 0.46 (0.64), residues: 78 loop : -1.26 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 315 HIS 0.005 0.001 HIS A1257 PHE 0.011 0.001 PHE A 942 TYR 0.012 0.001 TYR A 962 ARG 0.003 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5945 (ttm) cc_final: 0.5476 (ppp) REVERT: A 157 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8832 (ttm-80) REVERT: A 519 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7759 (mttp) REVERT: A 522 THR cc_start: 0.9272 (m) cc_final: 0.9061 (p) REVERT: A 582 THR cc_start: 0.9001 (m) cc_final: 0.8750 (p) REVERT: A 701 MET cc_start: 0.8210 (mmt) cc_final: 0.7927 (mmm) REVERT: A 707 GLU cc_start: 0.9039 (mp0) cc_final: 0.8705 (mp0) REVERT: A 880 SER cc_start: 0.9460 (OUTLIER) cc_final: 0.9192 (m) REVERT: A 942 PHE cc_start: 0.9069 (t80) cc_final: 0.8817 (t80) REVERT: A 946 GLN cc_start: 0.9235 (mm110) cc_final: 0.8798 (mm-40) REVERT: A 948 MET cc_start: 0.8895 (mmm) cc_final: 0.8632 (mmm) REVERT: A 959 PHE cc_start: 0.8663 (t80) cc_final: 0.8089 (t80) REVERT: A 986 MET cc_start: 0.8517 (mtp) cc_final: 0.8095 (ttp) REVERT: A 997 ASP cc_start: 0.9205 (m-30) cc_final: 0.8913 (m-30) REVERT: A 1084 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8443 (mt-10) REVERT: A 1166 SER cc_start: 0.8907 (m) cc_final: 0.8566 (p) REVERT: A 1216 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8467 (mm-30) REVERT: A 1252 LYS cc_start: 0.8736 (tptm) cc_final: 0.8459 (tppt) REVERT: A 1260 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8884 (tp) outliers start: 47 outliers final: 36 residues processed: 229 average time/residue: 0.1983 time to fit residues: 65.5081 Evaluate side-chains 234 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 100 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN A 930 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100011 restraints weight = 18855.427| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.46 r_work: 0.3132 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9138 Z= 0.166 Angle : 0.519 7.146 12365 Z= 0.271 Chirality : 0.038 0.158 1428 Planarity : 0.003 0.030 1555 Dihedral : 6.105 81.265 1306 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.27 % Allowed : 19.98 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1148 helix: 1.85 (0.19), residues: 747 sheet: 0.50 (0.63), residues: 78 loop : -1.20 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.005 0.001 HIS A1257 PHE 0.015 0.001 PHE A 851 TYR 0.011 0.001 TYR A 962 ARG 0.004 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5631 (ttm) cc_final: 0.5321 (ppp) REVERT: A 450 MET cc_start: 0.8449 (ptp) cc_final: 0.7823 (pmm) REVERT: A 519 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7689 (mttp) REVERT: A 701 MET cc_start: 0.8181 (mmt) cc_final: 0.7910 (mmm) REVERT: A 707 GLU cc_start: 0.9016 (mp0) cc_final: 0.8658 (mp0) REVERT: A 880 SER cc_start: 0.9426 (OUTLIER) cc_final: 0.9148 (m) REVERT: A 942 PHE cc_start: 0.8987 (t80) cc_final: 0.8772 (t80) REVERT: A 946 GLN cc_start: 0.9242 (mm110) cc_final: 0.8809 (mm-40) REVERT: A 948 MET cc_start: 0.8907 (mmm) cc_final: 0.8617 (mmm) REVERT: A 959 PHE cc_start: 0.8603 (t80) cc_final: 0.8060 (t80) REVERT: A 986 MET cc_start: 0.8483 (mtp) cc_final: 0.8039 (ttp) REVERT: A 997 ASP cc_start: 0.9182 (m-30) cc_final: 0.8873 (m-30) REVERT: A 1039 GLU cc_start: 0.7887 (mp0) cc_final: 0.7209 (tt0) REVERT: A 1084 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: A 1216 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8454 (mm-30) REVERT: A 1252 LYS cc_start: 0.8785 (tptm) cc_final: 0.8507 (tppt) REVERT: A 1260 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8879 (tp) outliers start: 40 outliers final: 33 residues processed: 227 average time/residue: 0.1969 time to fit residues: 63.3994 Evaluate side-chains 233 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101924 restraints weight = 18614.383| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.26 r_work: 0.3168 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9138 Z= 0.157 Angle : 0.525 7.154 12365 Z= 0.271 Chirality : 0.038 0.157 1428 Planarity : 0.003 0.030 1555 Dihedral : 5.898 76.536 1306 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.85 % Allowed : 21.05 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1148 helix: 1.91 (0.19), residues: 746 sheet: 0.64 (0.63), residues: 78 loop : -1.12 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 708 HIS 0.005 0.001 HIS A1257 PHE 0.013 0.001 PHE A 314 TYR 0.011 0.001 TYR A 962 ARG 0.004 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5537 (ttm) cc_final: 0.5236 (ppp) REVERT: A 227 LEU cc_start: 0.8495 (pp) cc_final: 0.8149 (mm) REVERT: A 519 LYS cc_start: 0.8182 (mtmt) cc_final: 0.7693 (mttm) REVERT: A 701 MET cc_start: 0.8010 (mmt) cc_final: 0.7598 (mmm) REVERT: A 707 GLU cc_start: 0.9019 (mp0) cc_final: 0.8648 (mp0) REVERT: A 880 SER cc_start: 0.9413 (OUTLIER) cc_final: 0.9121 (m) REVERT: A 942 PHE cc_start: 0.8976 (t80) cc_final: 0.8738 (t80) REVERT: A 946 GLN cc_start: 0.9216 (mm110) cc_final: 0.8801 (mm-40) REVERT: A 948 MET cc_start: 0.8882 (mmm) cc_final: 0.8572 (mmm) REVERT: A 959 PHE cc_start: 0.8561 (t80) cc_final: 0.8076 (t80) REVERT: A 986 MET cc_start: 0.8420 (mtp) cc_final: 0.8115 (ttp) REVERT: A 997 ASP cc_start: 0.9186 (m-30) cc_final: 0.8937 (m-30) REVERT: A 1159 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 1216 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8449 (mm-30) REVERT: A 1252 LYS cc_start: 0.8742 (tptm) cc_final: 0.8485 (tppt) REVERT: A 1260 LEU cc_start: 0.9157 (tp) cc_final: 0.8916 (tp) outliers start: 36 outliers final: 32 residues processed: 232 average time/residue: 0.1906 time to fit residues: 63.3513 Evaluate side-chains 229 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN A 990 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099909 restraints weight = 18761.995| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.19 r_work: 0.3126 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9138 Z= 0.207 Angle : 0.553 6.963 12365 Z= 0.289 Chirality : 0.039 0.169 1428 Planarity : 0.003 0.057 1555 Dihedral : 5.968 78.314 1306 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.74 % Allowed : 22.22 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1148 helix: 1.81 (0.19), residues: 747 sheet: 0.61 (0.63), residues: 78 loop : -1.12 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.004 0.001 HIS A1257 PHE 0.012 0.001 PHE A 303 TYR 0.010 0.001 TYR A 962 ARG 0.004 0.000 ARG A1233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8126 (tp30) cc_final: 0.6946 (mp0) REVERT: A 519 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7758 (mttm) REVERT: A 707 GLU cc_start: 0.9001 (mp0) cc_final: 0.8629 (mp0) REVERT: A 880 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9162 (m) REVERT: A 946 GLN cc_start: 0.9227 (mm110) cc_final: 0.8766 (mm-40) REVERT: A 948 MET cc_start: 0.8886 (mmm) cc_final: 0.8562 (mmm) REVERT: A 959 PHE cc_start: 0.8579 (t80) cc_final: 0.8102 (t80) REVERT: A 986 MET cc_start: 0.8431 (mtp) cc_final: 0.8037 (ttp) REVERT: A 997 ASP cc_start: 0.9182 (m-30) cc_final: 0.8916 (m-30) REVERT: A 1039 GLU cc_start: 0.7961 (mp0) cc_final: 0.7296 (tt0) REVERT: A 1159 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 1166 SER cc_start: 0.8874 (m) cc_final: 0.8548 (p) REVERT: A 1216 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8444 (mm-30) REVERT: A 1252 LYS cc_start: 0.8792 (tptm) cc_final: 0.8503 (tppt) REVERT: A 1260 LEU cc_start: 0.9146 (tp) cc_final: 0.8894 (tp) outliers start: 35 outliers final: 30 residues processed: 218 average time/residue: 0.1827 time to fit residues: 57.9530 Evaluate side-chains 230 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099450 restraints weight = 18769.035| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.25 r_work: 0.3131 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9138 Z= 0.191 Angle : 0.555 8.373 12365 Z= 0.288 Chirality : 0.038 0.160 1428 Planarity : 0.003 0.049 1555 Dihedral : 5.936 76.965 1306 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.63 % Allowed : 22.22 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1148 helix: 1.77 (0.19), residues: 751 sheet: 0.61 (0.63), residues: 78 loop : -1.08 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A1257 PHE 0.023 0.001 PHE A 942 TYR 0.011 0.001 TYR A 962 ARG 0.004 0.000 ARG A1233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.35 seconds wall clock time: 72 minutes 11.13 seconds (4331.13 seconds total)