Starting phenix.real_space_refine on Thu May 29 06:52:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykr_33895/05_2025/7ykr_33895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykr_33895/05_2025/7ykr_33895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ykr_33895/05_2025/7ykr_33895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykr_33895/05_2025/7ykr_33895.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykr_33895/05_2025/7ykr_33895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykr_33895/05_2025/7ykr_33895.cif" } resolution = 3.2 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= 0.006 sd= 0.102 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: 4 Type Number sf(0) Gaussians S 236 5.16 5 C 20384 2.51 5 N 5544 2.21 5 O 5760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31924 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 7981 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 998} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 162 Restraints were copied for chains: C, B, D Time building chain proxies: 21.02, per 1000 atoms: 0.66 Number of scatterers: 31924 At special positions: 0 Unit cell: (154.53, 154.53, 149.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 236 16.00 O 5760 8.00 N 5544 7.00 C 20384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS D 217 " - pdb=" SG CYS D 253 " distance=2.02 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: 8.07 Conformation dependent library (CDL) restraints added in 4.6 seconds 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7904 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 4 sheets defined 61.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.379A pdb=" N GLU A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.605A pdb=" N ARG A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.651A pdb=" N LEU A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.871A pdb=" N THR A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.876A pdb=" N VAL A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.544A pdb=" N LYS A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.397A pdb=" N LEU A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.603A pdb=" N ALA A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 removed outlier: 3.684A pdb=" N LEU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 3.691A pdb=" N PHE A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 428 through 432 removed outlier: 4.004A pdb=" N ALA A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 432 " --> pdb=" O THR A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 432' Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.616A pdb=" N ASP A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.563A pdb=" N GLU A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 489 through 498 removed outlier: 3.681A pdb=" N ASP A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.635A pdb=" N LEU A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE A 561 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.855A pdb=" N LEU A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 573 " --> pdb=" O HIS A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.555A pdb=" N LEU A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE A 595 " --> pdb=" O PRO A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU A 639 " --> pdb=" O ARG A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 659 through 668 removed outlier: 3.771A pdb=" N PHE A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS A 739 " --> pdb=" O PRO A 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 removed outlier: 3.846A pdb=" N TYR A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 840 " --> pdb=" O VAL A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.727A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 853 " --> pdb=" O GLN A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 877 removed outlier: 4.117A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 881 Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.624A pdb=" N TRP A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 913 removed outlier: 4.124A pdb=" N GLN A 911 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.556A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 937 removed outlier: 3.512A pdb=" N LEU A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 953 removed outlier: 3.516A pdb=" N ALA A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 966 Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.530A pdb=" N TYR A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1015 removed outlier: 3.514A pdb=" N PHE A1005 " --> pdb=" O PRO A1001 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A1031 " --> pdb=" O ALA A1027 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1033 " --> pdb=" O GLY A1029 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A1034 " --> pdb=" O ASP A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1057 removed outlier: 3.539A pdb=" N LYS A1041 " --> pdb=" O ASN A1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A1046 " --> pdb=" O ARG A1042 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1052 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.585A pdb=" N TRP A1061 " --> pdb=" O PRO A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1116 through 1121 removed outlier: 3.712A pdb=" N GLU A1119 " --> pdb=" O ALA A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1129 removed outlier: 3.791A pdb=" N ASP A1127 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.767A pdb=" N HIS A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1155 removed outlier: 4.190A pdb=" N ASP A1154 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1155 " --> pdb=" O ALA A1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1151 through 1155' Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.618A pdb=" N GLU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.604A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 165 " --> pdb=" O HIS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.651A pdb=" N LEU D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 213 removed outlier: 3.871A pdb=" N THR D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 239 through 246 removed outlier: 3.875A pdb=" N VAL D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.545A pdb=" N LYS D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 319 " --> pdb=" O VAL D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.397A pdb=" N LEU D 328 " --> pdb=" O MET D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET D 338 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 347 removed outlier: 3.603A pdb=" N ALA D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE D 347 " --> pdb=" O CYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL D 353 " --> pdb=" O HIS D 349 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 355 " --> pdb=" O ASP D 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 391 removed outlier: 3.683A pdb=" N LEU D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 391 " --> pdb=" O HIS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.692A pdb=" N PHE D 409 " --> pdb=" O ASN D 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 428 through 432 removed outlier: 4.004A pdb=" N ALA D 431 " --> pdb=" O GLN D 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN D 432 " --> pdb=" O THR D 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 428 through 432' Processing helix chain 'D' and resid 446 through 454 removed outlier: 3.615A pdb=" N ASP D 454 " --> pdb=" O TYR D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.563A pdb=" N GLU D 461 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 463 " --> pdb=" O SER D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 Processing helix chain 'D' and resid 489 through 498 removed outlier: 3.680A pdb=" N ASP D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 525 through 535 Processing helix chain 'D' and resid 547 through 555 removed outlier: 3.635A pdb=" N LEU D 551 " --> pdb=" O ASN D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE D 561 " --> pdb=" O TYR D 557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 566 " --> pdb=" O GLU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.855A pdb=" N LEU D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP D 573 " --> pdb=" O HIS D 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 581 through 589 removed outlier: 3.555A pdb=" N LEU D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE D 595 " --> pdb=" O PRO D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR D 617 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 629 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU D 639 " --> pdb=" O ARG D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 Processing helix chain 'D' and resid 659 through 668 removed outlier: 3.770A pdb=" N PHE D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR D 722 " --> pdb=" O PRO D 718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 744 " --> pdb=" O TYR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU D 754 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN D 756 " --> pdb=" O PHE D 752 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE D 759 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 762 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 763 " --> pdb=" O ILE D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 777 removed outlier: 3.847A pdb=" N TYR D 770 " --> pdb=" O PHE D 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL D 833 " --> pdb=" O LEU D 829 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 840 " --> pdb=" O VAL D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 853 removed outlier: 3.726A pdb=" N GLN D 852 " --> pdb=" O ILE D 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 853 " --> pdb=" O GLN D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 877 removed outlier: 4.116A pdb=" N LEU D 864 " --> pdb=" O GLU D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 881 Processing helix chain 'D' and resid 888 through 905 removed outlier: 3.623A pdb=" N TRP D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 913 removed outlier: 4.124A pdb=" N GLN D 911 " --> pdb=" O LEU D 908 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 912 " --> pdb=" O PHE D 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE D 913 " --> pdb=" O LEU D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 922 removed outlier: 3.556A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 937 removed outlier: 3.512A pdb=" N LEU D 930 " --> pdb=" O ILE D 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 932 " --> pdb=" O GLN D 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 953 removed outlier: 3.516A pdb=" N ALA D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 951 " --> pdb=" O ALA D 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 953 " --> pdb=" O TYR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 966 Processing helix chain 'D' and resid 969 through 977 Processing helix chain 'D' and resid 984 through 990 removed outlier: 3.530A pdb=" N TYR D 989 " --> pdb=" O PHE D 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1015 removed outlier: 3.514A pdb=" N PHE D1005 " --> pdb=" O PRO D1001 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D1006 " --> pdb=" O MET D1002 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY D1029 " --> pdb=" O GLY D1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE D1031 " --> pdb=" O ALA D1027 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D1033 " --> pdb=" O GLY D1029 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL D1034 " --> pdb=" O ASP D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1057 removed outlier: 3.539A pdb=" N LYS D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN D1046 " --> pdb=" O ARG D1042 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D1052 " --> pdb=" O VAL D1048 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D1056 " --> pdb=" O GLU D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1062 removed outlier: 3.585A pdb=" N TRP D1061 " --> pdb=" O PRO D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1089 Processing helix chain 'D' and resid 1116 through 1121 removed outlier: 3.713A pdb=" N GLU D1119 " --> pdb=" O ALA D1116 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1129 removed outlier: 3.790A pdb=" N ASP D1127 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D1128 " --> pdb=" O LYS D1124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D1129 " --> pdb=" O LEU D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1131 through 1143 removed outlier: 3.768A pdb=" N HIS D1137 " --> pdb=" O GLU D1133 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1155 removed outlier: 4.190A pdb=" N ASP D1154 " --> pdb=" O GLU D1151 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D1155 " --> pdb=" O ALA D1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1151 through 1155' Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.618A pdb=" N GLU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.604A pdb=" N ARG B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.652A pdb=" N LEU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.871A pdb=" N THR B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.876A pdb=" N VAL B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.545A pdb=" N LYS B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 319 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 removed outlier: 4.398A pdb=" N LEU B 328 " --> pdb=" O MET B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET B 338 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.603A pdb=" N ALA B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL B 353 " --> pdb=" O HIS B 349 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 removed outlier: 3.683A pdb=" N LEU B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 3.691A pdb=" N PHE B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.005A pdb=" N ALA B 431 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 432 " --> pdb=" O THR B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 432' Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.617A pdb=" N ASP B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.563A pdb=" N GLU B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 489 through 498 removed outlier: 3.681A pdb=" N ASP B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 525 through 535 Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.635A pdb=" N LEU B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE B 561 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.855A pdb=" N LEU B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 573 " --> pdb=" O HIS B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 573' Processing helix chain 'B' and resid 581 through 589 removed outlier: 3.554A pdb=" N LEU B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE B 595 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU B 639 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 Processing helix chain 'B' and resid 659 through 668 removed outlier: 3.770A pdb=" N PHE B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR B 722 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B 723 " --> pdb=" O ALA B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 744 " --> pdb=" O TYR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN B 756 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 removed outlier: 3.846A pdb=" N TYR B 770 " --> pdb=" O PHE B 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 853 removed outlier: 3.727A pdb=" N GLN B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 853 " --> pdb=" O GLN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 877 removed outlier: 4.117A pdb=" N LEU B 864 " --> pdb=" O GLU B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 881 Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.623A pdb=" N TRP B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 913 removed outlier: 4.125A pdb=" N GLN B 911 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 912 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 913 " --> pdb=" O LEU B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.556A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 937 removed outlier: 3.511A pdb=" N LEU B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 953 removed outlier: 3.516A pdb=" N ALA B 947 " --> pdb=" O ALA B 943 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 951 " --> pdb=" O ALA B 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 953 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 966 Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 984 through 990 removed outlier: 3.530A pdb=" N TYR B 989 " --> pdb=" O PHE B 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.513A pdb=" N PHE B1005 " --> pdb=" O PRO B1001 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B1006 " --> pdb=" O MET B1002 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B1031 " --> pdb=" O ALA B1027 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B1033 " --> pdb=" O GLY B1029 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B1034 " --> pdb=" O ASP B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1057 removed outlier: 3.538A pdb=" N LYS B1041 " --> pdb=" O ASN B1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B1045 " --> pdb=" O LYS B1041 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B1046 " --> pdb=" O ARG B1042 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B1052 " --> pdb=" O VAL B1048 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B1056 " --> pdb=" O GLU B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1062 removed outlier: 3.585A pdb=" N TRP B1061 " --> pdb=" O PRO B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1089 Processing helix chain 'B' and resid 1116 through 1121 removed outlier: 3.712A pdb=" N GLU B1119 " --> pdb=" O ALA B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1129 removed outlier: 3.790A pdb=" N ASP B1127 " --> pdb=" O ARG B1123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B1128 " --> pdb=" O LYS B1124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B1129 " --> pdb=" O LEU B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1143 removed outlier: 3.767A pdb=" N HIS B1137 " --> pdb=" O GLU B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1155 removed outlier: 4.190A pdb=" N ASP B1154 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B1155 " --> pdb=" O ALA B1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1151 through 1155' Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.617A pdb=" N GLU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 83 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.605A pdb=" N ARG C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA C 163 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.650A pdb=" N LEU C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 173 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.872A pdb=" N THR C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 239 through 246 removed outlier: 3.876A pdb=" N VAL C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.545A pdb=" N LYS C 316 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 319 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 329 removed outlier: 4.398A pdb=" N LEU C 328 " --> pdb=" O MET C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET C 338 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.602A pdb=" N ALA C 344 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL C 353 " --> pdb=" O HIS C 349 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 removed outlier: 3.683A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 3.691A pdb=" N PHE C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 428 through 432 removed outlier: 4.004A pdb=" N ALA C 431 " --> pdb=" O GLN C 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 432 " --> pdb=" O THR C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 428 through 432' Processing helix chain 'C' and resid 446 through 454 removed outlier: 3.615A pdb=" N ASP C 454 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.564A pdb=" N GLU C 461 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 Processing helix chain 'C' and resid 489 through 498 removed outlier: 3.681A pdb=" N ASP C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 547 through 555 removed outlier: 3.634A pdb=" N LEU C 551 " --> pdb=" O ASN C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE C 561 " --> pdb=" O TYR C 557 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 removed outlier: 3.854A pdb=" N LEU C 572 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP C 573 " --> pdb=" O HIS C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 569 through 573' Processing helix chain 'C' and resid 581 through 589 removed outlier: 3.554A pdb=" N LEU C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE C 595 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR C 617 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 629 Processing helix chain 'C' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU C 639 " --> pdb=" O ARG C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 Processing helix chain 'C' and resid 659 through 668 removed outlier: 3.770A pdb=" N PHE C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR C 722 " --> pdb=" O PRO C 718 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET C 723 " --> pdb=" O ALA C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS C 739 " --> pdb=" O PRO C 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 744 " --> pdb=" O TYR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU C 754 " --> pdb=" O LYS C 750 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN C 756 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 763 " --> pdb=" O ILE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 777 removed outlier: 3.846A pdb=" N TYR C 770 " --> pdb=" O PHE C 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 840 " --> pdb=" O VAL C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.726A pdb=" N GLN C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 853 " --> pdb=" O GLN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 877 removed outlier: 4.116A pdb=" N LEU C 864 " --> pdb=" O GLU C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 881 Processing helix chain 'C' and resid 888 through 905 removed outlier: 3.623A pdb=" N TRP C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 913 removed outlier: 4.125A pdb=" N GLN C 911 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 912 " --> pdb=" O PHE C 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 922 removed outlier: 3.557A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 937 removed outlier: 3.511A pdb=" N LEU C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 953 removed outlier: 3.517A pdb=" N ALA C 947 " --> pdb=" O ALA C 943 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 953 " --> pdb=" O TYR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 966 Processing helix chain 'C' and resid 969 through 977 Processing helix chain 'C' and resid 984 through 990 removed outlier: 3.529A pdb=" N TYR C 989 " --> pdb=" O PHE C 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1015 removed outlier: 3.514A pdb=" N PHE C1005 " --> pdb=" O PRO C1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C1006 " --> pdb=" O MET C1002 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY C1029 " --> pdb=" O GLY C1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C1031 " --> pdb=" O ALA C1027 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C1033 " --> pdb=" O GLY C1029 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C1034 " --> pdb=" O ASP C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1057 removed outlier: 3.538A pdb=" N LYS C1041 " --> pdb=" O ASN C1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C1046 " --> pdb=" O ARG C1042 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C1052 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C1056 " --> pdb=" O GLU C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1062 removed outlier: 3.586A pdb=" N TRP C1061 " --> pdb=" O PRO C1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1089 Processing helix chain 'C' and resid 1116 through 1121 removed outlier: 3.712A pdb=" N GLU C1119 " --> pdb=" O ALA C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1129 removed outlier: 3.790A pdb=" N ASP C1127 " --> pdb=" O ARG C1123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C1128 " --> pdb=" O LYS C1124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C1129 " --> pdb=" O LEU C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1131 through 1143 removed outlier: 3.767A pdb=" N HIS C1137 " --> pdb=" O GLU C1133 " (cutoff:3.500A) Processing helix chain 'C' and resid 1151 through 1155 removed outlier: 4.191A pdb=" N ASP C1154 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1155 " --> pdb=" O ALA C1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1151 through 1155' Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 672 Processing sheet with id=AA2, first strand: chain 'D' and resid 671 through 672 Processing sheet with id=AA3, first strand: chain 'B' and resid 671 through 672 Processing sheet with id=AA4, first strand: chain 'C' and resid 671 through 672 1140 hydrogen bonds defined for protein. 3276 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: 10.84 Time building geometry restraints manager: 9.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7403 1.33 - 1.45: 6661 1.45 - 1.57: 18088 1.57 - 1.70: 0 1.70 - 1.82: 388 Bond restraints: 32540 Sorted by residual: bond pdb=" CA LYS D 368 " pdb=" C LYS D 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.06e+01 bond pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.05e+01 bond pdb=" CA LYS B 368 " pdb=" C LYS B 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.03e+01 bond pdb=" CA LYS C 368 " pdb=" C LYS C 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.03e+01 bond pdb=" N GLN C 336 " pdb=" CA GLN C 336 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.05e+01 ... (remaining 32535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 43223 2.96 - 5.91: 741 5.91 - 8.87: 108 8.87 - 11.82: 25 11.82 - 14.78: 11 Bond angle restraints: 44108 Sorted by residual: angle pdb=" N LEU B 855 " pdb=" CA LEU B 855 " pdb=" C LEU B 855 " ideal model delta sigma weight residual 109.62 121.48 -11.86 1.50e+00 4.44e-01 6.25e+01 angle pdb=" N LEU D 855 " pdb=" CA LEU D 855 " pdb=" C LEU D 855 " ideal model delta sigma weight residual 109.62 121.46 -11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" N LEU C 855 " pdb=" CA LEU C 855 " pdb=" C LEU C 855 " ideal model delta sigma weight residual 109.62 121.45 -11.83 1.50e+00 4.44e-01 6.22e+01 angle pdb=" N LEU A 855 " pdb=" CA LEU A 855 " pdb=" C LEU A 855 " ideal model delta sigma weight residual 109.62 121.42 -11.80 1.50e+00 4.44e-01 6.19e+01 angle pdb=" N LYS D 854 " pdb=" CA LYS D 854 " pdb=" C LYS D 854 " ideal model delta sigma weight residual 111.11 119.31 -8.20 1.20e+00 6.94e-01 4.67e+01 ... (remaining 44103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 18492 15.20 - 30.40: 920 30.40 - 45.60: 252 45.60 - 60.80: 29 60.80 - 75.99: 31 Dihedral angle restraints: 19724 sinusoidal: 7560 harmonic: 12164 Sorted by residual: dihedral pdb=" CA ALA C 431 " pdb=" C ALA C 431 " pdb=" N GLN C 432 " pdb=" CA GLN C 432 " ideal model delta harmonic sigma weight residual 180.00 146.22 33.78 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA ALA B 431 " pdb=" C ALA B 431 " pdb=" N GLN B 432 " pdb=" CA GLN B 432 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA ALA A 431 " pdb=" C ALA A 431 " pdb=" N GLN A 432 " pdb=" CA GLN A 432 " ideal model delta harmonic sigma weight residual 180.00 146.27 33.73 0 5.00e+00 4.00e-02 4.55e+01 ... (remaining 19721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4717 0.100 - 0.199: 379 0.199 - 0.299: 32 0.299 - 0.399: 12 0.399 - 0.498: 4 Chirality restraints: 5144 Sorted by residual: chirality pdb=" CA LEU D 855 " pdb=" N LEU D 855 " pdb=" C LEU D 855 " pdb=" CB LEU D 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA LEU B 855 " pdb=" N LEU B 855 " pdb=" C LEU B 855 " pdb=" CB LEU B 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA LEU A 855 " pdb=" N LEU A 855 " pdb=" C LEU A 855 " pdb=" CB LEU A 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.16e+00 ... (remaining 5141 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 367 " 0.020 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ASP B 367 " -0.073 2.00e-02 2.50e+03 pdb=" O ASP B 367 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS B 368 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 367 " 0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ASP C 367 " -0.073 2.00e-02 2.50e+03 pdb=" O ASP C 367 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS C 368 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 367 " -0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ASP A 367 " 0.073 2.00e-02 2.50e+03 pdb=" O ASP A 367 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS A 368 " -0.024 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5231 2.75 - 3.29: 29389 3.29 - 3.83: 49245 3.83 - 4.36: 62940 4.36 - 4.90: 105076 Nonbonded interactions: 251881 Sorted by model distance: nonbonded pdb=" O ASP C 298 " pdb=" OD1 ASP C 298 " model vdw 2.215 3.040 nonbonded pdb=" O ASP D 298 " pdb=" OD1 ASP D 298 " model vdw 2.215 3.040 nonbonded pdb=" O ASP A 298 " pdb=" OD1 ASP A 298 " model vdw 2.215 3.040 nonbonded pdb=" O ASP B 298 " pdb=" OD1 ASP B 298 " model vdw 2.216 3.040 nonbonded pdb=" O ASP A 140 " pdb=" OH TYR A 178 " model vdw 2.326 3.040 ... (remaining 251876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 70.930 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1962 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 0.107 32544 Z= 0.362 Angle : 1.017 14.778 44116 Z= 0.555 Chirality : 0.063 0.498 5144 Planarity : 0.007 0.066 5616 Dihedral : 10.921 75.995 11808 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.83 % Allowed : 2.83 % Favored : 96.33 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -6.34 (0.08), residues: 4108 helix: -4.56 (0.04), residues: 2520 sheet: -0.73 (0.63), residues: 60 loop : -3.36 (0.12), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B1061 HIS 0.009 0.002 HIS C 482 PHE 0.024 0.003 PHE B 689 TYR 0.029 0.003 TYR B 857 ARG 0.006 0.001 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.33803 ( 1140) hydrogen bonds : angle 10.02824 ( 3276) SS BOND : bond 0.00614 ( 4) SS BOND : angle 0.66790 ( 8) covalent geometry : bond 0.00836 (32540) covalent geometry : angle 1.01715 (44108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 643 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.1680 (mtt) cc_final: 0.1329 (mtm) REVERT: A 388 LEU cc_start: 0.0745 (tp) cc_final: 0.0185 (tt) REVERT: A 568 HIS cc_start: 0.4186 (m90) cc_final: 0.3569 (m90) REVERT: A 648 HIS cc_start: 0.4221 (m90) cc_final: 0.3050 (m90) REVERT: A 889 THR cc_start: 0.3885 (m) cc_final: 0.3362 (p) REVERT: A 913 PHE cc_start: 0.4738 (m-10) cc_final: 0.4504 (m-10) REVERT: A 985 PHE cc_start: 0.4742 (t80) cc_final: 0.4142 (t80) REVERT: D 244 PHE cc_start: 0.4780 (m-80) cc_final: 0.4459 (m-80) REVERT: D 245 PHE cc_start: 0.3997 (m-10) cc_final: 0.3661 (m-10) REVERT: D 978 MET cc_start: -0.3443 (ptt) cc_final: -0.4128 (ttt) REVERT: D 991 ASN cc_start: 0.2106 (m-40) cc_final: 0.1582 (m-40) REVERT: D 1040 LEU cc_start: 0.3353 (tp) cc_final: 0.2316 (mp) REVERT: D 1119 GLU cc_start: 0.5597 (mp0) cc_final: 0.5177 (tt0) REVERT: B 854 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5472 (ttmt) REVERT: B 870 TYR cc_start: 0.5631 (m-10) cc_final: 0.3380 (m-10) REVERT: B 1131 MET cc_start: 0.6781 (mmt) cc_final: 0.6335 (mtm) REVERT: C 172 LEU cc_start: 0.6465 (mt) cc_final: 0.6244 (mt) outliers start: 28 outliers final: 5 residues processed: 666 average time/residue: 0.4411 time to fit residues: 459.9973 Evaluate side-chains 431 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 425 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain D residue 1000 VAL Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1000 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 0.9990 chunk 312 optimal weight: 0.0030 chunk 173 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 210 optimal weight: 50.0000 chunk 166 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 374 optimal weight: 0.0020 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 HIS A 370 HIS A 456 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN A 633 HIS A 734 HIS A 738 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1037 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS D 235 ASN D 246 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS D 462 ASN D 495 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 633 HIS D 667 GLN D 734 HIS D 738 GLN D 746 ASN D 753 HIS ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D1021 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 342 HIS B 370 HIS B 462 ASN B 530 GLN B 584 HIS B 734 HIS B 738 GLN ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 246 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 364 ASN C 370 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 ASN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN C 633 HIS ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN C 753 HIS ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 891 HIS C 991 ASN C1021 ASN C1050 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.184377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138251 restraints weight = 44126.162| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.86 r_work: 0.3559 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3176 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32544 Z= 0.127 Angle : 0.649 11.856 44116 Z= 0.342 Chirality : 0.042 0.253 5144 Planarity : 0.005 0.063 5616 Dihedral : 5.858 38.576 4453 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.07 % Allowed : 8.08 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.10), residues: 4108 helix: -2.90 (0.08), residues: 2540 sheet: 3.11 (0.57), residues: 40 loop : -2.74 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 383 HIS 0.011 0.001 HIS D 342 PHE 0.028 0.002 PHE C 261 TYR 0.020 0.002 TYR B 201 ARG 0.006 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1140) hydrogen bonds : angle 4.68537 ( 3276) SS BOND : bond 0.00433 ( 4) SS BOND : angle 0.56135 ( 8) covalent geometry : bond 0.00272 (32540) covalent geometry : angle 0.64869 (44108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 487 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.2389 (mtt) cc_final: 0.1962 (mtm) REVERT: A 318 MET cc_start: 0.2038 (mpp) cc_final: 0.0767 (ptt) REVERT: A 388 LEU cc_start: 0.1477 (tp) cc_final: 0.0705 (pp) REVERT: A 412 MET cc_start: 0.2551 (tpp) cc_final: 0.1917 (ppp) REVERT: A 568 HIS cc_start: 0.4179 (m90) cc_final: 0.3761 (m170) REVERT: A 585 LEU cc_start: 0.5075 (mt) cc_final: 0.4699 (mt) REVERT: A 617 TYR cc_start: 0.5039 (m-80) cc_final: 0.4282 (m-80) REVERT: A 630 MET cc_start: 0.3438 (mtt) cc_final: 0.2996 (mtt) REVERT: A 721 ASN cc_start: 0.6990 (m-40) cc_final: 0.6457 (m-40) REVERT: A 726 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5542 (m-70) REVERT: A 844 MET cc_start: 0.6660 (mmt) cc_final: 0.5817 (ppp) REVERT: A 865 ILE cc_start: 0.5960 (mm) cc_final: 0.5300 (tt) REVERT: A 1064 ARG cc_start: 0.6350 (ptm-80) cc_final: 0.5636 (ttp80) REVERT: D 312 ILE cc_start: 0.2983 (tp) cc_final: 0.2453 (tt) REVERT: D 775 MET cc_start: 0.5135 (mmt) cc_final: 0.4671 (mmt) REVERT: D 840 LEU cc_start: 0.4240 (OUTLIER) cc_final: 0.3925 (tt) REVERT: D 991 ASN cc_start: 0.3140 (m-40) cc_final: 0.2561 (m-40) REVERT: D 1083 PHE cc_start: 0.3763 (p90) cc_final: 0.2710 (m-80) REVERT: B 257 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6357 (pp20) REVERT: B 321 MET cc_start: 0.6825 (mmt) cc_final: 0.6034 (mmt) REVERT: B 562 GLU cc_start: 0.6027 (tt0) cc_final: 0.5786 (tm-30) REVERT: B 775 MET cc_start: 0.3891 (mmm) cc_final: 0.3469 (mmp) REVERT: B 870 TYR cc_start: 0.5472 (m-10) cc_final: 0.5080 (m-10) REVERT: B 1001 PRO cc_start: 0.5289 (Cg_exo) cc_final: 0.4968 (Cg_endo) REVERT: B 1002 MET cc_start: 0.3088 (mmt) cc_final: 0.2382 (pmm) REVERT: B 1016 PRO cc_start: 0.4182 (Cg_endo) cc_final: 0.3952 (Cg_exo) REVERT: C 338 MET cc_start: 0.0687 (OUTLIER) cc_final: 0.0113 (ptm) REVERT: C 491 ASN cc_start: 0.4554 (m-40) cc_final: 0.3633 (m-40) REVERT: C 494 ARG cc_start: 0.5039 (ptt180) cc_final: 0.4713 (tpt-90) REVERT: C 1000 VAL cc_start: 0.3177 (p) cc_final: 0.1930 (t) REVERT: C 1041 LYS cc_start: 0.3798 (mmtp) cc_final: 0.2817 (mtmm) outliers start: 36 outliers final: 14 residues processed: 508 average time/residue: 0.4000 time to fit residues: 334.0194 Evaluate side-chains 391 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 374 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 942 ILE Chi-restraints excluded: chain D residue 962 HIS Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1084 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 338 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 230 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 13 optimal weight: 0.0670 chunk 330 optimal weight: 0.8980 chunk 291 optimal weight: 7.9990 chunk 385 optimal weight: 0.8980 chunk 397 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 309 GLN A 349 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 342 HIS D 430 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D 991 ASN B 196 HIS B 246 GLN B 349 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 HIS B1075 ASN ** B1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 230 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 336 GLN C 349 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 543 HIS ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 HIS C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.192660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147489 restraints weight = 45913.948| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.99 r_work: 0.3638 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4195 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32544 Z= 0.155 Angle : 0.668 13.649 44116 Z= 0.350 Chirality : 0.042 0.195 5144 Planarity : 0.005 0.068 5616 Dihedral : 5.204 24.723 4440 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.58 % Allowed : 10.16 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 4108 helix: -1.67 (0.09), residues: 2516 sheet: 3.52 (0.51), residues: 40 loop : -2.60 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 247 HIS 0.066 0.002 HIS D 962 PHE 0.033 0.002 PHE B 261 TYR 0.024 0.002 TYR C 770 ARG 0.007 0.001 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 1140) hydrogen bonds : angle 4.39668 ( 3276) SS BOND : bond 0.00539 ( 4) SS BOND : angle 1.06234 ( 8) covalent geometry : bond 0.00331 (32540) covalent geometry : angle 0.66791 (44108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 484 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.3561 (tpp) cc_final: 0.2911 (ppp) REVERT: A 541 ARG cc_start: 0.4506 (mmp80) cc_final: 0.4163 (mmm-85) REVERT: A 568 HIS cc_start: 0.4837 (m90) cc_final: 0.4373 (m170) REVERT: A 721 ASN cc_start: 0.7547 (m-40) cc_final: 0.7012 (m-40) REVERT: A 844 MET cc_start: 0.6689 (mmt) cc_final: 0.5925 (ppp) REVERT: A 918 ILE cc_start: 0.6457 (tp) cc_final: 0.5198 (pt) REVERT: A 1141 LEU cc_start: 0.7983 (tp) cc_final: 0.7776 (tp) REVERT: D 201 TYR cc_start: 0.5734 (m-80) cc_final: 0.5109 (m-80) REVERT: D 258 MET cc_start: 0.4321 (ptp) cc_final: 0.0860 (tmm) REVERT: D 265 GLU cc_start: 0.4169 (mt-10) cc_final: 0.3570 (tp30) REVERT: D 312 ILE cc_start: 0.3082 (tp) cc_final: 0.2590 (tt) REVERT: D 571 LEU cc_start: 0.4353 (pp) cc_final: 0.4058 (pp) REVERT: D 829 LEU cc_start: 0.6914 (mt) cc_final: 0.6166 (pt) REVERT: D 935 MET cc_start: 0.5822 (ttt) cc_final: 0.5577 (ttp) REVERT: D 970 MET cc_start: 0.6075 (mmm) cc_final: 0.5249 (mtm) REVERT: D 1002 MET cc_start: 0.5570 (ppp) cc_final: 0.4605 (mtm) REVERT: D 1007 ILE cc_start: 0.3927 (mm) cc_final: 0.3261 (mt) REVERT: D 1030 ASP cc_start: 0.5920 (m-30) cc_final: 0.5293 (m-30) REVERT: D 1053 LEU cc_start: 0.5903 (tp) cc_final: 0.5459 (tp) REVERT: B 321 MET cc_start: 0.6798 (mmt) cc_final: 0.6064 (mmt) REVERT: B 337 LYS cc_start: 0.6372 (tppt) cc_final: 0.6151 (tppt) REVERT: B 362 ASP cc_start: 0.5393 (t0) cc_final: 0.5096 (t0) REVERT: B 599 MET cc_start: 0.5562 (ptm) cc_final: 0.5067 (ptm) REVERT: B 775 MET cc_start: 0.5242 (mmm) cc_final: 0.4913 (mmp) REVERT: B 1002 MET cc_start: 0.4244 (mmt) cc_final: 0.3970 (pmm) REVERT: B 1020 MET cc_start: 0.8289 (tpp) cc_final: 0.7562 (tpp) REVERT: B 1053 LEU cc_start: 0.5313 (tp) cc_final: 0.5062 (tt) REVERT: C 196 HIS cc_start: 0.4306 (OUTLIER) cc_final: 0.4101 (t70) REVERT: C 324 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4988 (tpp) REVERT: C 490 TYR cc_start: 0.4883 (t80) cc_final: 0.4114 (t80) REVERT: C 491 ASN cc_start: 0.5257 (m-40) cc_final: 0.4418 (m-40) REVERT: C 970 MET cc_start: 0.5528 (mmp) cc_final: 0.5246 (mmm) REVERT: C 973 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5342 (mp) REVERT: C 1002 MET cc_start: 0.6055 (mpp) cc_final: 0.5715 (mmm) outliers start: 53 outliers final: 18 residues processed: 518 average time/residue: 0.4002 time to fit residues: 339.6210 Evaluate side-chains 398 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 377 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 100 optimal weight: 20.0000 chunk 152 optimal weight: 0.6980 chunk 366 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 chunk 397 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 387 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 550 GLN A 570 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 842 ASN A 853 GLN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS A 991 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN D 667 GLN D 738 GLN D 776 ASN D 849 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 HIS C 161 HIS C 186 GLN C 190 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 224 ASN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN C 849 GLN ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.200662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155710 restraints weight = 47464.726| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.00 r_work: 0.3736 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5689 moved from start: 1.0244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 32544 Z= 0.175 Angle : 0.775 23.230 44116 Z= 0.395 Chirality : 0.045 0.262 5144 Planarity : 0.006 0.088 5616 Dihedral : 5.339 40.830 4440 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.35 % Allowed : 11.77 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.73 (0.12), residues: 4108 helix: -1.43 (0.09), residues: 2524 sheet: 3.45 (0.61), residues: 40 loop : -2.45 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 745 HIS 0.016 0.002 HIS B 408 PHE 0.032 0.002 PHE B 261 TYR 0.028 0.002 TYR B 621 ARG 0.016 0.001 ARG B 546 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1140) hydrogen bonds : angle 4.36400 ( 3276) SS BOND : bond 0.00252 ( 4) SS BOND : angle 1.01009 ( 8) covalent geometry : bond 0.00381 (32540) covalent geometry : angle 0.77528 (44108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 598 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5256 (ptp) REVERT: A 338 MET cc_start: 0.5738 (tmm) cc_final: 0.4071 (mtp) REVERT: A 412 MET cc_start: 0.4464 (tpp) cc_final: 0.3775 (ptt) REVERT: A 428 GLN cc_start: 0.6526 (mp10) cc_final: 0.5835 (tp40) REVERT: A 514 MET cc_start: 0.7270 (ptt) cc_final: 0.7022 (ptp) REVERT: A 630 MET cc_start: 0.8274 (mmt) cc_final: 0.8034 (mpp) REVERT: A 638 ASN cc_start: 0.8042 (p0) cc_final: 0.7638 (m110) REVERT: A 730 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8022 (pt0) REVERT: A 844 MET cc_start: 0.6470 (mmt) cc_final: 0.6087 (ppp) REVERT: A 984 ASP cc_start: 0.7577 (t0) cc_final: 0.6899 (t0) REVERT: A 1096 PHE cc_start: 0.7436 (m-80) cc_final: 0.7063 (m-80) REVERT: D 215 ASP cc_start: 0.6076 (m-30) cc_final: 0.4123 (t0) REVERT: D 265 GLU cc_start: 0.5005 (mt-10) cc_final: 0.4786 (tp30) REVERT: D 292 ILE cc_start: 0.3753 (OUTLIER) cc_final: 0.2975 (tp) REVERT: D 432 GLN cc_start: 0.3692 (tp-100) cc_final: 0.2981 (tm-30) REVERT: D 443 MET cc_start: 0.8067 (mmp) cc_final: 0.7794 (mmm) REVERT: D 607 TYR cc_start: 0.4716 (m-80) cc_final: 0.4512 (m-80) REVERT: D 630 MET cc_start: 0.5267 (mmp) cc_final: 0.4899 (mtt) REVERT: D 677 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.4046 (mtpp) REVERT: D 678 LYS cc_start: 0.6627 (mmtm) cc_final: 0.5882 (tttp) REVERT: D 845 ARG cc_start: 0.4987 (mtp-110) cc_final: 0.4291 (mpt180) REVERT: D 903 TRP cc_start: 0.8237 (m100) cc_final: 0.7124 (m100) REVERT: D 935 MET cc_start: 0.7409 (ttt) cc_final: 0.7197 (ttp) REVERT: D 970 MET cc_start: 0.7928 (mmm) cc_final: 0.7711 (mmm) REVERT: D 991 ASN cc_start: 0.6966 (m110) cc_final: 0.6756 (t0) REVERT: D 1089 ARG cc_start: 0.4085 (mmp80) cc_final: 0.3805 (mmt90) REVERT: B 321 MET cc_start: 0.6925 (mmt) cc_final: 0.6252 (mmt) REVERT: B 562 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 601 MET cc_start: 0.5849 (mmt) cc_final: 0.5618 (mmm) REVERT: B 612 MET cc_start: 0.8338 (tpp) cc_final: 0.7878 (tpt) REVERT: B 779 GLU cc_start: 0.7036 (mp0) cc_final: 0.6423 (mt-10) REVERT: B 959 GLN cc_start: 0.6896 (tm-30) cc_final: 0.6170 (tm-30) REVERT: B 989 TYR cc_start: 0.8713 (m-80) cc_final: 0.8427 (m-80) REVERT: B 1002 MET cc_start: 0.6615 (mmt) cc_final: 0.6169 (ptp) REVERT: B 1131 MET cc_start: 0.7365 (mmt) cc_final: 0.7020 (tmm) REVERT: C 275 HIS cc_start: 0.5920 (m-70) cc_final: 0.5581 (t70) REVERT: C 324 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5562 (tpt) REVERT: C 368 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6600 (tttp) REVERT: C 376 LEU cc_start: 0.7815 (tp) cc_final: 0.7462 (tp) REVERT: C 580 ASN cc_start: 0.6425 (m-40) cc_final: 0.6131 (m-40) REVERT: C 661 LYS cc_start: 0.7641 (mptm) cc_final: 0.7396 (mmmt) REVERT: C 723 MET cc_start: 0.5950 (mmm) cc_final: 0.5003 (mmt) REVERT: C 996 ASP cc_start: 0.6772 (t70) cc_final: 0.6377 (t70) REVERT: C 1015 MET cc_start: 0.7854 (tpt) cc_final: 0.7582 (tpt) outliers start: 79 outliers final: 24 residues processed: 651 average time/residue: 0.4074 time to fit residues: 432.5720 Evaluate side-chains 461 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 433 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 1084 CYS Chi-restraints excluded: chain D residue 1119 GLU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 900 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 243 optimal weight: 0.0050 chunk 341 optimal weight: 3.9990 chunk 251 optimal weight: 0.3980 chunk 323 optimal weight: 0.7980 chunk 207 optimal weight: 40.0000 chunk 319 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 301 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 309 GLN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 746 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS C 196 HIS C 230 HIS C 235 ASN ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.190631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140120 restraints weight = 46092.439| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.49 r_work: 0.3545 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 1.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32544 Z= 0.181 Angle : 0.729 21.748 44116 Z= 0.374 Chirality : 0.045 0.288 5144 Planarity : 0.005 0.071 5616 Dihedral : 5.068 21.797 4440 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.23 % Favored : 92.75 % Rotamer: Outliers : 2.15 % Allowed : 15.46 % Favored : 82.39 % 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: -2.19 (0.12), residues: 4108 helix: -0.92 (0.10), residues: 2475 sheet: 3.25 (0.64), residues: 40 loop : -2.36 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 383 HIS 0.010 0.001 HIS D 565 PHE 0.056 0.002 PHE A 261 TYR 0.028 0.002 TYR C 851 ARG 0.012 0.001 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 1140) hydrogen bonds : angle 4.35292 ( 3276) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.90747 ( 8) covalent geometry : bond 0.00392 (32540) covalent geometry : angle 0.72903 (44108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 638 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7129 (mt-10) REVERT: A 226 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6279 (t80) REVERT: A 278 ASP cc_start: 0.5806 (t70) cc_final: 0.5586 (t0) REVERT: A 422 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 428 GLN cc_start: 0.6445 (mp10) cc_final: 0.6151 (tp40) REVERT: A 443 MET cc_start: 0.7844 (mpp) cc_final: 0.7610 (mmm) REVERT: A 578 ASP cc_start: 0.7976 (m-30) cc_final: 0.7400 (t0) REVERT: A 620 TYR cc_start: 0.8263 (t80) cc_final: 0.7841 (t80) REVERT: A 730 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8296 (pt0) REVERT: A 769 ILE cc_start: 0.8553 (mm) cc_final: 0.8171 (mp) REVERT: A 844 MET cc_start: 0.6632 (mmt) cc_final: 0.6144 (ppp) REVERT: A 935 MET cc_start: 0.6056 (ptt) cc_final: 0.5815 (ttp) REVERT: A 984 ASP cc_start: 0.8126 (t0) cc_final: 0.7351 (t0) REVERT: A 989 TYR cc_start: 0.8250 (m-80) cc_final: 0.7942 (m-80) REVERT: A 1096 PHE cc_start: 0.7886 (m-80) cc_final: 0.7487 (m-80) REVERT: D 241 MET cc_start: 0.5282 (ppp) cc_final: 0.5071 (ptm) REVERT: D 292 ILE cc_start: 0.4306 (OUTLIER) cc_final: 0.2758 (tt) REVERT: D 338 MET cc_start: 0.3244 (tpp) cc_final: 0.0967 (mmt) REVERT: D 443 MET cc_start: 0.8374 (mmp) cc_final: 0.8119 (mmm) REVERT: D 593 HIS cc_start: 0.7925 (t-90) cc_final: 0.7269 (m90) REVERT: D 599 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6620 (mmm) REVERT: D 677 LYS cc_start: 0.5490 (OUTLIER) cc_final: 0.4219 (mtpp) REVERT: D 678 LYS cc_start: 0.6877 (mmtm) cc_final: 0.5882 (tmtt) REVERT: D 746 ASN cc_start: 0.7805 (m110) cc_final: 0.7499 (m-40) REVERT: D 845 ARG cc_start: 0.5520 (mtp-110) cc_final: 0.4555 (mpt90) REVERT: D 915 GLN cc_start: 0.7801 (tp-100) cc_final: 0.6386 (mp10) REVERT: D 982 GLU cc_start: 0.8249 (pt0) cc_final: 0.7637 (pm20) REVERT: D 1032 GLU cc_start: 0.7902 (tp30) cc_final: 0.7118 (tp30) REVERT: D 1089 ARG cc_start: 0.4826 (mmp80) cc_final: 0.4470 (mmt90) REVERT: D 1131 MET cc_start: 0.5504 (ttt) cc_final: 0.4901 (tpt) REVERT: B 258 MET cc_start: 0.5187 (tmm) cc_final: 0.4933 (ttm) REVERT: B 321 MET cc_start: 0.6552 (mmt) cc_final: 0.5999 (mmt) REVERT: B 362 ASP cc_start: 0.5925 (t0) cc_final: 0.5699 (t0) REVERT: B 370 HIS cc_start: 0.7113 (t-90) cc_final: 0.6903 (t-90) REVERT: B 380 ARG cc_start: 0.8072 (tpt170) cc_final: 0.7739 (mmm160) REVERT: B 383 TRP cc_start: 0.6221 (m-90) cc_final: 0.5892 (m-90) REVERT: B 407 LEU cc_start: 0.7388 (mt) cc_final: 0.6981 (mt) REVERT: B 483 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: B 486 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6737 (tpp-160) REVERT: B 487 TYR cc_start: 0.7776 (m-80) cc_final: 0.7415 (m-80) REVERT: B 538 LEU cc_start: 0.7967 (mt) cc_final: 0.7435 (mt) REVERT: B 557 TYR cc_start: 0.7442 (m-80) cc_final: 0.7044 (m-80) REVERT: B 615 ILE cc_start: 0.7243 (mm) cc_final: 0.7043 (mt) REVERT: B 635 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8272 (mt-10) REVERT: B 673 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8194 (ttmm) REVERT: B 730 GLU cc_start: 0.8360 (tp30) cc_final: 0.7475 (pt0) REVERT: B 779 GLU cc_start: 0.7055 (mp0) cc_final: 0.6733 (mt-10) REVERT: B 912 ARG cc_start: 0.7204 (mtt90) cc_final: 0.6789 (ttm110) REVERT: B 1002 MET cc_start: 0.7370 (mmt) cc_final: 0.6205 (ptp) REVERT: B 1032 GLU cc_start: 0.8176 (tp30) cc_final: 0.7671 (tp30) REVERT: B 1131 MET cc_start: 0.7417 (mmt) cc_final: 0.6557 (ptm) REVERT: C 196 HIS cc_start: 0.6317 (OUTLIER) cc_final: 0.5704 (t-90) REVERT: C 324 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6233 (tpp) REVERT: C 368 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7346 (tttp) REVERT: C 443 MET cc_start: 0.8690 (tpp) cc_final: 0.8435 (mmm) REVERT: C 620 TYR cc_start: 0.7290 (t80) cc_final: 0.6897 (t80) REVERT: C 661 LYS cc_start: 0.8373 (mptm) cc_final: 0.8060 (mmmm) REVERT: C 681 LYS cc_start: 0.7641 (ptpp) cc_final: 0.6611 (tppt) REVERT: C 856 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.5097 (p-80) REVERT: C 996 ASP cc_start: 0.7521 (t70) cc_final: 0.6944 (t0) REVERT: C 1032 GLU cc_start: 0.8389 (tp30) cc_final: 0.8009 (tp30) outliers start: 72 outliers final: 27 residues processed: 684 average time/residue: 0.3880 time to fit residues: 433.1685 Evaluate side-chains 513 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 478 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1050 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 199 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 50.0000 chunk 285 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 411 optimal weight: 0.0270 chunk 26 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN D 432 GLN D 456 HIS ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 235 ASN ** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS B 608 ASN B 738 GLN B 856 HIS B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS C 387 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.184140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129313 restraints weight = 45566.009| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.04 r_work: 0.3427 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 1.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32544 Z= 0.127 Angle : 0.637 15.489 44116 Z= 0.326 Chirality : 0.042 0.277 5144 Planarity : 0.005 0.060 5616 Dihedral : 4.743 26.368 4440 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.88 % Allowed : 18.21 % Favored : 79.92 % 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: -1.61 (0.13), residues: 4108 helix: -0.41 (0.10), residues: 2468 sheet: 3.45 (0.64), residues: 40 loop : -2.19 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C1061 HIS 0.013 0.001 HIS D 565 PHE 0.033 0.001 PHE A 261 TYR 0.039 0.001 TYR D 620 ARG 0.028 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 1140) hydrogen bonds : angle 3.99863 ( 3276) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.61173 ( 8) covalent geometry : bond 0.00290 (32540) covalent geometry : angle 0.63651 (44108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 556 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.1123 (mmt) cc_final: 0.0907 (mmt) REVERT: A 278 ASP cc_start: 0.5934 (t70) cc_final: 0.5730 (t0) REVERT: A 321 MET cc_start: 0.5483 (tpt) cc_final: 0.4661 (tpt) REVERT: A 428 GLN cc_start: 0.6698 (mp10) cc_final: 0.6392 (tp40) REVERT: A 443 MET cc_start: 0.8071 (mpp) cc_final: 0.7853 (mmm) REVERT: A 504 PHE cc_start: 0.6624 (m-80) cc_final: 0.5611 (t80) REVERT: A 578 ASP cc_start: 0.8102 (m-30) cc_final: 0.7107 (t0) REVERT: A 646 ASP cc_start: 0.7628 (p0) cc_final: 0.6253 (m-30) REVERT: A 730 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8510 (pt0) REVERT: A 984 ASP cc_start: 0.8274 (t0) cc_final: 0.7538 (t0) REVERT: A 1032 GLU cc_start: 0.8094 (tp30) cc_final: 0.7861 (tp30) REVERT: A 1037 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7186 (p0) REVERT: D 190 HIS cc_start: 0.5299 (t-90) cc_final: 0.5088 (t-90) REVERT: D 245 PHE cc_start: 0.7436 (t80) cc_final: 0.7147 (t80) REVERT: D 258 MET cc_start: 0.4727 (pmm) cc_final: 0.4490 (pmm) REVERT: D 432 GLN cc_start: 0.4582 (tp-100) cc_final: 0.4134 (tm-30) REVERT: D 572 LEU cc_start: 0.8850 (tp) cc_final: 0.8384 (tp) REVERT: D 590 ASN cc_start: 0.7734 (t0) cc_final: 0.7521 (t0) REVERT: D 593 HIS cc_start: 0.8232 (t-90) cc_final: 0.7811 (m-70) REVERT: D 677 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.4894 (mtpp) REVERT: D 678 LYS cc_start: 0.7340 (mmtm) cc_final: 0.6773 (tmtt) REVERT: D 746 ASN cc_start: 0.8046 (m110) cc_final: 0.7774 (m-40) REVERT: D 748 TYR cc_start: 0.6495 (p90) cc_final: 0.6094 (p90) REVERT: D 845 ARG cc_start: 0.5747 (mtp-110) cc_final: 0.4633 (mtt-85) REVERT: D 915 GLN cc_start: 0.8221 (tp-100) cc_final: 0.6644 (mp10) REVERT: D 1032 GLU cc_start: 0.8202 (tp30) cc_final: 0.7833 (tp30) REVERT: D 1131 MET cc_start: 0.5941 (ttt) cc_final: 0.5260 (tpt) REVERT: B 355 TYR cc_start: 0.6938 (t80) cc_final: 0.6735 (t80) REVERT: B 362 ASP cc_start: 0.5798 (t0) cc_final: 0.5529 (t0) REVERT: B 380 ARG cc_start: 0.8010 (tpt170) cc_final: 0.7307 (mmm160) REVERT: B 383 TRP cc_start: 0.6609 (m-90) cc_final: 0.6068 (m-90) REVERT: B 463 LEU cc_start: 0.7422 (mm) cc_final: 0.7170 (mt) REVERT: B 557 TYR cc_start: 0.7698 (m-80) cc_final: 0.7446 (m-10) REVERT: B 615 ILE cc_start: 0.7342 (mm) cc_final: 0.7089 (mt) REVERT: B 659 MET cc_start: 0.8738 (ptt) cc_final: 0.8515 (ptt) REVERT: B 673 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8247 (ttmm) REVERT: B 677 LYS cc_start: 0.7742 (mppt) cc_final: 0.7170 (mtpt) REVERT: B 730 GLU cc_start: 0.8474 (tp30) cc_final: 0.7885 (pt0) REVERT: B 912 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7303 (ttm110) REVERT: B 989 TYR cc_start: 0.8626 (m-80) cc_final: 0.8197 (m-80) REVERT: B 1002 MET cc_start: 0.7712 (mmt) cc_final: 0.6461 (ptp) REVERT: B 1032 GLU cc_start: 0.8280 (tp30) cc_final: 0.7883 (tp30) REVERT: B 1064 ARG cc_start: 0.7492 (tpt90) cc_final: 0.6963 (tmm160) REVERT: C 154 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7358 (tp30) REVERT: C 237 SER cc_start: 0.7477 (m) cc_final: 0.6778 (p) REVERT: C 324 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6543 (tpp) REVERT: C 351 ASP cc_start: 0.6820 (m-30) cc_final: 0.6544 (m-30) REVERT: C 368 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7395 (tttp) REVERT: C 388 LEU cc_start: 0.7823 (tp) cc_final: 0.7360 (tp) REVERT: C 456 HIS cc_start: 0.7286 (m-70) cc_final: 0.6940 (m-70) REVERT: C 494 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.7628 (tmm-80) REVERT: C 625 GLU cc_start: 0.7910 (tt0) cc_final: 0.7414 (pt0) REVERT: C 635 GLU cc_start: 0.8197 (tp30) cc_final: 0.7792 (tt0) REVERT: C 641 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6337 (mtm) REVERT: C 661 LYS cc_start: 0.8736 (mptm) cc_final: 0.8417 (mmmm) REVERT: C 681 LYS cc_start: 0.8303 (ptpp) cc_final: 0.7562 (tppt) REVERT: C 996 ASP cc_start: 0.7888 (t70) cc_final: 0.7266 (t0) REVERT: C 1032 GLU cc_start: 0.8527 (tp30) cc_final: 0.8039 (tp30) REVERT: C 1068 MET cc_start: 0.6411 (pmm) cc_final: 0.5827 (mmp) outliers start: 63 outliers final: 31 residues processed: 598 average time/residue: 0.4084 time to fit residues: 398.3092 Evaluate side-chains 496 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 461 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 977 SER Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 641 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 23 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 320 optimal weight: 0.0020 chunk 344 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS D 540 HIS ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 HIS ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN C 849 GLN C 853 GLN C 856 HIS C 962 HIS C1046 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.174806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117930 restraints weight = 44922.714| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.97 r_work: 0.3345 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 1.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32544 Z= 0.141 Angle : 0.663 15.840 44116 Z= 0.338 Chirality : 0.043 0.305 5144 Planarity : 0.005 0.073 5616 Dihedral : 4.757 22.779 4440 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.26 % Allowed : 18.47 % Favored : 79.26 % 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: -1.53 (0.13), residues: 4108 helix: -0.36 (0.10), residues: 2542 sheet: 3.34 (0.67), residues: 40 loop : -2.19 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C1061 HIS 0.009 0.001 HIS C 856 PHE 0.023 0.001 PHE B 261 TYR 0.023 0.001 TYR D 620 ARG 0.010 0.001 ARG C1064 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 1140) hydrogen bonds : angle 4.04981 ( 3276) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.78081 ( 8) covalent geometry : bond 0.00317 (32540) covalent geometry : angle 0.66295 (44108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 586 time to evaluate : 3.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.4561 (mtm) cc_final: 0.4263 (mpp) REVERT: A 226 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6319 (t80) REVERT: A 275 HIS cc_start: 0.8369 (m90) cc_final: 0.7536 (m-70) REVERT: A 278 ASP cc_start: 0.6615 (t70) cc_final: 0.6343 (t0) REVERT: A 321 MET cc_start: 0.5810 (tpt) cc_final: 0.5515 (tpp) REVERT: A 337 LYS cc_start: 0.6337 (OUTLIER) cc_final: 0.5766 (tptt) REVERT: A 428 GLN cc_start: 0.6923 (mp10) cc_final: 0.6705 (tp40) REVERT: A 450 TYR cc_start: 0.7998 (m-10) cc_final: 0.7718 (m-10) REVERT: A 458 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8098 (ttp80) REVERT: A 470 ILE cc_start: 0.7628 (mm) cc_final: 0.7368 (mm) REVERT: A 477 ASN cc_start: 0.7800 (m110) cc_final: 0.7563 (m110) REVERT: A 534 ASN cc_start: 0.8748 (t0) cc_final: 0.8342 (m-40) REVERT: A 539 LEU cc_start: 0.9112 (mt) cc_final: 0.8842 (mt) REVERT: A 578 ASP cc_start: 0.8154 (m-30) cc_final: 0.7452 (t0) REVERT: A 620 TYR cc_start: 0.8688 (t80) cc_final: 0.8216 (t80) REVERT: A 644 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7216 (ttp-110) REVERT: A 646 ASP cc_start: 0.8068 (p0) cc_final: 0.6870 (m-30) REVERT: A 730 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8503 (pt0) REVERT: A 844 MET cc_start: 0.6950 (mmt) cc_final: 0.6387 (ppp) REVERT: A 984 ASP cc_start: 0.8259 (t0) cc_final: 0.7543 (t0) REVERT: A 1032 GLU cc_start: 0.8144 (tp30) cc_final: 0.7912 (tp30) REVERT: A 1037 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7561 (p0) REVERT: A 1053 LEU cc_start: 0.7602 (mt) cc_final: 0.7360 (mm) REVERT: D 293 SER cc_start: 0.7751 (p) cc_final: 0.7432 (t) REVERT: D 346 MET cc_start: 0.6654 (mmm) cc_final: 0.6304 (mmm) REVERT: D 432 GLN cc_start: 0.5393 (tp-100) cc_final: 0.5078 (tm-30) REVERT: D 457 ILE cc_start: 0.7279 (mt) cc_final: 0.6574 (mt) REVERT: D 593 HIS cc_start: 0.8568 (t-90) cc_final: 0.8187 (m90) REVERT: D 601 MET cc_start: 0.9094 (ttm) cc_final: 0.8803 (ttm) REVERT: D 611 ASP cc_start: 0.8608 (m-30) cc_final: 0.8355 (m-30) REVERT: D 632 THR cc_start: 0.8961 (m) cc_final: 0.8705 (p) REVERT: D 677 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5215 (mtpp) REVERT: D 678 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7139 (tmtt) REVERT: D 723 MET cc_start: 0.8279 (mtt) cc_final: 0.8075 (mtp) REVERT: D 845 ARG cc_start: 0.6191 (mtp-110) cc_final: 0.5083 (mtt-85) REVERT: D 860 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6522 (pt0) REVERT: D 876 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8529 (ptt) REVERT: D 905 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6782 (mmm-85) REVERT: D 1032 GLU cc_start: 0.8232 (tp30) cc_final: 0.7791 (tp30) REVERT: D 1131 MET cc_start: 0.6226 (ttt) cc_final: 0.5541 (tpt) REVERT: B 175 MET cc_start: 0.6632 (mpp) cc_final: 0.6358 (mpp) REVERT: B 297 HIS cc_start: 0.8045 (m170) cc_final: 0.7824 (m170) REVERT: B 298 ASP cc_start: 0.8660 (t0) cc_final: 0.8208 (m-30) REVERT: B 321 MET cc_start: 0.6077 (mmt) cc_final: 0.5811 (mmt) REVERT: B 362 ASP cc_start: 0.6466 (t0) cc_final: 0.6142 (t0) REVERT: B 534 ASN cc_start: 0.8857 (t0) cc_final: 0.8651 (m-40) REVERT: B 659 MET cc_start: 0.8643 (ptt) cc_final: 0.8337 (ptt) REVERT: B 673 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8321 (ttmm) REVERT: B 677 LYS cc_start: 0.7923 (mppt) cc_final: 0.7567 (mtpt) REVERT: B 730 GLU cc_start: 0.8731 (tp30) cc_final: 0.8283 (pt0) REVERT: B 746 ASN cc_start: 0.8545 (t0) cc_final: 0.8336 (m-40) REVERT: B 760 TYR cc_start: 0.7593 (t80) cc_final: 0.6831 (t80) REVERT: B 912 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7456 (mtt-85) REVERT: B 978 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8202 (ttm) REVERT: B 1032 GLU cc_start: 0.8266 (tp30) cc_final: 0.7980 (tp30) REVERT: B 1064 ARG cc_start: 0.7704 (tpt90) cc_final: 0.7087 (tmm160) REVERT: B 1131 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.5335 (tmm) REVERT: C 154 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7376 (tp30) REVERT: C 196 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.5855 (t-90) REVERT: C 237 SER cc_start: 0.8192 (m) cc_final: 0.7426 (p) REVERT: C 292 ILE cc_start: 0.7258 (pt) cc_final: 0.7017 (pt) REVERT: C 324 MET cc_start: 0.7145 (mmp) cc_final: 0.6910 (tpp) REVERT: C 351 ASP cc_start: 0.7333 (m-30) cc_final: 0.6265 (p0) REVERT: C 368 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7707 (tttp) REVERT: C 450 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6618 (m-10) REVERT: C 487 TYR cc_start: 0.8597 (m-80) cc_final: 0.8350 (m-80) REVERT: C 625 GLU cc_start: 0.7957 (tt0) cc_final: 0.7585 (pt0) REVERT: C 635 GLU cc_start: 0.8425 (tp30) cc_final: 0.8010 (tt0) REVERT: C 661 LYS cc_start: 0.8790 (mptm) cc_final: 0.8532 (mmmt) REVERT: C 681 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8206 (tppt) REVERT: C 839 ILE cc_start: 0.8078 (mt) cc_final: 0.7799 (mp) REVERT: C 840 LEU cc_start: 0.8516 (tp) cc_final: 0.8241 (tt) REVERT: C 844 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6323 (mmt) REVERT: C 984 ASP cc_start: 0.8234 (t0) cc_final: 0.8032 (t0) REVERT: C 996 ASP cc_start: 0.8120 (t70) cc_final: 0.7642 (t0) REVERT: C 1032 GLU cc_start: 0.8481 (tp30) cc_final: 0.7950 (tp30) REVERT: C 1045 MET cc_start: 0.7409 (ptt) cc_final: 0.6917 (tpp) REVERT: C 1048 VAL cc_start: 0.8061 (p) cc_final: 0.7853 (m) REVERT: C 1049 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7280 (tp) outliers start: 76 outliers final: 38 residues processed: 621 average time/residue: 0.4033 time to fit residues: 408.1860 Evaluate side-chains 537 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 487 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 979 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 599 MET Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain C residue 1049 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 0.1980 chunk 245 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 299 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 350 optimal weight: 0.0000 chunk 366 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 GLN D 275 HIS D 309 GLN D 476 ASN D 580 ASN D 590 ASN D1046 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN C 296 GLN C 408 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.175247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120042 restraints weight = 45162.036| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.78 r_work: 0.3381 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 1.7092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32544 Z= 0.107 Angle : 0.601 14.137 44116 Z= 0.304 Chirality : 0.041 0.239 5144 Planarity : 0.004 0.065 5616 Dihedral : 4.494 23.208 4440 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.76 % Allowed : 20.50 % Favored : 77.74 % 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: -1.07 (0.13), residues: 4108 helix: 0.00 (0.11), residues: 2498 sheet: 3.44 (0.68), residues: 40 loop : -1.95 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1091 HIS 0.007 0.001 HIS A 342 PHE 0.019 0.001 PHE B 261 TYR 0.023 0.001 TYR D 620 ARG 0.009 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 1140) hydrogen bonds : angle 3.82410 ( 3276) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.72909 ( 8) covalent geometry : bond 0.00234 (32540) covalent geometry : angle 0.60128 (44108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 518 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.4727 (mtm) cc_final: 0.4432 (mpp) REVERT: A 226 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6330 (t80) REVERT: A 275 HIS cc_start: 0.8457 (m90) cc_final: 0.7622 (m-70) REVERT: A 278 ASP cc_start: 0.6959 (t70) cc_final: 0.6671 (t0) REVERT: A 321 MET cc_start: 0.6267 (tpt) cc_final: 0.5824 (tpp) REVERT: A 324 MET cc_start: 0.6683 (mmp) cc_final: 0.6421 (mmt) REVERT: A 428 GLN cc_start: 0.7308 (mp10) cc_final: 0.6861 (tp40) REVERT: A 450 TYR cc_start: 0.8124 (m-10) cc_final: 0.7699 (m-10) REVERT: A 458 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.8149 (ttp80) REVERT: A 539 LEU cc_start: 0.9088 (mt) cc_final: 0.8829 (mt) REVERT: A 578 ASP cc_start: 0.8398 (m-30) cc_final: 0.7694 (t0) REVERT: A 620 TYR cc_start: 0.8704 (t80) cc_final: 0.8279 (t80) REVERT: A 630 MET cc_start: 0.9252 (mtp) cc_final: 0.9034 (mtp) REVERT: A 646 ASP cc_start: 0.7975 (p0) cc_final: 0.6925 (m-30) REVERT: A 730 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8625 (pt0) REVERT: A 844 MET cc_start: 0.7045 (mmt) cc_final: 0.6423 (ppp) REVERT: A 853 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6987 (tm-30) REVERT: A 984 ASP cc_start: 0.8377 (t0) cc_final: 0.7755 (t0) REVERT: A 1037 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 1053 LEU cc_start: 0.7819 (mt) cc_final: 0.7454 (mt) REVERT: D 175 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.4508 (pmm) REVERT: D 432 GLN cc_start: 0.6161 (tp-100) cc_final: 0.5730 (tm-30) REVERT: D 593 HIS cc_start: 0.8609 (t-90) cc_final: 0.8329 (m90) REVERT: D 601 MET cc_start: 0.9166 (ttm) cc_final: 0.8896 (ttm) REVERT: D 611 ASP cc_start: 0.8647 (m-30) cc_final: 0.8380 (m-30) REVERT: D 632 THR cc_start: 0.9106 (m) cc_final: 0.8867 (p) REVERT: D 678 LYS cc_start: 0.7611 (mmtm) cc_final: 0.7400 (tmtt) REVERT: D 693 GLN cc_start: 0.8672 (pp30) cc_final: 0.8350 (pt0) REVERT: D 769 ILE cc_start: 0.7704 (mm) cc_final: 0.7410 (mp) REVERT: D 842 ASN cc_start: 0.6746 (t0) cc_final: 0.6460 (t0) REVERT: D 845 ARG cc_start: 0.6575 (mtp-110) cc_final: 0.5533 (mtt-85) REVERT: D 860 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6741 (pt0) REVERT: D 1032 GLU cc_start: 0.8320 (tp30) cc_final: 0.7870 (tp30) REVERT: D 1131 MET cc_start: 0.6173 (ttt) cc_final: 0.5475 (tpt) REVERT: B 175 MET cc_start: 0.6615 (mpp) cc_final: 0.6296 (mpp) REVERT: B 297 HIS cc_start: 0.8098 (m170) cc_final: 0.7854 (m170) REVERT: B 321 MET cc_start: 0.6343 (mmt) cc_final: 0.6053 (mmt) REVERT: B 362 ASP cc_start: 0.6739 (t0) cc_final: 0.6474 (t0) REVERT: B 443 MET cc_start: 0.7986 (ppp) cc_final: 0.7756 (ptm) REVERT: B 601 MET cc_start: 0.8694 (mtt) cc_final: 0.8361 (mtt) REVERT: B 673 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8134 (mtmm) REVERT: B 677 LYS cc_start: 0.8065 (mppt) cc_final: 0.7808 (mtpt) REVERT: B 730 GLU cc_start: 0.8750 (tp30) cc_final: 0.8450 (pt0) REVERT: B 746 ASN cc_start: 0.8671 (t0) cc_final: 0.8443 (m-40) REVERT: B 760 TYR cc_start: 0.7720 (t80) cc_final: 0.7125 (t80) REVERT: B 877 VAL cc_start: 0.8480 (t) cc_final: 0.8201 (m) REVERT: B 989 TYR cc_start: 0.8611 (m-80) cc_final: 0.8219 (m-80) REVERT: B 1032 GLU cc_start: 0.8410 (tp30) cc_final: 0.7899 (tp30) REVERT: B 1064 ARG cc_start: 0.7741 (tpt90) cc_final: 0.7481 (tmt170) REVERT: B 1131 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5728 (tmm) REVERT: C 237 SER cc_start: 0.8272 (m) cc_final: 0.7512 (p) REVERT: C 324 MET cc_start: 0.7191 (mmp) cc_final: 0.6575 (mmm) REVERT: C 351 ASP cc_start: 0.7407 (m-30) cc_final: 0.6362 (p0) REVERT: C 368 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7686 (tttp) REVERT: C 450 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6978 (m-10) REVERT: C 559 GLU cc_start: 0.8634 (tp30) cc_final: 0.8359 (mt-10) REVERT: C 635 GLU cc_start: 0.8410 (tp30) cc_final: 0.8063 (tt0) REVERT: C 661 LYS cc_start: 0.8928 (mptm) cc_final: 0.8701 (mmmt) REVERT: C 681 LYS cc_start: 0.8821 (ptpp) cc_final: 0.8410 (tppt) REVERT: C 844 MET cc_start: 0.6958 (tmm) cc_final: 0.6337 (mmt) REVERT: C 884 ASP cc_start: 0.7976 (m-30) cc_final: 0.7614 (p0) REVERT: C 996 ASP cc_start: 0.8026 (t70) cc_final: 0.7558 (t0) REVERT: C 1032 GLU cc_start: 0.8541 (tp30) cc_final: 0.8087 (tp30) REVERT: C 1048 VAL cc_start: 0.8249 (p) cc_final: 0.8032 (m) REVERT: C 1049 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7594 (tp) outliers start: 59 outliers final: 31 residues processed: 550 average time/residue: 0.3893 time to fit residues: 358.9157 Evaluate side-chains 500 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 463 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 590 ASN Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 1054 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 1049 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 293 optimal weight: 3.9990 chunk 387 optimal weight: 7.9990 chunk 137 optimal weight: 0.0980 chunk 185 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 320 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS D1046 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 777 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108202 restraints weight = 44600.075| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.72 r_work: 0.3211 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 1.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 32544 Z= 0.150 Angle : 0.685 14.036 44116 Z= 0.347 Chirality : 0.044 0.269 5144 Planarity : 0.005 0.070 5616 Dihedral : 4.780 23.852 4440 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.47 % Favored : 92.50 % Rotamer: Outliers : 1.91 % Allowed : 20.05 % Favored : 78.04 % 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: -1.25 (0.13), residues: 4108 helix: -0.14 (0.10), residues: 2524 sheet: 3.05 (0.69), residues: 40 loop : -2.03 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 383 HIS 0.014 0.001 HIS A 342 PHE 0.022 0.002 PHE D1011 TYR 0.025 0.002 TYR D 620 ARG 0.008 0.001 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1140) hydrogen bonds : angle 4.03472 ( 3276) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.68425 ( 8) covalent geometry : bond 0.00353 (32540) covalent geometry : angle 0.68495 (44108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 542 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.5017 (mtm) cc_final: 0.4696 (mpp) REVERT: A 226 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 235 ASN cc_start: 0.6808 (m110) cc_final: 0.6399 (m110) REVERT: A 278 ASP cc_start: 0.7299 (t70) cc_final: 0.7059 (t0) REVERT: A 318 MET cc_start: 0.6551 (mmm) cc_final: 0.5948 (mmm) REVERT: A 321 MET cc_start: 0.7056 (tpt) cc_final: 0.6773 (tpp) REVERT: A 366 LEU cc_start: 0.7818 (mm) cc_final: 0.7558 (mm) REVERT: A 384 LYS cc_start: 0.8879 (tptp) cc_final: 0.8652 (ttmm) REVERT: A 391 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6221 (ptp90) REVERT: A 428 GLN cc_start: 0.7712 (mp10) cc_final: 0.7389 (tp40) REVERT: A 436 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.5096 (tp) REVERT: A 458 ARG cc_start: 0.8568 (ttp-170) cc_final: 0.8043 (ptt180) REVERT: A 578 ASP cc_start: 0.8446 (m-30) cc_final: 0.7762 (t0) REVERT: A 646 ASP cc_start: 0.8165 (p0) cc_final: 0.7279 (m-30) REVERT: A 730 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8567 (pt0) REVERT: A 844 MET cc_start: 0.6909 (mmt) cc_final: 0.6451 (ppp) REVERT: A 853 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 935 MET cc_start: 0.7151 (ttp) cc_final: 0.6776 (ttp) REVERT: A 984 ASP cc_start: 0.8382 (t0) cc_final: 0.7691 (t0) REVERT: A 989 TYR cc_start: 0.8616 (m-80) cc_final: 0.8232 (m-80) REVERT: A 1032 GLU cc_start: 0.8186 (tp30) cc_final: 0.7928 (tp30) REVERT: A 1037 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7933 (p0) REVERT: A 1053 LEU cc_start: 0.7857 (mt) cc_final: 0.7623 (mm) REVERT: D 175 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.4825 (pmm) REVERT: D 338 MET cc_start: 0.6516 (tpp) cc_final: 0.6131 (tpp) REVERT: D 381 SER cc_start: 0.9216 (t) cc_final: 0.8855 (p) REVERT: D 432 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7130 (tm-30) REVERT: D 450 TYR cc_start: 0.5390 (m-10) cc_final: 0.4508 (m-10) REVERT: D 509 SER cc_start: 0.9372 (p) cc_final: 0.9126 (m) REVERT: D 593 HIS cc_start: 0.8611 (t-90) cc_final: 0.8279 (m-70) REVERT: D 693 GLN cc_start: 0.8883 (pp30) cc_final: 0.8670 (pt0) REVERT: D 841 LEU cc_start: 0.7811 (mm) cc_final: 0.7591 (mm) REVERT: D 845 ARG cc_start: 0.6615 (mtp-110) cc_final: 0.5542 (mtt-85) REVERT: D 905 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7722 (mmm-85) REVERT: D 1032 GLU cc_start: 0.8379 (tp30) cc_final: 0.7947 (tp30) REVERT: D 1131 MET cc_start: 0.5786 (ttt) cc_final: 0.5279 (tpt) REVERT: D 1146 MET cc_start: 0.5690 (mmm) cc_final: 0.3249 (ttt) REVERT: B 156 LYS cc_start: 0.6645 (mtpm) cc_final: 0.6030 (mppt) REVERT: B 175 MET cc_start: 0.6839 (mpp) cc_final: 0.6530 (mpp) REVERT: B 298 ASP cc_start: 0.8694 (t70) cc_final: 0.8321 (m-30) REVERT: B 321 MET cc_start: 0.6351 (mmt) cc_final: 0.6076 (mmt) REVERT: B 324 MET cc_start: 0.7759 (mmt) cc_final: 0.7420 (mmp) REVERT: B 355 TYR cc_start: 0.7471 (t80) cc_final: 0.6822 (t80) REVERT: B 362 ASP cc_start: 0.7232 (t0) cc_final: 0.7003 (t0) REVERT: B 384 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8945 (mtmt) REVERT: B 501 LYS cc_start: 0.7396 (mttm) cc_final: 0.7091 (mtmt) REVERT: B 578 ASP cc_start: 0.8394 (p0) cc_final: 0.7631 (t0) REVERT: B 730 GLU cc_start: 0.8802 (tp30) cc_final: 0.8504 (pt0) REVERT: B 760 TYR cc_start: 0.8082 (t80) cc_final: 0.7290 (t80) REVERT: B 764 LEU cc_start: 0.7377 (tp) cc_final: 0.6903 (tp) REVERT: B 877 VAL cc_start: 0.8815 (t) cc_final: 0.8586 (m) REVERT: B 911 GLN cc_start: 0.8939 (tt0) cc_final: 0.8718 (tt0) REVERT: B 1018 LEU cc_start: 0.8846 (tp) cc_final: 0.8575 (tp) REVERT: B 1032 GLU cc_start: 0.8439 (tp30) cc_final: 0.8004 (tp30) REVERT: B 1068 MET cc_start: 0.7795 (pmm) cc_final: 0.7228 (mmt) REVERT: C 219 ARG cc_start: 0.8553 (mtm180) cc_final: 0.8311 (mtm-85) REVERT: C 223 ASN cc_start: 0.8198 (m-40) cc_final: 0.7988 (m110) REVERT: C 324 MET cc_start: 0.7594 (mmp) cc_final: 0.6956 (mmm) REVERT: C 351 ASP cc_start: 0.8185 (m-30) cc_final: 0.7383 (p0) REVERT: C 458 ARG cc_start: 0.7727 (ttt90) cc_final: 0.7384 (ttp-110) REVERT: C 501 LYS cc_start: 0.7862 (mttm) cc_final: 0.7602 (mtmt) REVERT: C 599 MET cc_start: 0.9357 (mtp) cc_final: 0.9094 (mtp) REVERT: C 661 LYS cc_start: 0.8918 (mptm) cc_final: 0.8712 (mmmm) REVERT: C 681 LYS cc_start: 0.9007 (ptpp) cc_final: 0.8747 (tppt) REVERT: C 746 ASN cc_start: 0.8215 (t0) cc_final: 0.7533 (m-40) REVERT: C 842 ASN cc_start: 0.7944 (m-40) cc_final: 0.7432 (t0) REVERT: C 844 MET cc_start: 0.6876 (tmm) cc_final: 0.6556 (mmt) REVERT: C 872 SER cc_start: 0.8827 (m) cc_final: 0.8224 (p) REVERT: C 884 ASP cc_start: 0.8075 (m-30) cc_final: 0.7777 (p0) REVERT: C 996 ASP cc_start: 0.8298 (t70) cc_final: 0.7810 (t0) REVERT: C 1032 GLU cc_start: 0.8515 (tp30) cc_final: 0.7862 (tp30) REVERT: C 1045 MET cc_start: 0.7986 (ttp) cc_final: 0.7258 (ttp) REVERT: C 1048 VAL cc_start: 0.8515 (p) cc_final: 0.8210 (m) REVERT: C 1063 GLN cc_start: 0.8012 (pp30) cc_final: 0.7158 (pm20) outliers start: 64 outliers final: 37 residues processed: 574 average time/residue: 0.3860 time to fit residues: 366.3907 Evaluate side-chains 500 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 458 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 625 GLU Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1054 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain C residue 1049 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 chunk 309 optimal weight: 60.0000 chunk 88 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D1046 GLN D1134 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 304 HIS B 522 GLN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 295 GLN ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS C 570 HIS ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 HIS C1121 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093456 restraints weight = 45024.871| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.86 r_work: 0.2955 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 2.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 32544 Z= 0.293 Angle : 0.886 16.438 44116 Z= 0.451 Chirality : 0.052 0.257 5144 Planarity : 0.006 0.131 5616 Dihedral : 5.861 29.743 4440 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.82 % Allowed : 20.62 % Favored : 77.56 % 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: -1.92 (0.12), residues: 4108 helix: -0.72 (0.10), residues: 2542 sheet: 1.17 (0.71), residues: 55 loop : -2.22 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 867 HIS 0.018 0.002 HIS B 190 PHE 0.032 0.003 PHE D 948 TYR 0.025 0.002 TYR D 450 ARG 0.014 0.001 ARG D 371 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 1140) hydrogen bonds : angle 4.54847 ( 3276) SS BOND : bond 0.00356 ( 4) SS BOND : angle 0.91153 ( 8) covalent geometry : bond 0.00720 (32540) covalent geometry : angle 0.88620 (44108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 535 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 HIS cc_start: 0.7331 (m90) cc_final: 0.7023 (m90) REVERT: A 223 ASN cc_start: 0.8853 (m-40) cc_final: 0.8612 (m-40) REVERT: A 239 LYS cc_start: 0.8768 (tppt) cc_final: 0.8493 (mtmt) REVERT: A 368 LYS cc_start: 0.7652 (mmtp) cc_final: 0.7337 (mmtt) REVERT: A 458 ARG cc_start: 0.8701 (ttp-170) cc_final: 0.8474 (ttp80) REVERT: A 501 LYS cc_start: 0.8090 (mttm) cc_final: 0.7701 (mtpt) REVERT: A 730 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8547 (pt0) REVERT: A 824 ARG cc_start: 0.7907 (mpp-170) cc_final: 0.7209 (mtp-110) REVERT: A 872 SER cc_start: 0.8811 (m) cc_final: 0.8157 (p) REVERT: A 935 MET cc_start: 0.7281 (ttp) cc_final: 0.6927 (ttp) REVERT: A 984 ASP cc_start: 0.8313 (t0) cc_final: 0.7990 (t0) REVERT: A 1032 GLU cc_start: 0.8038 (tp30) cc_final: 0.7726 (tp30) REVERT: D 175 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.5990 (ptp) REVERT: D 237 SER cc_start: 0.8483 (m) cc_final: 0.8145 (p) REVERT: D 416 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7776 (ttm-80) REVERT: D 509 SER cc_start: 0.9333 (p) cc_final: 0.9096 (m) REVERT: D 554 MET cc_start: 0.8846 (ptm) cc_final: 0.8553 (ttp) REVERT: D 589 GLU cc_start: 0.8764 (pt0) cc_final: 0.8475 (pt0) REVERT: D 593 HIS cc_start: 0.8846 (t-90) cc_final: 0.8420 (m90) REVERT: D 630 MET cc_start: 0.9186 (mtp) cc_final: 0.8929 (mtp) REVERT: D 677 LYS cc_start: 0.7433 (mptt) cc_final: 0.7171 (mtpt) REVERT: D 693 GLN cc_start: 0.8966 (pp30) cc_final: 0.8761 (pt0) REVERT: D 779 GLU cc_start: 0.8436 (pt0) cc_final: 0.8203 (pp20) REVERT: D 842 ASN cc_start: 0.7872 (t0) cc_final: 0.7632 (t0) REVERT: D 860 GLU cc_start: 0.6462 (mt-10) cc_final: 0.6217 (pt0) REVERT: D 912 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7704 (mtt90) REVERT: D 984 ASP cc_start: 0.8233 (t0) cc_final: 0.8010 (t0) REVERT: D 1032 GLU cc_start: 0.8265 (tp30) cc_final: 0.7670 (tp30) REVERT: D 1131 MET cc_start: 0.6067 (ttt) cc_final: 0.5521 (tpt) REVERT: D 1140 ARG cc_start: 0.6914 (ttp-110) cc_final: 0.6173 (tpp-160) REVERT: D 1146 MET cc_start: 0.5851 (mmm) cc_final: 0.3855 (ttt) REVERT: B 154 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7096 (tp30) REVERT: B 156 LYS cc_start: 0.6352 (mtpm) cc_final: 0.6140 (mppt) REVERT: B 211 ILE cc_start: 0.8807 (tt) cc_final: 0.8397 (pt) REVERT: B 219 ARG cc_start: 0.8856 (mtm180) cc_final: 0.8545 (mtm110) REVERT: B 278 ASP cc_start: 0.6540 (t70) cc_final: 0.6164 (t70) REVERT: B 355 TYR cc_start: 0.7722 (t80) cc_final: 0.7373 (t80) REVERT: B 384 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8889 (mtmm) REVERT: B 501 LYS cc_start: 0.8084 (mttm) cc_final: 0.7765 (mtmt) REVERT: B 730 GLU cc_start: 0.8785 (tp30) cc_final: 0.8459 (pt0) REVERT: B 821 ARG cc_start: 0.6649 (tmm160) cc_final: 0.6326 (ttp80) REVERT: B 840 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8295 (mt) REVERT: B 877 VAL cc_start: 0.8929 (t) cc_final: 0.8695 (m) REVERT: B 1032 GLU cc_start: 0.8265 (tp30) cc_final: 0.7636 (tp30) REVERT: C 154 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7928 (tp30) REVERT: C 166 LEU cc_start: 0.7952 (mt) cc_final: 0.7642 (mm) REVERT: C 324 MET cc_start: 0.8244 (mmp) cc_final: 0.7821 (mpp) REVERT: C 458 ARG cc_start: 0.8734 (ttt90) cc_final: 0.8104 (ttp80) REVERT: C 730 GLU cc_start: 0.8302 (pp20) cc_final: 0.7804 (pp20) REVERT: C 746 ASN cc_start: 0.8326 (t0) cc_final: 0.7937 (m-40) REVERT: C 842 ASN cc_start: 0.8058 (m-40) cc_final: 0.7742 (t0) REVERT: C 847 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7537 (mt) REVERT: C 884 ASP cc_start: 0.8462 (m-30) cc_final: 0.7967 (p0) REVERT: C 1032 GLU cc_start: 0.8427 (tp30) cc_final: 0.7924 (tp30) REVERT: C 1045 MET cc_start: 0.8392 (ttp) cc_final: 0.7676 (ttp) REVERT: C 1063 GLN cc_start: 0.8358 (pp30) cc_final: 0.7284 (pm20) outliers start: 61 outliers final: 28 residues processed: 570 average time/residue: 0.3993 time to fit residues: 371.7262 Evaluate side-chains 459 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 428 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 540 HIS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 355 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 288 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 320 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 313 optimal weight: 50.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN D 271 HIS ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN D 495 GLN D 574 GLN D 753 HIS D 962 HIS B 157 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 432 GLN B 495 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1121 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094882 restraints weight = 44681.230| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.82 r_work: 0.2969 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 2.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32544 Z= 0.189 Angle : 0.708 14.292 44116 Z= 0.360 Chirality : 0.046 0.252 5144 Planarity : 0.005 0.070 5616 Dihedral : 5.161 23.383 4440 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.19 % Allowed : 21.81 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 4108 helix: -0.45 (0.10), residues: 2592 sheet: 1.07 (0.72), residues: 60 loop : -2.21 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 383 HIS 0.008 0.001 HIS A 370 PHE 0.026 0.002 PHE A 420 TYR 0.022 0.002 TYR C 620 ARG 0.007 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1140) hydrogen bonds : angle 4.10624 ( 3276) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.59473 ( 8) covalent geometry : bond 0.00466 (32540) covalent geometry : angle 0.70823 (44108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18063.81 seconds wall clock time: 312 minutes 10.09 seconds (18730.09 seconds total)