Starting phenix.real_space_refine on Fri Jun 27 12:06:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykr_33895/06_2025/7ykr_33895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykr_33895/06_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_33895/06_2025/7ykr_33895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykr_33895/06_2025/7ykr_33895.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykr_33895/06_2025/7ykr_33895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykr_33895/06_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-5710/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: 20.70, per 1000 atoms: 0.65 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: 7.34 Conformation dependent library (CDL) restraints added in 4.3 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: 3.88 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: 10.59 Time building geometry restraints manager: 8.77 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: 0.25 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 71.310 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.620 ------------------------------------------------------------------------------- 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 : 3.595 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: 0.4679 time to fit residues: 489.3699 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 : 3.445 ------------------------------------------------------------------------------- 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 = 0.184384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138248 restraints weight = 44129.502| |-----------------------------------------------------------------------------| 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: 0.3172 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 0.56136 ( 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 : 3.333 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: 0.2392 (mtt) cc_final: 0.1963 (mtm) REVERT: A 318 MET cc_start: 0.2025 (mpp) cc_final: 0.0765 (ptt) REVERT: A 388 LEU cc_start: 0.1483 (tp) cc_final: 0.0709 (pp) REVERT: A 412 MET cc_start: 0.2528 (tpp) cc_final: 0.1896 (ppp) REVERT: A 568 HIS cc_start: 0.4202 (m90) cc_final: 0.3776 (m170) REVERT: A 585 LEU cc_start: 0.5085 (mt) cc_final: 0.4707 (mt) REVERT: A 617 TYR cc_start: 0.5064 (m-80) cc_final: 0.4308 (m-80) REVERT: A 630 MET cc_start: 0.3408 (mtt) cc_final: 0.2976 (mtt) REVERT: A 721 ASN cc_start: 0.6993 (m-40) cc_final: 0.6469 (m-40) REVERT: A 726 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5564 (m-70) REVERT: A 844 MET cc_start: 0.6691 (mmt) cc_final: 0.5837 (ppp) REVERT: A 865 ILE cc_start: 0.5965 (mm) cc_final: 0.5296 (tt) REVERT: A 1064 ARG cc_start: 0.6332 (ptm-80) cc_final: 0.5623 (ttp80) REVERT: D 312 ILE cc_start: 0.2990 (tp) cc_final: 0.2454 (tt) REVERT: D 775 MET cc_start: 0.5162 (mmt) cc_final: 0.4689 (mmt) REVERT: D 840 LEU cc_start: 0.4213 (OUTLIER) cc_final: 0.3893 (tt) REVERT: D 991 ASN cc_start: 0.3130 (m-40) cc_final: 0.2554 (m-40) REVERT: D 1083 PHE cc_start: 0.3788 (p90) cc_final: 0.2727 (m-80) REVERT: B 257 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6356 (pp20) REVERT: B 321 MET cc_start: 0.6859 (mmt) cc_final: 0.6057 (mmt) REVERT: B 562 GLU cc_start: 0.6025 (tt0) cc_final: 0.5797 (tm-30) REVERT: B 775 MET cc_start: 0.3899 (mmm) cc_final: 0.3483 (mmp) REVERT: B 870 TYR cc_start: 0.5528 (m-10) cc_final: 0.5129 (m-10) REVERT: B 1001 PRO cc_start: 0.5291 (Cg_exo) cc_final: 0.4998 (Cg_endo) REVERT: B 1002 MET cc_start: 0.3072 (mmt) cc_final: 0.2399 (pmm) REVERT: B 1016 PRO cc_start: 0.4217 (Cg_endo) cc_final: 0.3991 (Cg_exo) REVERT: C 338 MET cc_start: 0.0622 (OUTLIER) cc_final: 0.0080 (ptm) REVERT: C 491 ASN cc_start: 0.4535 (m-40) cc_final: 0.3623 (m-40) REVERT: C 494 ARG cc_start: 0.4982 (ptt180) cc_final: 0.4679 (tpt-90) REVERT: C 1000 VAL cc_start: 0.3212 (p) cc_final: 0.1955 (t) REVERT: C 1041 LYS cc_start: 0.3755 (mmtp) cc_final: 0.2787 (mtmm) outliers start: 36 outliers final: 14 residues processed: 508 average time/residue: 0.4151 time to fit residues: 348.7018 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 : 3.919 ------------------------------------------------------------------------------- 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: 0.0870 chunk 39 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 13 optimal weight: 0.0670 chunk 330 optimal weight: 0.0980 chunk 291 optimal weight: 0.1980 chunk 385 optimal weight: 0.0970 chunk 397 optimal weight: 0.0970 chunk 344 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 overall best weight: 0.0892 ------------------------------------------------------------------------------- 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 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 349 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** 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** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN D 574 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS B 349 HIS B 522 GLN B 550 GLN ** 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 ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 565 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 852 GLN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.188213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142091 restraints weight = 44841.896| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.93 r_work: 0.3598 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3250 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 32544 Z= 0.103 Angle : 0.584 10.392 44116 Z= 0.305 Chirality : 0.040 0.175 5144 Planarity : 0.004 0.070 5616 Dihedral : 5.223 22.539 4440 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.10 % Allowed : 10.70 % Favored : 88.20 % 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: -1.77 (0.09), residues: 2488 sheet: 3.55 (0.54), residues: 40 loop : -2.37 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 745 HIS 0.016 0.001 HIS D 962 PHE 0.043 0.001 PHE B 261 TYR 0.018 0.001 TYR C 770 ARG 0.004 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 1140) hydrogen bonds : angle 4.23895 ( 3276) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.76077 ( 8) covalent geometry : bond 0.00215 (32540) covalent geometry : angle 0.58383 (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 441 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 404 time to evaluate : 3.633 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 412 MET cc_start: 0.2532 (tpp) cc_final: 0.1978 (ppp) REVERT: A 423 GLN cc_start: 0.5011 (mp10) cc_final: 0.4722 (tp-100) REVERT: A 568 HIS cc_start: 0.3982 (m90) cc_final: 0.3477 (m170) REVERT: A 585 LEU cc_start: 0.5365 (mt) cc_final: 0.4936 (mt) REVERT: A 617 TYR cc_start: 0.4934 (m-80) cc_final: 0.4314 (m-80) REVERT: A 630 MET cc_start: 0.3848 (mtt) cc_final: 0.3387 (mtt) REVERT: A 721 ASN cc_start: 0.7027 (m-40) cc_final: 0.6453 (m-40) REVERT: A 726 HIS cc_start: 0.6190 (OUTLIER) cc_final: 0.4933 (m-70) REVERT: A 844 MET cc_start: 0.6382 (mmt) cc_final: 0.5730 (ppp) REVERT: A 1064 ARG cc_start: 0.6348 (ptm-80) cc_final: 0.5620 (ttp80) REVERT: A 1122 ARG cc_start: 0.5101 (tmm160) cc_final: 0.4552 (mmm160) REVERT: A 1131 MET cc_start: 0.5202 (ttt) cc_final: 0.4282 (mtp) REVERT: D 201 TYR cc_start: 0.5631 (m-80) cc_final: 0.5267 (m-80) REVERT: D 215 ASP cc_start: 0.5772 (m-30) cc_final: 0.3910 (t0) REVERT: D 258 MET cc_start: 0.4177 (ptp) cc_final: 0.0821 (tmm) REVERT: D 312 ILE cc_start: 0.3021 (tp) cc_final: 0.2467 (tt) REVERT: D 598 LEU cc_start: 0.0630 (mt) cc_final: -0.0018 (mt) REVERT: D 991 ASN cc_start: 0.3365 (m-40) cc_final: 0.2891 (m-40) REVERT: D 1002 MET cc_start: 0.4475 (ppp) cc_final: 0.3948 (ppp) REVERT: B 241 MET cc_start: 0.2284 (ptp) cc_final: 0.1585 (ptp) REVERT: B 258 MET cc_start: 0.3974 (tmm) cc_final: 0.3687 (ttp) REVERT: B 259 ILE cc_start: 0.5534 (tp) cc_final: 0.4839 (mt) REVERT: B 321 MET cc_start: 0.6913 (mmt) cc_final: 0.6678 (mmp) REVERT: B 652 THR cc_start: 0.3250 (m) cc_final: 0.2101 (p) REVERT: B 775 MET cc_start: 0.4048 (mmm) cc_final: 0.3732 (mmp) REVERT: B 870 TYR cc_start: 0.5273 (m-10) cc_final: 0.5047 (m-10) REVERT: B 951 LEU cc_start: 0.4499 (mt) cc_final: 0.4186 (mp) REVERT: B 1002 MET cc_start: 0.3004 (mmt) cc_final: 0.2688 (pmm) REVERT: B 1016 PRO cc_start: 0.4622 (Cg_endo) cc_final: 0.4314 (Cg_exo) REVERT: B 1043 LEU cc_start: 0.4823 (mt) cc_final: 0.4241 (mt) REVERT: C 338 MET cc_start: 0.0600 (OUTLIER) cc_final: 0.0349 (ptm) REVERT: C 491 ASN cc_start: 0.4565 (m-40) cc_final: 0.3395 (m-40) REVERT: C 571 LEU cc_start: 0.1602 (OUTLIER) cc_final: 0.1383 (mp) REVERT: C 659 MET cc_start: 0.1418 (pmm) cc_final: 0.1159 (pmm) REVERT: C 922 MET cc_start: 0.3881 (mpp) cc_final: 0.2469 (mmm) REVERT: C 1146 MET cc_start: 0.0496 (mmm) cc_final: 0.0133 (mmm) outliers start: 37 outliers final: 14 residues processed: 428 average time/residue: 0.4294 time to fit residues: 308.4763 Evaluate side-chains 377 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 360 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 962 HIS Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 630 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 100 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 366 optimal weight: 0.9980 chunk 328 optimal weight: 0.4980 chunk 397 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 345 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 HIS A 430 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 584 HIS D 667 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN B 849 GLN ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN C 777 ASN C 852 GLN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150048 restraints weight = 45587.895| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.34 r_work: 0.3683 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4248 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32544 Z= 0.141 Angle : 0.642 14.457 44116 Z= 0.331 Chirality : 0.041 0.198 5144 Planarity : 0.005 0.069 5616 Dihedral : 4.922 29.510 4440 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.79 % Allowed : 10.88 % Favored : 87.34 % 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: -2.42 (0.12), residues: 4108 helix: -1.13 (0.10), residues: 2496 sheet: 0.88 (0.71), residues: 60 loop : -2.36 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 745 HIS 0.050 0.001 HIS D 962 PHE 0.037 0.002 PHE D 944 TYR 0.031 0.002 TYR D 994 ARG 0.005 0.000 ARG A1042 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 1140) hydrogen bonds : angle 4.14249 ( 3276) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.74901 ( 8) covalent geometry : bond 0.00310 (32540) covalent geometry : angle 0.64220 (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 527 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 467 time to evaluate : 3.501 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 338 MET cc_start: 0.4050 (tmm) cc_final: 0.3485 (mtp) REVERT: A 412 MET cc_start: 0.3313 (tpp) cc_final: 0.2959 (ppp) REVERT: A 568 HIS cc_start: 0.4790 (m90) cc_final: 0.4504 (m170) REVERT: A 721 ASN cc_start: 0.7368 (m-40) cc_final: 0.6957 (m-40) REVERT: A 844 MET cc_start: 0.6627 (mmt) cc_final: 0.6054 (ppp) REVERT: A 1012 MET cc_start: 0.6549 (ptt) cc_final: 0.6194 (ptt) REVERT: A 1131 MET cc_start: 0.5050 (ttt) cc_final: 0.4280 (mtp) REVERT: A 1141 LEU cc_start: 0.7995 (tp) cc_final: 0.7755 (tp) REVERT: D 201 TYR cc_start: 0.5588 (m-80) cc_final: 0.4960 (m-80) REVERT: D 312 ILE cc_start: 0.3051 (tp) cc_final: 0.2642 (tt) REVERT: D 571 LEU cc_start: 0.4799 (OUTLIER) cc_final: 0.4436 (pp) REVERT: D 584 HIS cc_start: 0.0537 (m-70) cc_final: 0.0156 (m-70) REVERT: D 970 MET cc_start: 0.6102 (mmm) cc_final: 0.5332 (mtm) REVERT: D 991 ASN cc_start: 0.4981 (m-40) cc_final: 0.4339 (m-40) REVERT: D 1002 MET cc_start: 0.5584 (ppp) cc_final: 0.4703 (mtm) REVERT: D 1030 ASP cc_start: 0.6029 (m-30) cc_final: 0.5476 (m-30) REVERT: B 314 ILE cc_start: 0.5094 (mt) cc_final: 0.4803 (mp) REVERT: B 318 MET cc_start: 0.5998 (mpp) cc_final: 0.5668 (mpp) REVERT: B 321 MET cc_start: 0.6956 (mmt) cc_final: 0.6229 (mmt) REVERT: B 362 ASP cc_start: 0.5145 (t0) cc_final: 0.4871 (t0) REVERT: B 775 MET cc_start: 0.5472 (mmm) cc_final: 0.4772 (mmp) REVERT: B 876 MET cc_start: 0.6748 (ppp) cc_final: 0.6182 (tmm) REVERT: B 912 ARG cc_start: 0.6432 (mtt90) cc_final: 0.6195 (ttm110) REVERT: B 935 MET cc_start: 0.5429 (mpp) cc_final: 0.4029 (mmp) REVERT: B 1053 LEU cc_start: 0.5093 (tp) cc_final: 0.4811 (tt) REVERT: B 1146 MET cc_start: 0.5684 (mmm) cc_final: 0.4046 (ppp) REVERT: C 196 HIS cc_start: 0.4321 (OUTLIER) cc_final: 0.4093 (t70) REVERT: C 338 MET cc_start: 0.0778 (tpp) cc_final: -0.0018 (ptm) REVERT: C 412 MET cc_start: 0.5514 (mpp) cc_final: 0.4513 (ptp) REVERT: C 774 MET cc_start: 0.3921 (mmp) cc_final: 0.2552 (mtm) REVERT: C 973 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5477 (mp) outliers start: 60 outliers final: 22 residues processed: 511 average time/residue: 0.5021 time to fit residues: 427.4997 Evaluate side-chains 390 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1084 CYS Chi-restraints excluded: chain B residue 346 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 938 SER Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 973 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 243 optimal weight: 0.0770 chunk 341 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 323 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 319 optimal weight: 0.9980 chunk 395 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 chunk 301 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN D 157 GLN D 161 HIS D 177 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN D 574 GLN D 584 HIS D 738 GLN D 776 ASN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 525 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN ** B1135 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 224 ASN ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 849 GLN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.198642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154339 restraints weight = 46617.205| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.29 r_work: 0.3704 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5074 moved from start: 0.8767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32544 Z= 0.136 Angle : 0.656 12.797 44116 Z= 0.336 Chirality : 0.042 0.188 5144 Planarity : 0.005 0.072 5616 Dihedral : 4.851 33.033 4440 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.85 % Allowed : 12.57 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.94 (0.13), residues: 4108 helix: -0.74 (0.10), residues: 2436 sheet: 1.26 (0.75), residues: 60 loop : -2.17 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 903 HIS 0.012 0.001 HIS C 449 PHE 0.039 0.002 PHE B 261 TYR 0.040 0.002 TYR C 450 ARG 0.011 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1140) hydrogen bonds : angle 4.19773 ( 3276) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.72926 ( 8) covalent geometry : bond 0.00298 (32540) covalent geometry : angle 0.65561 (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 585 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 523 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.5863 (ptt) cc_final: 0.4839 (ptt) REVERT: A 261 PHE cc_start: 0.5710 (m-10) cc_final: 0.5440 (m-10) REVERT: A 412 MET cc_start: 0.3821 (tpp) cc_final: 0.2844 (pmm) REVERT: A 428 GLN cc_start: 0.6753 (mp10) cc_final: 0.6088 (tp40) REVERT: A 430 GLN cc_start: 0.2614 (mm-40) cc_final: 0.1993 (mm110) REVERT: A 638 ASN cc_start: 0.7454 (p0) cc_final: 0.7061 (m110) REVERT: A 721 ASN cc_start: 0.7453 (m-40) cc_final: 0.7103 (m-40) REVERT: A 844 MET cc_start: 0.6459 (mmt) cc_final: 0.5897 (ppp) REVERT: A 848 ILE cc_start: 0.6459 (tt) cc_final: 0.5992 (pt) REVERT: A 984 ASP cc_start: 0.7168 (t0) cc_final: 0.6624 (t0) REVERT: A 1131 MET cc_start: 0.5232 (ttt) cc_final: 0.4574 (mtp) REVERT: D 201 TYR cc_start: 0.5501 (m-80) cc_final: 0.4734 (m-80) REVERT: D 241 MET cc_start: 0.5067 (OUTLIER) cc_final: 0.4853 (tmm) REVERT: D 258 MET cc_start: 0.3742 (ptp) cc_final: 0.0743 (tmm) REVERT: D 292 ILE cc_start: 0.2474 (OUTLIER) cc_final: 0.1858 (tt) REVERT: D 312 ILE cc_start: 0.3405 (tp) cc_final: 0.2801 (tt) REVERT: D 351 ASP cc_start: 0.5604 (t0) cc_final: 0.4920 (p0) REVERT: D 599 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.3756 (mmp) REVERT: D 630 MET cc_start: 0.4713 (mmp) cc_final: 0.3985 (mtt) REVERT: D 677 LYS cc_start: 0.4545 (OUTLIER) cc_final: 0.4256 (mmtm) REVERT: D 678 LYS cc_start: 0.6582 (mmtm) cc_final: 0.5264 (tmtt) REVERT: D 845 ARG cc_start: 0.4830 (mtp-110) cc_final: 0.4199 (mpt180) REVERT: D 935 MET cc_start: 0.7332 (ttt) cc_final: 0.7065 (ttp) REVERT: D 1053 LEU cc_start: 0.6417 (tp) cc_final: 0.6162 (tp) REVERT: B 200 ILE cc_start: 0.4738 (mt) cc_final: 0.3975 (tt) REVERT: B 258 MET cc_start: 0.5034 (tmm) cc_final: 0.4571 (ttm) REVERT: B 314 ILE cc_start: 0.5035 (mt) cc_final: 0.4761 (mp) REVERT: B 318 MET cc_start: 0.6092 (mpp) cc_final: 0.5814 (mpp) REVERT: B 321 MET cc_start: 0.6813 (mmt) cc_final: 0.6264 (mmt) REVERT: B 355 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.5259 (m-80) REVERT: B 408 HIS cc_start: 0.5723 (m90) cc_final: 0.5462 (m90) REVERT: B 450 TYR cc_start: 0.4476 (OUTLIER) cc_final: 0.4049 (m-10) REVERT: B 743 MET cc_start: 0.6232 (mmp) cc_final: 0.5602 (ttt) REVERT: B 779 GLU cc_start: 0.6973 (mp0) cc_final: 0.6347 (mt-10) REVERT: B 903 TRP cc_start: 0.5879 (m100) cc_final: 0.4714 (m100) REVERT: B 912 ARG cc_start: 0.6809 (mtt90) cc_final: 0.6477 (ttm110) REVERT: B 935 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6709 (mmm) REVERT: B 1020 MET cc_start: 0.8713 (tpt) cc_final: 0.8432 (mmm) REVERT: B 1131 MET cc_start: 0.7007 (mmt) cc_final: 0.5796 (ptm) REVERT: B 1142 ILE cc_start: 0.7428 (mt) cc_final: 0.7034 (mt) REVERT: B 1146 MET cc_start: 0.5741 (mmm) cc_final: 0.4173 (ppp) REVERT: C 305 LEU cc_start: 0.5710 (mt) cc_final: 0.5463 (mt) REVERT: C 578 ASP cc_start: 0.6399 (m-30) cc_final: 0.6140 (m-30) REVERT: C 661 LYS cc_start: 0.7440 (mptm) cc_final: 0.7194 (mmmt) REVERT: C 743 MET cc_start: 0.5926 (tpp) cc_final: 0.5687 (ttp) REVERT: C 774 MET cc_start: 0.5041 (mmp) cc_final: 0.4150 (mtm) REVERT: C 984 ASP cc_start: 0.7510 (m-30) cc_final: 0.7271 (m-30) REVERT: C 1002 MET cc_start: 0.6730 (mpp) cc_final: 0.5761 (pmm) REVERT: C 1032 GLU cc_start: 0.6580 (tp30) cc_final: 0.5834 (tt0) outliers start: 62 outliers final: 23 residues processed: 564 average time/residue: 0.4351 time to fit residues: 400.7298 Evaluate side-chains 440 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 410 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 992 THR Chi-restraints excluded: chain D residue 1119 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 355 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1059 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 199 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 104 optimal weight: 50.0000 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 0.0070 chunk 219 optimal weight: 9.9990 chunk 411 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 246 optimal weight: 0.0870 chunk 98 optimal weight: 10.0000 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN D 275 HIS ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 456 HIS D 574 GLN D 849 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS B 891 HIS B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 540 HIS ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.198226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153061 restraints weight = 46533.819| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.39 r_work: 0.3683 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 1.0063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32544 Z= 0.120 Angle : 0.613 9.976 44116 Z= 0.313 Chirality : 0.041 0.195 5144 Planarity : 0.004 0.059 5616 Dihedral : 4.526 20.746 4440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.46 % Allowed : 14.84 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.55 (0.13), residues: 4108 helix: -0.44 (0.10), residues: 2480 sheet: 4.30 (0.65), residues: 40 loop : -2.05 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 745 HIS 0.008 0.001 HIS D 342 PHE 0.030 0.001 PHE B 261 TYR 0.030 0.001 TYR D 623 ARG 0.008 0.001 ARG D 546 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 1140) hydrogen bonds : angle 3.96386 ( 3276) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.70115 ( 8) covalent geometry : bond 0.00267 (32540) covalent geometry : angle 0.61301 (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 549 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 500 time to evaluate : 3.606 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 258 MET cc_start: 0.6316 (ptt) cc_final: 0.5072 (ptp) REVERT: A 261 PHE cc_start: 0.5486 (m-10) cc_final: 0.5020 (m-10) REVERT: A 338 MET cc_start: 0.4454 (tmm) cc_final: 0.3696 (mtp) REVERT: A 412 MET cc_start: 0.4589 (tpp) cc_final: 0.4254 (pmm) REVERT: A 487 TYR cc_start: 0.5017 (m-80) cc_final: 0.4759 (m-80) REVERT: A 638 ASN cc_start: 0.7964 (p0) cc_final: 0.7516 (m-40) REVERT: A 721 ASN cc_start: 0.7549 (m-40) cc_final: 0.7228 (m110) REVERT: A 844 MET cc_start: 0.6422 (mmt) cc_final: 0.6043 (ppp) REVERT: A 984 ASP cc_start: 0.7547 (t0) cc_final: 0.6949 (t0) REVERT: A 1096 PHE cc_start: 0.7090 (m-80) cc_final: 0.6846 (m-80) REVERT: A 1131 MET cc_start: 0.5121 (ttt) cc_final: 0.4471 (mtp) REVERT: D 215 ASP cc_start: 0.6020 (m-30) cc_final: 0.4053 (t0) REVERT: D 292 ILE cc_start: 0.3270 (OUTLIER) cc_final: 0.2286 (tp) REVERT: D 312 ILE cc_start: 0.3275 (tp) cc_final: 0.2701 (tt) REVERT: D 351 ASP cc_start: 0.5833 (t0) cc_final: 0.5160 (p0) REVERT: D 432 GLN cc_start: 0.4121 (tp-100) cc_final: 0.3553 (tm-30) REVERT: D 443 MET cc_start: 0.7964 (mmp) cc_final: 0.7292 (mmm) REVERT: D 571 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5991 (pp) REVERT: D 607 TYR cc_start: 0.4619 (m-80) cc_final: 0.4408 (m-80) REVERT: D 630 MET cc_start: 0.4915 (mmp) cc_final: 0.4597 (mtt) REVERT: D 638 ASN cc_start: 0.7707 (p0) cc_final: 0.6763 (p0) REVERT: D 677 LYS cc_start: 0.4964 (OUTLIER) cc_final: 0.4455 (mmtm) REVERT: D 678 LYS cc_start: 0.6367 (mmtm) cc_final: 0.5447 (tmtt) REVERT: D 845 ARG cc_start: 0.4896 (mtp-110) cc_final: 0.4175 (mpt180) REVERT: D 935 MET cc_start: 0.7679 (ttt) cc_final: 0.7411 (ttp) REVERT: D 954 LYS cc_start: 0.6828 (mmmt) cc_final: 0.6472 (mttm) REVERT: D 991 ASN cc_start: 0.6493 (m-40) cc_final: 0.6012 (m-40) REVERT: D 1002 MET cc_start: 0.7646 (mmm) cc_final: 0.7435 (mmm) REVERT: B 258 MET cc_start: 0.5287 (tmm) cc_final: 0.4957 (ttm) REVERT: B 321 MET cc_start: 0.6571 (mmt) cc_final: 0.5956 (mmt) REVERT: B 743 MET cc_start: 0.6957 (mmp) cc_final: 0.6703 (ttp) REVERT: B 779 GLU cc_start: 0.6869 (mp0) cc_final: 0.6516 (mt-10) REVERT: B 876 MET cc_start: 0.7219 (ppp) cc_final: 0.6895 (tmm) REVERT: B 912 ARG cc_start: 0.6947 (mtt90) cc_final: 0.6531 (ttm110) REVERT: B 935 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7103 (mmm) REVERT: B 959 GLN cc_start: 0.6974 (tp40) cc_final: 0.6125 (tm-30) REVERT: B 1018 LEU cc_start: 0.8255 (tp) cc_final: 0.7756 (mp) REVERT: B 1020 MET cc_start: 0.8739 (tpt) cc_final: 0.8503 (mmm) REVERT: B 1131 MET cc_start: 0.7400 (mmt) cc_final: 0.6372 (ptm) REVERT: B 1142 ILE cc_start: 0.7411 (mt) cc_final: 0.7039 (mt) REVERT: B 1146 MET cc_start: 0.5733 (mmm) cc_final: 0.4279 (ppp) REVERT: C 321 MET cc_start: 0.5422 (mmm) cc_final: 0.5219 (mpp) REVERT: C 368 LYS cc_start: 0.7151 (ttmt) cc_final: 0.6688 (tttp) REVERT: C 487 TYR cc_start: 0.6614 (m-80) cc_final: 0.6097 (m-80) REVERT: C 578 ASP cc_start: 0.7024 (m-30) cc_final: 0.6781 (m-30) REVERT: C 641 MET cc_start: 0.3957 (pmm) cc_final: 0.3386 (pmm) REVERT: C 661 LYS cc_start: 0.7787 (mptm) cc_final: 0.7576 (mmmt) REVERT: C 766 PHE cc_start: 0.3436 (m-80) cc_final: 0.3133 (m-10) REVERT: C 774 MET cc_start: 0.5195 (mmp) cc_final: 0.4365 (mtp) REVERT: C 996 ASP cc_start: 0.6469 (t70) cc_final: 0.6071 (t0) outliers start: 49 outliers final: 23 residues processed: 534 average time/residue: 0.4528 time to fit residues: 403.0305 Evaluate side-chains 437 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 410 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 966 SER Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 571 LEU 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: 9.9990 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 319 optimal weight: 0.1980 chunk 224 optimal weight: 8.9990 chunk 320 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 275 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 296 GLN ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS D 547 ASN D 574 GLN D 580 ASN ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS B 177 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS B 849 GLN B 911 GLN B1037 ASN C 190 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C 565 HIS C 580 ASN C 842 ASN C 849 GLN C 853 GLN ** C1121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.188795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132331 restraints weight = 45630.577| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.08 r_work: 0.3452 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 1.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 32544 Z= 0.228 Angle : 0.933 21.010 44116 Z= 0.479 Chirality : 0.051 0.266 5144 Planarity : 0.006 0.085 5616 Dihedral : 6.139 41.159 4440 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.15 % Favored : 91.82 % Rotamer: Outliers : 2.26 % Allowed : 15.97 % Favored : 81.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.51 (0.12), residues: 4108 helix: -1.19 (0.10), residues: 2492 sheet: 1.29 (0.73), residues: 55 loop : -2.44 (0.14), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 383 HIS 0.014 0.002 HIS D 518 PHE 0.041 0.003 PHE D 965 TYR 0.033 0.003 TYR C 450 ARG 0.012 0.001 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.05605 ( 1140) hydrogen bonds : angle 4.92515 ( 3276) SS BOND : bond 0.00551 ( 4) SS BOND : angle 2.03323 ( 8) covalent geometry : bond 0.00526 (32540) covalent geometry : angle 0.93265 (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 803 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 727 time to evaluate : 3.349 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 165 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7060 (tt0) REVERT: A 241 MET cc_start: 0.1552 (mmt) cc_final: 0.1259 (mmt) REVERT: A 275 HIS cc_start: 0.8119 (m90) cc_final: 0.7842 (m-70) REVERT: A 278 ASP cc_start: 0.6440 (t70) cc_final: 0.6143 (t0) REVERT: A 454 ASP cc_start: 0.7410 (p0) cc_final: 0.6971 (p0) REVERT: A 530 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8145 (tp-100) REVERT: A 578 ASP cc_start: 0.7928 (m-30) cc_final: 0.7028 (t0) REVERT: A 589 GLU cc_start: 0.8650 (pt0) cc_final: 0.7953 (pt0) REVERT: A 611 ASP cc_start: 0.8278 (m-30) cc_final: 0.8030 (m-30) REVERT: A 620 TYR cc_start: 0.8663 (t80) cc_final: 0.8390 (t80) REVERT: A 646 ASP cc_start: 0.7607 (t0) cc_final: 0.7194 (m-30) REVERT: A 844 MET cc_start: 0.6951 (mmt) cc_final: 0.6382 (ppp) REVERT: A 852 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: A 912 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7814 (mtm-85) REVERT: A 984 ASP cc_start: 0.8328 (t0) cc_final: 0.7630 (t0) REVERT: A 1032 GLU cc_start: 0.7947 (tp30) cc_final: 0.7629 (tp30) REVERT: A 1096 PHE cc_start: 0.8058 (m-80) cc_final: 0.7694 (m-80) REVERT: D 267 ASN cc_start: 0.6815 (m-40) cc_final: 0.5849 (m-40) REVERT: D 346 MET cc_start: 0.6320 (mmt) cc_final: 0.5758 (mmm) REVERT: D 351 ASP cc_start: 0.7522 (t0) cc_final: 0.6840 (p0) REVERT: D 352 ILE cc_start: 0.6125 (mp) cc_final: 0.5346 (mt) REVERT: D 457 ILE cc_start: 0.6766 (mt) cc_final: 0.6441 (mt) REVERT: D 458 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7692 (ttt-90) REVERT: D 470 ILE cc_start: 0.8051 (mm) cc_final: 0.7683 (mm) REVERT: D 593 HIS cc_start: 0.8599 (t-90) cc_final: 0.8236 (m170) REVERT: D 625 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7920 (mt-10) REVERT: D 677 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5017 (mtpt) REVERT: D 678 LYS cc_start: 0.7656 (mmtm) cc_final: 0.6953 (tmtt) REVERT: D 681 LYS cc_start: 0.8494 (tptp) cc_final: 0.8274 (mmmt) REVERT: D 775 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7647 (mmm) REVERT: D 844 MET cc_start: 0.7082 (tpp) cc_final: 0.6866 (mmp) REVERT: D 845 ARG cc_start: 0.5747 (mtp-110) cc_final: 0.4865 (mpt180) REVERT: D 954 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7488 (mttp) REVERT: D 991 ASN cc_start: 0.7787 (m-40) cc_final: 0.7489 (t0) REVERT: D 999 LYS cc_start: 0.8445 (tptm) cc_final: 0.8132 (ttpt) REVERT: D 1030 ASP cc_start: 0.8960 (m-30) cc_final: 0.8730 (m-30) REVERT: D 1032 GLU cc_start: 0.8175 (tp30) cc_final: 0.7592 (tp30) REVERT: D 1131 MET cc_start: 0.5578 (ttt) cc_final: 0.5128 (tpt) REVERT: B 321 MET cc_start: 0.6481 (mmt) cc_final: 0.5966 (mmt) REVERT: B 355 TYR cc_start: 0.7000 (t80) cc_final: 0.6763 (t80) REVERT: B 384 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8405 (mttm) REVERT: B 477 ASN cc_start: 0.7110 (t0) cc_final: 0.6643 (m110) REVERT: B 608 ASN cc_start: 0.7564 (t0) cc_final: 0.7322 (t0) REVERT: B 677 LYS cc_start: 0.7764 (mppt) cc_final: 0.7432 (mtpt) REVERT: B 730 GLU cc_start: 0.8740 (tp30) cc_final: 0.8045 (pt0) REVERT: B 778 ILE cc_start: 0.8104 (tp) cc_final: 0.7808 (mt) REVERT: B 882 GLN cc_start: 0.6892 (mp10) cc_final: 0.6501 (mp10) REVERT: B 967 ASN cc_start: 0.7654 (p0) cc_final: 0.7411 (p0) REVERT: B 984 ASP cc_start: 0.8314 (t0) cc_final: 0.7725 (t0) REVERT: B 997 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7680 (mt0) REVERT: B 1032 GLU cc_start: 0.8213 (tp30) cc_final: 0.7708 (tp30) REVERT: B 1146 MET cc_start: 0.5794 (mmm) cc_final: 0.4412 (ppp) REVERT: C 293 SER cc_start: 0.6901 (t) cc_final: 0.6408 (p) REVERT: C 298 ASP cc_start: 0.8379 (t0) cc_final: 0.8110 (t0) REVERT: C 359 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6391 (mm-30) REVERT: C 368 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7680 (tttp) REVERT: C 369 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 388 LEU cc_start: 0.8069 (tp) cc_final: 0.7769 (tp) REVERT: C 398 VAL cc_start: 0.8245 (m) cc_final: 0.7863 (p) REVERT: C 416 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.6713 (ttt180) REVERT: C 454 ASP cc_start: 0.7063 (m-30) cc_final: 0.6818 (m-30) REVERT: C 562 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 578 ASP cc_start: 0.8202 (m-30) cc_final: 0.7980 (m-30) REVERT: C 635 GLU cc_start: 0.8681 (tp30) cc_final: 0.8445 (tt0) REVERT: C 661 LYS cc_start: 0.8375 (mptm) cc_final: 0.8145 (mmmt) REVERT: C 820 GLU cc_start: 0.6865 (tt0) cc_final: 0.6655 (tt0) REVERT: C 996 ASP cc_start: 0.8388 (t70) cc_final: 0.7829 (t0) REVERT: C 1048 VAL cc_start: 0.7711 (p) cc_final: 0.7431 (m) REVERT: C 1061 TRP cc_start: 0.5965 (p-90) cc_final: 0.5551 (p90) outliers start: 76 outliers final: 20 residues processed: 763 average time/residue: 0.4742 time to fit residues: 587.2493 Evaluate side-chains 518 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 495 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 775 MET Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain C residue 897 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 245 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 366 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 387 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS A 997 GLN A1075 ASN D 309 GLN D 349 HIS D 574 GLN D 667 GLN D 738 GLN ** D 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS ** D 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1059 HIS B 235 ASN B 543 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 HIS B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119689 restraints weight = 45055.778| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.01 r_work: 0.3300 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 1.7365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32544 Z= 0.138 Angle : 0.693 14.745 44116 Z= 0.350 Chirality : 0.044 0.261 5144 Planarity : 0.005 0.062 5616 Dihedral : 5.040 38.182 4440 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.58 % Allowed : 18.98 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.77 (0.13), residues: 4108 helix: -0.57 (0.10), residues: 2532 sheet: 1.65 (0.75), residues: 55 loop : -2.23 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 745 HIS 0.019 0.001 HIS C 856 PHE 0.043 0.002 PHE A 261 TYR 0.033 0.002 TYR A 227 ARG 0.008 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 1140) hydrogen bonds : angle 4.11641 ( 3276) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.06329 ( 8) covalent geometry : bond 0.00319 (32540) covalent geometry : angle 0.69274 (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 633 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 580 time to evaluate : 5.242 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 226 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6149 (t80) REVERT: A 275 HIS cc_start: 0.8344 (m90) cc_final: 0.7785 (m-70) REVERT: A 278 ASP cc_start: 0.6621 (t70) cc_final: 0.6218 (t0) REVERT: A 324 MET cc_start: 0.6289 (mmp) cc_final: 0.6049 (mmt) REVERT: A 337 LYS cc_start: 0.6533 (mmtm) cc_final: 0.6092 (tptt) REVERT: A 578 ASP cc_start: 0.7979 (m-30) cc_final: 0.7488 (t0) REVERT: A 620 TYR cc_start: 0.8628 (t80) cc_final: 0.8161 (t80) REVERT: A 625 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7889 (mp0) REVERT: A 634 GLU cc_start: 0.8270 (mp0) cc_final: 0.7850 (mp0) REVERT: A 764 LEU cc_start: 0.7002 (tp) cc_final: 0.6737 (tp) REVERT: A 844 MET cc_start: 0.6903 (mmt) cc_final: 0.6291 (ppp) REVERT: A 852 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: A 935 MET cc_start: 0.7010 (ttp) cc_final: 0.6629 (ttp) REVERT: A 984 ASP cc_start: 0.8147 (t0) cc_final: 0.7791 (t0) REVERT: A 989 TYR cc_start: 0.8527 (m-80) cc_final: 0.8002 (m-80) REVERT: A 1032 GLU cc_start: 0.8035 (tp30) cc_final: 0.7759 (tp30) REVERT: A 1131 MET cc_start: 0.5326 (ttt) cc_final: 0.4511 (mtp) REVERT: D 231 GLU cc_start: 0.6527 (mm-30) cc_final: 0.6118 (mm-30) REVERT: D 235 ASN cc_start: 0.7015 (m110) cc_final: 0.6388 (m110) REVERT: D 346 MET cc_start: 0.6308 (mmt) cc_final: 0.6095 (mmm) REVERT: D 351 ASP cc_start: 0.7619 (t0) cc_final: 0.7100 (p0) REVERT: D 352 ILE cc_start: 0.6311 (mp) cc_final: 0.6042 (mt) REVERT: D 380 ARG cc_start: 0.7191 (mmm-85) cc_final: 0.6867 (mmm-85) REVERT: D 432 GLN cc_start: 0.5171 (tp-100) cc_final: 0.4618 (tm-30) REVERT: D 439 GLU cc_start: 0.7723 (tp30) cc_final: 0.7246 (mt-10) REVERT: D 509 SER cc_start: 0.8834 (m) cc_final: 0.8617 (p) REVERT: D 593 HIS cc_start: 0.8492 (t-90) cc_final: 0.8178 (m90) REVERT: D 625 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8034 (mt-10) REVERT: D 678 LYS cc_start: 0.7550 (mmtm) cc_final: 0.7237 (tmtt) REVERT: D 769 ILE cc_start: 0.8142 (mm) cc_final: 0.7909 (mt) REVERT: D 775 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7766 (mmm) REVERT: D 842 ASN cc_start: 0.6680 (t0) cc_final: 0.6451 (t0) REVERT: D 845 ARG cc_start: 0.6123 (mtp-110) cc_final: 0.5103 (mtt-85) REVERT: D 954 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7342 (mttm) REVERT: D 991 ASN cc_start: 0.7877 (m-40) cc_final: 0.7639 (m-40) REVERT: D 999 LYS cc_start: 0.8507 (tptm) cc_final: 0.8117 (ttpt) REVERT: D 1032 GLU cc_start: 0.8115 (tp30) cc_final: 0.7533 (tp30) REVERT: D 1052 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 1131 MET cc_start: 0.5471 (ttt) cc_final: 0.5060 (tpt) REVERT: B 318 MET cc_start: 0.8031 (mpp) cc_final: 0.7782 (mtt) REVERT: B 321 MET cc_start: 0.6365 (mmt) cc_final: 0.6022 (mmt) REVERT: B 355 TYR cc_start: 0.6959 (t80) cc_final: 0.6757 (t80) REVERT: B 362 ASP cc_start: 0.6510 (t0) cc_final: 0.6253 (t0) REVERT: B 384 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8599 (mttt) REVERT: B 610 LEU cc_start: 0.8968 (mt) cc_final: 0.8605 (mp) REVERT: B 677 LYS cc_start: 0.7780 (mppt) cc_final: 0.7481 (mtpt) REVERT: B 730 GLU cc_start: 0.8751 (tp30) cc_final: 0.8256 (pt0) REVERT: B 877 VAL cc_start: 0.8023 (t) cc_final: 0.7749 (m) REVERT: B 882 GLN cc_start: 0.7006 (mp10) cc_final: 0.6805 (mp10) REVERT: B 910 LEU cc_start: 0.8579 (tt) cc_final: 0.8318 (tt) REVERT: B 997 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7804 (mt0) REVERT: B 1032 GLU cc_start: 0.8320 (tp30) cc_final: 0.7722 (tp30) REVERT: B 1064 ARG cc_start: 0.8129 (tmm160) cc_final: 0.7389 (tmm-80) REVERT: B 1131 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5669 (tmm) REVERT: B 1146 MET cc_start: 0.5809 (mmm) cc_final: 0.4571 (ppp) REVERT: C 154 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7525 (tp30) REVERT: C 219 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7894 (mtm-85) REVERT: C 298 ASP cc_start: 0.8601 (t0) cc_final: 0.8226 (t0) REVERT: C 338 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6547 (mmt) REVERT: C 368 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7610 (tttp) REVERT: C 398 VAL cc_start: 0.8211 (m) cc_final: 0.7903 (p) REVERT: C 416 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.6706 (ttt180) REVERT: C 635 GLU cc_start: 0.8505 (tp30) cc_final: 0.8176 (tt0) REVERT: C 661 LYS cc_start: 0.8702 (mptm) cc_final: 0.8488 (mmmt) REVERT: C 746 ASN cc_start: 0.7588 (t0) cc_final: 0.6897 (m-40) REVERT: C 820 GLU cc_start: 0.7222 (tt0) cc_final: 0.6942 (tt0) REVERT: C 844 MET cc_start: 0.6734 (tmm) cc_final: 0.6277 (mmt) REVERT: C 996 ASP cc_start: 0.8283 (t70) cc_final: 0.7747 (t0) REVERT: C 1032 GLU cc_start: 0.8158 (tp30) cc_final: 0.7710 (tp30) REVERT: C 1048 VAL cc_start: 0.7797 (p) cc_final: 0.7592 (m) outliers start: 53 outliers final: 18 residues processed: 610 average time/residue: 0.4927 time to fit residues: 501.6905 Evaluate side-chains 500 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 477 time to evaluate : 3.959 ------------------------------------------------------------------------------- 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 774 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 852 GLN Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 775 MET Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 962 HIS Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 979 MET 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 338 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 1065 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 293 optimal weight: 1.9990 chunk 387 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 205 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN A1121 GLN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 580 ASN D 667 GLN D 777 ASN D 962 HIS D 997 GLN ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1121 GLN B 297 HIS B 449 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN B1135 GLN C 157 GLN ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 408 HIS C 462 ASN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111165 restraints weight = 44688.220| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.95 r_work: 0.3230 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 1.8227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 32544 Z= 0.150 Angle : 0.699 12.642 44116 Z= 0.353 Chirality : 0.044 0.248 5144 Planarity : 0.005 0.066 5616 Dihedral : 4.942 35.831 4440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.31 % Allowed : 20.86 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.44 (0.13), residues: 4108 helix: -0.30 (0.10), residues: 2518 sheet: 1.91 (0.75), residues: 55 loop : -2.11 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 745 HIS 0.033 0.001 HIS D 962 PHE 0.034 0.002 PHE D 965 TYR 0.018 0.001 TYR D 838 ARG 0.008 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1140) hydrogen bonds : angle 4.05552 ( 3276) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.79497 ( 8) covalent geometry : bond 0.00336 (32540) covalent geometry : angle 0.69880 (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 562 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 518 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6269 (t80) REVERT: A 235 ASN cc_start: 0.6571 (m110) cc_final: 0.6051 (m110) REVERT: A 261 PHE cc_start: 0.5491 (m-80) cc_final: 0.5197 (m-80) REVERT: A 458 ARG cc_start: 0.8366 (ttp-170) cc_final: 0.8014 (ttp80) REVERT: A 578 ASP cc_start: 0.8225 (m-30) cc_final: 0.7704 (t0) REVERT: A 620 TYR cc_start: 0.8707 (t80) cc_final: 0.8339 (t80) REVERT: A 844 MET cc_start: 0.6817 (mmt) cc_final: 0.6356 (ppp) REVERT: A 910 LEU cc_start: 0.8825 (tt) cc_final: 0.8529 (mp) REVERT: A 935 MET cc_start: 0.7109 (ttp) cc_final: 0.6806 (ttp) REVERT: A 989 TYR cc_start: 0.8590 (m-80) cc_final: 0.8147 (m-80) REVERT: A 1020 MET cc_start: 0.8970 (mmm) cc_final: 0.8712 (mmm) REVERT: A 1032 GLU cc_start: 0.8054 (tp30) cc_final: 0.7782 (tp30) REVERT: A 1096 PHE cc_start: 0.8392 (m-80) cc_final: 0.8189 (m-80) REVERT: A 1131 MET cc_start: 0.5373 (ttt) cc_final: 0.4677 (mtm) REVERT: D 231 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6797 (mm-30) REVERT: D 235 ASN cc_start: 0.7364 (m110) cc_final: 0.6851 (m110) REVERT: D 318 MET cc_start: 0.8041 (ptm) cc_final: 0.7617 (ptm) REVERT: D 351 ASP cc_start: 0.8001 (t0) cc_final: 0.7741 (p0) REVERT: D 352 ILE cc_start: 0.7084 (mp) cc_final: 0.6801 (mt) REVERT: D 381 SER cc_start: 0.8906 (t) cc_final: 0.8693 (p) REVERT: D 432 GLN cc_start: 0.6279 (tp-100) cc_final: 0.5807 (tm-30) REVERT: D 593 HIS cc_start: 0.8630 (t-90) cc_final: 0.8380 (m-70) REVERT: D 625 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8235 (mt-10) REVERT: D 677 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.5906 (mtpp) REVERT: D 730 GLU cc_start: 0.8625 (pm20) cc_final: 0.8150 (pm20) REVERT: D 769 ILE cc_start: 0.8365 (mm) cc_final: 0.8110 (mt) REVERT: D 775 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7911 (mmm) REVERT: D 845 ARG cc_start: 0.6498 (mtp-110) cc_final: 0.5520 (mtt-85) REVERT: D 989 TYR cc_start: 0.8689 (m-80) cc_final: 0.8306 (m-80) REVERT: D 991 ASN cc_start: 0.7838 (m-40) cc_final: 0.7553 (m110) REVERT: D 999 LYS cc_start: 0.8509 (tptm) cc_final: 0.8115 (ttpt) REVERT: D 1032 GLU cc_start: 0.8273 (tp30) cc_final: 0.7701 (tp30) REVERT: D 1089 ARG cc_start: 0.5449 (mmp80) cc_final: 0.5202 (tpp80) REVERT: D 1131 MET cc_start: 0.5474 (ttt) cc_final: 0.5138 (tpt) REVERT: D 1140 ARG cc_start: 0.6658 (ttp-110) cc_final: 0.5757 (tpp-160) REVERT: D 1146 MET cc_start: 0.4626 (mtt) cc_final: 0.3484 (ttt) REVERT: B 321 MET cc_start: 0.6574 (mmt) cc_final: 0.6221 (mmt) REVERT: B 324 MET cc_start: 0.7725 (mmt) cc_final: 0.7341 (mmp) REVERT: B 362 ASP cc_start: 0.7080 (t0) cc_final: 0.6729 (t0) REVERT: B 384 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8835 (mtmt) REVERT: B 477 ASN cc_start: 0.7230 (t0) cc_final: 0.6615 (m110) REVERT: B 677 LYS cc_start: 0.8047 (mppt) cc_final: 0.7790 (mtpt) REVERT: B 730 GLU cc_start: 0.8720 (tp30) cc_final: 0.8423 (pt0) REVERT: B 746 ASN cc_start: 0.8549 (t0) cc_final: 0.8179 (m-40) REVERT: B 877 VAL cc_start: 0.8404 (t) cc_final: 0.8130 (m) REVERT: B 882 GLN cc_start: 0.6924 (mp10) cc_final: 0.6604 (mp10) REVERT: B 984 ASP cc_start: 0.8062 (t0) cc_final: 0.7579 (t0) REVERT: B 997 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7811 (mt0) REVERT: B 1032 GLU cc_start: 0.8297 (tp30) cc_final: 0.7748 (tp30) REVERT: B 1048 VAL cc_start: 0.8481 (p) cc_final: 0.8217 (m) REVERT: B 1131 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.4742 (tmm) REVERT: B 1142 ILE cc_start: 0.7673 (mt) cc_final: 0.7359 (mt) REVERT: B 1146 MET cc_start: 0.5832 (mmm) cc_final: 0.4595 (ppp) REVERT: C 154 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7654 (tp30) REVERT: C 219 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8218 (mtm-85) REVERT: C 223 ASN cc_start: 0.8220 (t0) cc_final: 0.7638 (m110) REVERT: C 298 ASP cc_start: 0.8594 (t0) cc_final: 0.8340 (m-30) REVERT: C 338 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6768 (mmt) REVERT: C 398 VAL cc_start: 0.8330 (m) cc_final: 0.8082 (p) REVERT: C 416 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.6923 (ttt-90) REVERT: C 450 TYR cc_start: 0.7822 (m-10) cc_final: 0.7497 (m-80) REVERT: C 458 ARG cc_start: 0.7413 (ttt90) cc_final: 0.7071 (mpt180) REVERT: C 559 GLU cc_start: 0.8744 (tp30) cc_final: 0.8469 (mt-10) REVERT: C 635 GLU cc_start: 0.8448 (tp30) cc_final: 0.8212 (tt0) REVERT: C 661 LYS cc_start: 0.8748 (mptm) cc_final: 0.8545 (mmmt) REVERT: C 693 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: C 746 ASN cc_start: 0.7758 (t0) cc_final: 0.7176 (m-40) REVERT: C 844 MET cc_start: 0.6813 (tmm) cc_final: 0.6596 (mmt) REVERT: C 872 SER cc_start: 0.8715 (m) cc_final: 0.8239 (p) REVERT: C 884 ASP cc_start: 0.7773 (m-30) cc_final: 0.7460 (p0) REVERT: C 996 ASP cc_start: 0.8282 (t70) cc_final: 0.7739 (t0) REVERT: C 1032 GLU cc_start: 0.8348 (tp30) cc_final: 0.7860 (tp30) REVERT: C 1048 VAL cc_start: 0.8196 (p) cc_final: 0.7957 (m) outliers start: 44 outliers final: 24 residues processed: 543 average time/residue: 0.4005 time to fit residues: 359.0027 Evaluate side-chains 470 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 440 time to evaluate : 3.673 ------------------------------------------------------------------------------- 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 672 THR Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 775 MET Chi-restraints excluded: chain D residue 828 ILE 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 398 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 1037 ASN Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 693 GLN Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 411 optimal weight: 6.9990 chunk 309 optimal weight: 60.0000 chunk 88 optimal weight: 0.7980 chunk 350 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 387 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN A 491 ASN A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A 991 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN D 275 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 HIS D 574 GLN ** D 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 742 GLN ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN C 161 HIS C 223 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN C 309 GLN C 432 GLN C 456 HIS C 534 ASN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106802 restraints weight = 44376.756| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.55 r_work: 0.3009 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 2.0207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.160 32544 Z= 0.271 Angle : 0.900 18.209 44116 Z= 0.459 Chirality : 0.051 0.276 5144 Planarity : 0.006 0.085 5616 Dihedral : 6.018 38.323 4440 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.42 % Favored : 91.53 % Rotamer: Outliers : 1.31 % Allowed : 21.36 % Favored : 77.32 % Cbeta Deviations : 0.03 % 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: -2.06 (0.12), residues: 4108 helix: -0.85 (0.10), residues: 2560 sheet: 1.41 (0.71), residues: 55 loop : -2.26 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 745 HIS 0.019 0.002 HIS D 753 PHE 0.040 0.003 PHE B 261 TYR 0.033 0.003 TYR D 623 ARG 0.025 0.001 ARG B1036 Details of bonding type rmsd hydrogen bonds : bond 0.05293 ( 1140) hydrogen bonds : angle 4.56087 ( 3276) SS BOND : bond 0.00296 ( 4) SS BOND : angle 1.09583 ( 8) covalent geometry : bond 0.00660 (32540) covalent geometry : angle 0.89963 (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 562 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 518 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5698 (t80) REVERT: A 239 LYS cc_start: 0.8540 (tptt) cc_final: 0.8314 (mtmt) REVERT: A 241 MET cc_start: 0.6944 (mmt) cc_final: 0.6358 (tpp) REVERT: A 391 ARG cc_start: 0.7452 (ttp80) cc_final: 0.6985 (ttm170) REVERT: A 420 PHE cc_start: 0.8388 (t80) cc_final: 0.8088 (t80) REVERT: A 458 ARG cc_start: 0.8756 (ttp-170) cc_final: 0.8407 (ttp80) REVERT: A 501 LYS cc_start: 0.8422 (mttm) cc_final: 0.8189 (mtmt) REVERT: A 717 LEU cc_start: 0.8198 (mt) cc_final: 0.7936 (mp) REVERT: A 824 ARG cc_start: 0.7789 (mpp-170) cc_final: 0.6980 (mtp-110) REVERT: A 844 MET cc_start: 0.7223 (mmt) cc_final: 0.6921 (ppp) REVERT: A 864 LEU cc_start: 0.8560 (mp) cc_final: 0.8116 (tp) REVERT: A 935 MET cc_start: 0.7448 (ttp) cc_final: 0.7089 (ttp) REVERT: A 1002 MET cc_start: 0.9297 (mmm) cc_final: 0.9087 (mmt) REVERT: A 1032 GLU cc_start: 0.8466 (tp30) cc_final: 0.8153 (tp30) REVERT: A 1063 GLN cc_start: 0.8421 (tp40) cc_final: 0.8176 (tp40) REVERT: D 175 MET cc_start: 0.5926 (ptm) cc_final: 0.5649 (ptm) REVERT: D 283 GLU cc_start: 0.7126 (pt0) cc_final: 0.6532 (pt0) REVERT: D 324 MET cc_start: 0.7794 (mmp) cc_final: 0.7475 (mmt) REVERT: D 384 LYS cc_start: 0.9252 (tppt) cc_final: 0.9039 (ttmm) REVERT: D 432 GLN cc_start: 0.7352 (tp-100) cc_final: 0.6761 (tm-30) REVERT: D 554 MET cc_start: 0.9075 (ptm) cc_final: 0.8846 (ttp) REVERT: D 625 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8623 (mt-10) REVERT: D 842 ASN cc_start: 0.8128 (t0) cc_final: 0.7912 (t0) REVERT: D 845 ARG cc_start: 0.6997 (mtp-110) cc_final: 0.5962 (mtt180) REVERT: D 912 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7674 (mtt90) REVERT: D 1032 GLU cc_start: 0.8804 (tp30) cc_final: 0.8307 (tp30) REVERT: D 1140 ARG cc_start: 0.6986 (ttp-110) cc_final: 0.6123 (tpp-160) REVERT: B 156 LYS cc_start: 0.6632 (mtpm) cc_final: 0.6405 (mppt) REVERT: B 219 ARG cc_start: 0.8766 (mtm180) cc_final: 0.8515 (mtm110) REVERT: B 324 MET cc_start: 0.7962 (mmt) cc_final: 0.7698 (mpp) REVERT: B 355 TYR cc_start: 0.7926 (t80) cc_final: 0.7427 (t80) REVERT: B 369 GLU cc_start: 0.8324 (pt0) cc_final: 0.7819 (pp20) REVERT: B 384 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9092 (mtmm) REVERT: B 388 LEU cc_start: 0.8638 (mp) cc_final: 0.8309 (tp) REVERT: B 400 ASP cc_start: 0.7479 (p0) cc_final: 0.7272 (p0) REVERT: B 501 LYS cc_start: 0.7821 (mttm) cc_final: 0.7573 (mtmt) REVERT: B 530 GLN cc_start: 0.8947 (tt0) cc_final: 0.8566 (tp40) REVERT: B 601 MET cc_start: 0.9429 (mtt) cc_final: 0.9090 (mtt) REVERT: B 730 GLU cc_start: 0.8983 (tp30) cc_final: 0.8617 (pt0) REVERT: B 746 ASN cc_start: 0.8658 (t0) cc_final: 0.8346 (m110) REVERT: B 821 ARG cc_start: 0.6789 (tmm160) cc_final: 0.6362 (ttp80) REVERT: B 997 GLN cc_start: 0.8602 (mm-40) cc_final: 0.7978 (mt0) REVERT: B 1002 MET cc_start: 0.7490 (ptp) cc_final: 0.6724 (mmm) REVERT: B 1018 LEU cc_start: 0.8995 (tp) cc_final: 0.8789 (tp) REVERT: B 1032 GLU cc_start: 0.8780 (tp30) cc_final: 0.8276 (tp30) REVERT: B 1081 LEU cc_start: 0.8015 (mm) cc_final: 0.7799 (mm) REVERT: B 1131 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.4896 (tmm) REVERT: C 154 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7901 (tp30) REVERT: C 166 LEU cc_start: 0.8135 (mt) cc_final: 0.7904 (mm) REVERT: C 398 VAL cc_start: 0.8675 (m) cc_final: 0.8306 (p) REVERT: C 458 ARG cc_start: 0.8579 (ttt90) cc_final: 0.8116 (ttp-170) REVERT: C 630 MET cc_start: 0.9241 (mtp) cc_final: 0.9022 (mtp) REVERT: C 746 ASN cc_start: 0.8555 (t0) cc_final: 0.8205 (m-40) REVERT: C 777 ASN cc_start: 0.8911 (m-40) cc_final: 0.8711 (m-40) REVERT: C 824 ARG cc_start: 0.7540 (tmm-80) cc_final: 0.7094 (mtp180) REVERT: C 844 MET cc_start: 0.7147 (tmm) cc_final: 0.6737 (mmt) REVERT: C 884 ASP cc_start: 0.8214 (m-30) cc_final: 0.7811 (p0) REVERT: C 887 ILE cc_start: 0.8289 (mm) cc_final: 0.8070 (mm) outliers start: 44 outliers final: 17 residues processed: 544 average time/residue: 0.4338 time to fit residues: 383.0539 Evaluate side-chains 431 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 412 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 1065 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 355 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 288 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 chunk 338 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 219 optimal weight: 0.0980 chunk 313 optimal weight: 50.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 HIS ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 HIS D 161 HIS ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN B 223 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 HIS B1037 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 ASN C 570 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.159477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104006 restraints weight = 44300.959| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.85 r_work: 0.3113 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 2.0353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32544 Z= 0.120 Angle : 0.674 13.069 44116 Z= 0.339 Chirality : 0.042 0.222 5144 Planarity : 0.004 0.070 5616 Dihedral : 4.936 32.952 4440 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.86 % Allowed : 22.62 % Favored : 76.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.42 (0.13), residues: 4108 helix: -0.31 (0.10), residues: 2571 sheet: 2.13 (0.74), residues: 55 loop : -2.11 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 745 HIS 0.015 0.001 HIS A1136 PHE 0.029 0.001 PHE B 261 TYR 0.020 0.001 TYR C 490 ARG 0.009 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1140) hydrogen bonds : angle 3.96134 ( 3276) SS BOND : bond 0.00392 ( 4) SS BOND : angle 1.07959 ( 8) covalent geometry : bond 0.00274 (32540) covalent geometry : angle 0.67391 (44108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19696.38 seconds wall clock time: 345 minutes 42.49 seconds (20742.49 seconds total)