Starting phenix.real_space_refine on Tue Aug 26 00:00:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykr_33895/08_2025/7ykr_33895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykr_33895/08_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_33895/08_2025/7ykr_33895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykr_33895/08_2025/7ykr_33895.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykr_33895/08_2025/7ykr_33895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykr_33895/08_2025/7ykr_33895.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 10, 'TYR:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 8, 'PHE:plan': 3, 'ARG:plan': 7, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 162 Restraints were copied for chains: D, B, C Time building chain proxies: 10.25, per 1000 atoms: 0.32 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 D 217 " - pdb=" SG CYS D 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.44 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: 6.34 Time building geometry restraints manager: 3.70 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.830 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.006 0.001 ARG B 974 TYR 0.029 0.003 TYR B 857 PHE 0.024 0.003 PHE B 689 TRP 0.033 0.004 TRP B1061 HIS 0.009 0.002 HIS C 482 Details of bonding type rmsd covalent geometry : bond 0.00836 (32540) covalent geometry : angle 1.01715 (44108) SS BOND : bond 0.00614 ( 4) SS BOND : angle 0.66790 ( 8) hydrogen bonds : bond 0.33803 ( 1140) hydrogen bonds : angle 10.02824 ( 3276) *********************** 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 : 1.190 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: 0.1328 (mtm) REVERT: A 388 LEU cc_start: 0.0745 (tp) cc_final: 0.0187 (tt) REVERT: A 568 HIS cc_start: 0.4186 (m90) cc_final: 0.3580 (m90) REVERT: A 648 HIS cc_start: 0.4221 (m90) cc_final: 0.3049 (m90) REVERT: A 889 THR cc_start: 0.3885 (m) cc_final: 0.3364 (p) REVERT: A 913 PHE cc_start: 0.4738 (m-10) cc_final: 0.4494 (m-10) REVERT: A 985 PHE cc_start: 0.4742 (t80) cc_final: 0.4141 (t80) REVERT: D 244 PHE cc_start: 0.4780 (m-80) cc_final: 0.4458 (m-80) REVERT: D 245 PHE cc_start: 0.3997 (m-10) cc_final: 0.3664 (m-10) REVERT: D 978 MET cc_start: -0.3443 (ptt) cc_final: -0.4127 (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: 0.2317 (mp) REVERT: D 1119 GLU cc_start: 0.5597 (mp0) cc_final: 0.5174 (tt0) REVERT: B 854 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5474 (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: 0.6333 (mtm) REVERT: C 172 LEU cc_start: 0.6465 (mt) cc_final: 0.6245 (mt) outliers start: 28 outliers final: 5 residues processed: 666 average time/residue: 0.2293 time to fit residues: 240.2413 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 : 1.248 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 235 ASN 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 746 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1037 ASN ** A1135 GLN ** 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 565 HIS 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 ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS 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** B 959 GLN 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 C 534 ASN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** 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 863 ASN 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: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137121 restraints weight = 44735.726| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.89 r_work: 0.3541 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3133 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32544 Z= 0.137 Angle : 0.653 12.087 44116 Z= 0.346 Chirality : 0.042 0.287 5144 Planarity : 0.005 0.062 5616 Dihedral : 5.882 40.000 4453 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.10 % Allowed : 8.10 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.33 (0.10), residues: 4108 helix: -2.87 (0.08), residues: 2536 sheet: 0.27 (0.69), residues: 60 loop : -2.73 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 636 TYR 0.020 0.001 TYR D 178 PHE 0.026 0.001 PHE C 261 TRP 0.027 0.002 TRP C 383 HIS 0.008 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00274 (32540) covalent geometry : angle 0.65292 (44108) SS BOND : bond 0.00393 ( 4) SS BOND : angle 0.56834 ( 8) hydrogen bonds : bond 0.03810 ( 1140) hydrogen bonds : angle 4.69401 ( 3276) *********************** 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 510 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 473 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.2260 (mtt) cc_final: 0.1892 (mtm) REVERT: A 229 ILE cc_start: 0.3398 (tp) cc_final: 0.3110 (mt) REVERT: A 258 MET cc_start: 0.5528 (mtm) cc_final: 0.5178 (ptt) REVERT: A 261 PHE cc_start: 0.5769 (m-10) cc_final: 0.5497 (m-10) REVERT: A 412 MET cc_start: 0.2538 (tpp) cc_final: 0.2036 (ppp) REVERT: A 568 HIS cc_start: 0.4102 (m90) cc_final: 0.3631 (m170) REVERT: A 585 LEU cc_start: 0.5230 (mt) cc_final: 0.4611 (mt) REVERT: A 630 MET cc_start: 0.3465 (mtt) cc_final: 0.2976 (mtt) REVERT: A 721 ASN cc_start: 0.6991 (m-40) cc_final: 0.6463 (m-40) REVERT: A 726 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5494 (m-70) REVERT: A 865 ILE cc_start: 0.5997 (mm) cc_final: 0.5334 (tt) REVERT: A 1064 ARG cc_start: 0.6352 (ptm-80) cc_final: 0.5638 (ttp80) REVERT: A 1138 LEU cc_start: 0.7004 (mp) cc_final: 0.6803 (mt) REVERT: D 312 ILE cc_start: 0.3104 (tp) cc_final: 0.2619 (tt) REVERT: D 775 MET cc_start: 0.5006 (mmt) cc_final: 0.4602 (mmt) REVERT: D 840 LEU cc_start: 0.4072 (OUTLIER) cc_final: 0.3753 (tt) REVERT: D 991 ASN cc_start: 0.3132 (m-40) cc_final: 0.2548 (m-40) REVERT: D 1083 PHE cc_start: 0.3757 (p90) cc_final: 0.2696 (m-80) REVERT: B 257 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6217 (tp30) REVERT: B 321 MET cc_start: 0.6821 (mmt) cc_final: 0.5998 (mmt) REVERT: B 339 THR cc_start: 0.5884 (m) cc_final: 0.5276 (p) REVERT: B 775 MET cc_start: 0.3865 (mmm) cc_final: 0.3472 (mmp) REVERT: B 870 TYR cc_start: 0.5442 (m-10) cc_final: 0.5077 (m-10) REVERT: B 1001 PRO cc_start: 0.5179 (Cg_exo) cc_final: 0.4937 (Cg_endo) REVERT: B 1002 MET cc_start: 0.3159 (mmt) cc_final: 0.2513 (pmm) REVERT: B 1016 PRO cc_start: 0.4289 (Cg_endo) cc_final: 0.4064 (Cg_exo) REVERT: C 245 PHE cc_start: 0.4904 (m-10) cc_final: 0.4556 (m-10) REVERT: C 336 GLN cc_start: 0.4209 (tt0) cc_final: 0.3703 (tt0) REVERT: C 338 MET cc_start: 0.0813 (OUTLIER) cc_final: 0.0128 (ptm) REVERT: C 491 ASN cc_start: 0.4584 (m-40) cc_final: 0.3634 (m-40) REVERT: C 494 ARG cc_start: 0.4941 (ptt180) cc_final: 0.4570 (tpt-90) REVERT: C 498 ASP cc_start: 0.3596 (p0) cc_final: 0.3118 (t70) REVERT: C 1000 VAL cc_start: 0.3011 (p) cc_final: 0.1599 (t) REVERT: C 1002 MET cc_start: 0.5215 (mpp) cc_final: 0.4987 (mpt) REVERT: C 1041 LYS cc_start: 0.3691 (mmtp) cc_final: 0.2724 (mtmm) outliers start: 37 outliers final: 11 residues processed: 495 average time/residue: 0.1969 time to fit residues: 161.3148 Evaluate side-chains 396 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 382 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 264 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 312 optimal weight: 50.0000 chunk 146 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 309 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 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 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 246 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** 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 C 190 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS C 296 GLN C 309 GLN C 349 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 HIS C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.197878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154691 restraints weight = 47277.665| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.38 r_work: 0.3704 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32544 Z= 0.225 Angle : 0.787 15.740 44116 Z= 0.411 Chirality : 0.045 0.316 5144 Planarity : 0.006 0.074 5616 Dihedral : 5.456 28.356 4440 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.06 % Allowed : 9.65 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.12), residues: 4108 helix: -1.76 (0.09), residues: 2480 sheet: 3.57 (0.51), residues: 40 loop : -2.49 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1089 TYR 0.025 0.002 TYR C 892 PHE 0.031 0.003 PHE A 900 TRP 0.029 0.003 TRP A 383 HIS 0.077 0.002 HIS D 962 Details of bonding type rmsd covalent geometry : bond 0.00450 (32540) covalent geometry : angle 0.78701 (44108) SS BOND : bond 0.00449 ( 4) SS BOND : angle 1.38778 ( 8) hydrogen bonds : bond 0.04749 ( 1140) hydrogen bonds : angle 4.71033 ( 3276) *********************** 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 618 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 549 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.4496 (OUTLIER) cc_final: 0.4174 (tt0) REVERT: A 318 MET cc_start: 0.1974 (mmm) cc_final: -0.0118 (mtm) REVERT: A 412 MET cc_start: 0.4321 (tpp) cc_final: 0.3896 (ppp) REVERT: A 616 ASP cc_start: 0.6311 (m-30) cc_final: 0.5998 (m-30) REVERT: A 721 ASN cc_start: 0.7651 (m-40) cc_final: 0.7101 (m110) REVERT: A 753 HIS cc_start: 0.3713 (t-90) cc_final: 0.3510 (t70) REVERT: A 844 MET cc_start: 0.6651 (mmt) cc_final: 0.6029 (ppp) REVERT: A 876 MET cc_start: 0.6752 (mtm) cc_final: 0.6416 (mtm) REVERT: A 1015 MET cc_start: 0.8076 (mmm) cc_final: 0.7819 (mmp) REVERT: A 1141 LEU cc_start: 0.7995 (tp) cc_final: 0.7742 (tp) REVERT: D 201 TYR cc_start: 0.5993 (m-80) cc_final: 0.5183 (m-80) REVERT: D 215 ASP cc_start: 0.6134 (m-30) cc_final: 0.4180 (t0) REVERT: D 245 PHE cc_start: 0.6669 (t80) cc_final: 0.6384 (t80) REVERT: D 258 MET cc_start: 0.4591 (ptp) cc_final: 0.1072 (tmm) REVERT: D 265 GLU cc_start: 0.4575 (mt-10) cc_final: 0.3548 (tp30) REVERT: D 312 ILE cc_start: 0.2989 (OUTLIER) cc_final: 0.2414 (tt) REVERT: D 318 MET cc_start: 0.5324 (ptt) cc_final: 0.5069 (ppp) REVERT: D 630 MET cc_start: 0.4435 (mmp) cc_final: 0.3864 (mtt) REVERT: D 775 MET cc_start: 0.5270 (mmt) cc_final: 0.4558 (mmt) REVERT: D 845 ARG cc_start: 0.4459 (mtp-110) cc_final: 0.3981 (mpt180) REVERT: D 935 MET cc_start: 0.6860 (ttt) cc_final: 0.6585 (ttp) REVERT: D 970 MET cc_start: 0.7004 (mmm) cc_final: 0.6766 (mmm) REVERT: D 1002 MET cc_start: 0.6221 (ppp) cc_final: 0.5940 (mpp) REVERT: D 1007 ILE cc_start: 0.4906 (mm) cc_final: 0.4432 (mm) REVERT: D 1010 VAL cc_start: 0.5884 (p) cc_final: 0.5642 (p) REVERT: D 1053 LEU cc_start: 0.6363 (tp) cc_final: 0.5677 (mt) REVERT: B 200 ILE cc_start: 0.3712 (mt) cc_final: 0.3299 (tt) REVERT: B 226 TYR cc_start: 0.3916 (m-80) cc_final: 0.3286 (m-80) REVERT: B 318 MET cc_start: 0.6257 (mpp) cc_final: 0.5823 (mpp) REVERT: B 321 MET cc_start: 0.6739 (mmt) cc_final: 0.5958 (mmt) REVERT: B 337 LYS cc_start: 0.6468 (tppt) cc_final: 0.6206 (tppt) REVERT: B 476 ASN cc_start: 0.6606 (m-40) cc_final: 0.6343 (m-40) REVERT: B 514 MET cc_start: 0.6703 (ttt) cc_final: 0.6328 (ttt) REVERT: B 557 TYR cc_start: 0.5164 (m-80) cc_final: 0.4871 (m-80) REVERT: B 588 MET cc_start: 0.7326 (ptp) cc_final: 0.7089 (ptp) REVERT: B 599 MET cc_start: 0.6519 (ptm) cc_final: 0.6219 (ptm) REVERT: B 612 MET cc_start: 0.8127 (tpp) cc_final: 0.7869 (tpt) REVERT: B 775 MET cc_start: 0.5991 (mmm) cc_final: 0.5647 (mmp) REVERT: B 897 ILE cc_start: 0.7528 (mt) cc_final: 0.7323 (mt) REVERT: B 903 TRP cc_start: 0.5701 (m100) cc_final: 0.5065 (m100) REVERT: B 935 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.5835 (mmm) REVERT: B 1002 MET cc_start: 0.5140 (mmt) cc_final: 0.4800 (pmm) REVERT: B 1045 MET cc_start: 0.4563 (ptt) cc_final: 0.4269 (ptp) REVERT: B 1075 ASN cc_start: 0.4581 (OUTLIER) cc_final: 0.4376 (t0) REVERT: B 1142 ILE cc_start: 0.7632 (mt) cc_final: 0.7238 (mt) REVERT: B 1146 MET cc_start: 0.5578 (mmm) cc_final: 0.4108 (ppp) REVERT: C 324 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.5054 (tpt) REVERT: C 412 MET cc_start: 0.5622 (mpp) cc_final: 0.5084 (ptp) REVERT: C 490 TYR cc_start: 0.5861 (t80) cc_final: 0.4881 (t80) REVERT: C 491 ASN cc_start: 0.5646 (m-40) cc_final: 0.4854 (m-40) REVERT: C 494 ARG cc_start: 0.5948 (ptt180) cc_final: 0.5701 (tpt-90) REVERT: C 743 MET cc_start: 0.5906 (tpp) cc_final: 0.5664 (tmm) REVERT: C 835 ILE cc_start: 0.6845 (mm) cc_final: 0.6217 (pt) REVERT: C 897 ILE cc_start: 0.6752 (mt) cc_final: 0.6384 (mt) REVERT: C 970 MET cc_start: 0.6888 (mmp) cc_final: 0.6621 (mmm) REVERT: C 983 LEU cc_start: 0.7611 (mt) cc_final: 0.7310 (mp) REVERT: C 996 ASP cc_start: 0.6014 (t70) cc_final: 0.5668 (t0) REVERT: C 1146 MET cc_start: 0.0782 (mmm) cc_final: 0.0434 (mmm) outliers start: 69 outliers final: 22 residues processed: 599 average time/residue: 0.1997 time to fit residues: 194.7789 Evaluate side-chains 440 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 413 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 1084 CYS 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 648 HIS 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 1075 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1000 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 189 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS A 550 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN A 853 GLN A 863 ASN ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 525 HIS D 550 GLN D 667 GLN D 738 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D1094 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 408 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** B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 HIS C 190 HIS C 196 HIS C 224 ASN C 230 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 842 ASN C1050 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149611 restraints weight = 47062.702| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.04 r_work: 0.3691 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.9597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32544 Z= 0.136 Angle : 0.638 11.860 44116 Z= 0.330 Chirality : 0.041 0.178 5144 Planarity : 0.005 0.082 5616 Dihedral : 4.957 25.585 4440 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.70 % Allowed : 12.90 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.12), residues: 4108 helix: -1.11 (0.10), residues: 2492 sheet: 3.86 (0.62), residues: 40 loop : -2.29 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 912 TYR 0.020 0.002 TYR A 487 PHE 0.034 0.002 PHE B 261 TRP 0.023 0.002 TRP B 247 HIS 0.009 0.001 HIS C 962 Details of bonding type rmsd covalent geometry : bond 0.00297 (32540) covalent geometry : angle 0.63787 (44108) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.62291 ( 8) hydrogen bonds : bond 0.03286 ( 1140) hydrogen bonds : angle 4.07928 ( 3276) *********************** 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 602 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 545 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6127 (ptp) cc_final: 0.5913 (ptp) REVERT: A 380 ARG cc_start: 0.6067 (mmm160) cc_final: 0.5866 (mmm160) REVERT: A 412 MET cc_start: 0.4464 (tpp) cc_final: 0.4041 (pmm) REVERT: A 428 GLN cc_start: 0.6432 (mp10) cc_final: 0.5797 (tp40) REVERT: A 529 VAL cc_start: 0.8392 (p) cc_final: 0.8159 (m) REVERT: A 616 ASP cc_start: 0.7383 (m-30) cc_final: 0.6990 (m-30) REVERT: A 721 ASN cc_start: 0.7660 (m-40) cc_final: 0.7450 (m-40) REVERT: A 844 MET cc_start: 0.6624 (mmt) cc_final: 0.6170 (ppp) REVERT: A 984 ASP cc_start: 0.7525 (t0) cc_final: 0.6912 (t0) REVERT: A 1020 MET cc_start: 0.8560 (mmm) cc_final: 0.8234 (mmm) REVERT: A 1131 MET cc_start: 0.4568 (ptm) cc_final: 0.4274 (ptp) REVERT: D 215 ASP cc_start: 0.6158 (m-30) cc_final: 0.4214 (t0) REVERT: D 292 ILE cc_start: 0.2813 (OUTLIER) cc_final: 0.1855 (tp) REVERT: D 338 MET cc_start: 0.1485 (tpp) cc_final: 0.1100 (mmt) REVERT: D 432 GLN cc_start: 0.2823 (tp40) cc_final: 0.2231 (tm-30) REVERT: D 443 MET cc_start: 0.7982 (mmp) cc_final: 0.7418 (mmm) REVERT: D 599 MET cc_start: 0.4648 (OUTLIER) cc_final: 0.2805 (tpp) REVERT: D 630 MET cc_start: 0.5333 (mmp) cc_final: 0.4723 (mtt) REVERT: D 638 ASN cc_start: 0.7498 (p0) cc_final: 0.6738 (p0) REVERT: D 678 LYS cc_start: 0.6347 (mmtm) cc_final: 0.5101 (tmtt) REVERT: D 845 ARG cc_start: 0.4917 (mtp-110) cc_final: 0.4259 (mpt180) REVERT: D 935 MET cc_start: 0.7649 (ttt) cc_final: 0.7391 (ttp) REVERT: D 1094 ASN cc_start: 0.6699 (OUTLIER) cc_final: 0.6354 (p0) REVERT: B 258 MET cc_start: 0.5079 (tmm) cc_final: 0.4869 (ttm) REVERT: B 314 ILE cc_start: 0.5503 (mm) cc_final: 0.5260 (mm) REVERT: B 321 MET cc_start: 0.6795 (mmt) cc_final: 0.6142 (mmt) REVERT: B 337 LYS cc_start: 0.6853 (tppt) cc_final: 0.6493 (tppt) REVERT: B 383 TRP cc_start: 0.4921 (m-90) cc_final: 0.4642 (m-90) REVERT: B 408 HIS cc_start: 0.6267 (m90) cc_final: 0.5985 (m90) REVERT: B 601 MET cc_start: 0.4827 (mmt) cc_final: 0.4386 (mtt) REVERT: B 612 MET cc_start: 0.8283 (tpp) cc_final: 0.7651 (tpt) REVERT: B 625 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7784 (mm-30) REVERT: B 779 GLU cc_start: 0.6909 (mp0) cc_final: 0.6390 (mt-10) REVERT: B 935 MET cc_start: 0.7556 (mpp) cc_final: 0.7132 (mmm) REVERT: B 1002 MET cc_start: 0.6286 (mmt) cc_final: 0.5653 (pmm) REVERT: B 1131 MET cc_start: 0.6943 (mmt) cc_final: 0.5773 (ptp) REVERT: B 1142 ILE cc_start: 0.7417 (mt) cc_final: 0.7086 (mt) REVERT: B 1146 MET cc_start: 0.5658 (mmm) cc_final: 0.4191 (ppp) REVERT: C 258 MET cc_start: 0.5819 (tmm) cc_final: 0.5279 (tmm) REVERT: C 324 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5387 (tpt) REVERT: C 368 LYS cc_start: 0.7064 (ttmt) cc_final: 0.6527 (ttpp) REVERT: C 383 TRP cc_start: 0.4665 (m100) cc_final: 0.4178 (m100) REVERT: C 491 ASN cc_start: 0.5911 (m-40) cc_final: 0.4871 (m-40) REVERT: C 656 ILE cc_start: 0.4888 (mt) cc_final: 0.4506 (mt) REVERT: C 912 ARG cc_start: 0.6220 (ttp-110) cc_final: 0.5971 (ttp-170) REVERT: C 982 GLU cc_start: 0.7681 (pt0) cc_final: 0.7459 (pm20) REVERT: C 996 ASP cc_start: 0.6676 (t70) cc_final: 0.6278 (t0) REVERT: C 1045 MET cc_start: 0.5365 (ptt) cc_final: 0.5153 (tpp) REVERT: C 1146 MET cc_start: 0.0935 (mmm) cc_final: 0.0366 (mmt) outliers start: 57 outliers final: 23 residues processed: 584 average time/residue: 0.1721 time to fit residues: 165.9518 Evaluate side-chains 452 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 425 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 992 THR Chi-restraints excluded: chain D residue 1084 CYS Chi-restraints excluded: chain D residue 1094 ASN Chi-restraints excluded: chain D residue 1119 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 1050 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 336 optimal weight: 0.4980 chunk 351 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 358 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 85 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.0020 chunk 223 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 246 GLN D 275 HIS ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS ** D 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS ** D1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS C 196 HIS C 230 HIS ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 HIS C 911 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148231 restraints weight = 46957.023| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.45 r_work: 0.3660 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 1.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 32544 Z= 0.109 Angle : 0.591 9.770 44116 Z= 0.303 Chirality : 0.040 0.176 5144 Planarity : 0.004 0.064 5616 Dihedral : 4.596 21.531 4440 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.97 % Allowed : 14.75 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.13), residues: 4108 helix: -0.54 (0.10), residues: 2448 sheet: 4.16 (0.64), residues: 40 loop : -2.00 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 728 TYR 0.027 0.001 TYR C 490 PHE 0.029 0.001 PHE B 261 TRP 0.023 0.001 TRP B1091 HIS 0.030 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00237 (32540) covalent geometry : angle 0.59087 (44108) SS BOND : bond 0.00440 ( 4) SS BOND : angle 1.38449 ( 8) hydrogen bonds : bond 0.03013 ( 1140) hydrogen bonds : angle 3.95587 ( 3276) *********************** 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 564 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 498 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.2637 (mmm) cc_final: 0.2376 (mmm) REVERT: A 380 ARG cc_start: 0.6573 (mmm160) cc_final: 0.6224 (mmm160) REVERT: A 428 GLN cc_start: 0.6584 (mp10) cc_final: 0.6055 (tp40) REVERT: A 616 ASP cc_start: 0.7557 (m-30) cc_final: 0.7153 (m-30) REVERT: A 836 VAL cc_start: 0.7585 (t) cc_final: 0.7317 (m) REVERT: A 844 MET cc_start: 0.6596 (mmt) cc_final: 0.6141 (ppp) REVERT: A 853 GLN cc_start: 0.5813 (tp-100) cc_final: 0.5316 (mp-120) REVERT: A 876 MET cc_start: 0.7331 (mtm) cc_final: 0.7105 (mtm) REVERT: A 982 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 984 ASP cc_start: 0.7782 (t0) cc_final: 0.6891 (t0) REVERT: A 988 THR cc_start: 0.7672 (t) cc_final: 0.7033 (t) REVERT: A 1045 MET cc_start: 0.6407 (mpp) cc_final: 0.6070 (mpp) REVERT: A 1131 MET cc_start: 0.5031 (ptm) cc_final: 0.4644 (ptp) REVERT: D 215 ASP cc_start: 0.6086 (m-30) cc_final: 0.4168 (t0) REVERT: D 245 PHE cc_start: 0.7308 (t80) cc_final: 0.6910 (t80) REVERT: D 292 ILE cc_start: 0.3455 (OUTLIER) cc_final: 0.2539 (tp) REVERT: D 295 GLN cc_start: 0.7127 (mp10) cc_final: 0.6904 (mm110) REVERT: D 432 GLN cc_start: 0.3800 (tp40) cc_final: 0.3431 (tm-30) REVERT: D 443 MET cc_start: 0.8088 (mmp) cc_final: 0.7748 (mmm) REVERT: D 562 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6338 (mt-10) REVERT: D 599 MET cc_start: 0.4944 (OUTLIER) cc_final: 0.1019 (tpp) REVERT: D 630 MET cc_start: 0.5497 (mmp) cc_final: 0.5043 (mtt) REVERT: D 678 LYS cc_start: 0.6519 (mmtm) cc_final: 0.5828 (tmtt) REVERT: D 775 MET cc_start: 0.5975 (mmt) cc_final: 0.5391 (mmt) REVERT: D 845 ARG cc_start: 0.4985 (mtp-110) cc_final: 0.4259 (mpt180) REVERT: D 935 MET cc_start: 0.7742 (ttt) cc_final: 0.7531 (ttp) REVERT: D 1131 MET cc_start: 0.5104 (ttt) cc_final: 0.4452 (tpt) REVERT: B 208 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4661 (ptp-110) REVERT: B 258 MET cc_start: 0.5309 (tmm) cc_final: 0.5052 (ttm) REVERT: B 314 ILE cc_start: 0.5688 (mm) cc_final: 0.4929 (mp) REVERT: B 318 MET cc_start: 0.6503 (mpp) cc_final: 0.6094 (mpp) REVERT: B 321 MET cc_start: 0.6661 (mmt) cc_final: 0.6027 (mmt) REVERT: B 383 TRP cc_start: 0.5123 (m-90) cc_final: 0.4882 (m-10) REVERT: B 562 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7109 (mt-10) REVERT: B 601 MET cc_start: 0.5378 (mmt) cc_final: 0.5081 (mtt) REVERT: B 625 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 779 GLU cc_start: 0.6883 (mp0) cc_final: 0.6499 (mt-10) REVERT: B 882 GLN cc_start: 0.5826 (mp10) cc_final: 0.5484 (mp10) REVERT: B 935 MET cc_start: 0.7844 (mpp) cc_final: 0.7203 (mmm) REVERT: B 1002 MET cc_start: 0.6703 (mmt) cc_final: 0.6088 (ptp) REVERT: B 1032 GLU cc_start: 0.7814 (tp30) cc_final: 0.7606 (tp30) REVERT: B 1064 ARG cc_start: 0.7494 (tpt90) cc_final: 0.7139 (tmm160) REVERT: B 1131 MET cc_start: 0.7211 (mmt) cc_final: 0.6097 (ptp) REVERT: B 1142 ILE cc_start: 0.7420 (mt) cc_final: 0.7101 (mt) REVERT: B 1146 MET cc_start: 0.5622 (mmm) cc_final: 0.4217 (ppp) REVERT: C 324 MET cc_start: 0.6045 (mmp) cc_final: 0.5772 (tpp) REVERT: C 368 LYS cc_start: 0.7061 (ttmt) cc_final: 0.6598 (tttp) REVERT: C 376 LEU cc_start: 0.8077 (tp) cc_final: 0.7845 (tp) REVERT: C 383 TRP cc_start: 0.5022 (m100) cc_final: 0.4692 (m100) REVERT: C 487 TYR cc_start: 0.6460 (m-80) cc_final: 0.6170 (m-80) REVERT: C 588 MET cc_start: 0.4472 (mtt) cc_final: 0.4222 (mtt) REVERT: C 630 MET cc_start: 0.4899 (OUTLIER) cc_final: 0.4684 (tpp) REVERT: C 723 MET cc_start: 0.6085 (mmm) cc_final: 0.5801 (mmt) REVERT: C 996 ASP cc_start: 0.6852 (t70) cc_final: 0.6418 (t0) REVERT: C 1135 GLN cc_start: 0.5592 (OUTLIER) cc_final: 0.5371 (tp40) REVERT: C 1146 MET cc_start: 0.1082 (mmm) cc_final: 0.0610 (mmt) outliers start: 66 outliers final: 40 residues processed: 537 average time/residue: 0.1837 time to fit residues: 164.4848 Evaluate side-chains 469 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 424 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 774 MET 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 A residue 978 MET Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 445 CYS Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 890 ILE Chi-restraints excluded: chain D residue 962 HIS Chi-restraints excluded: chain D residue 986 VAL Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 429 THR 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 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain B residue 1037 ASN Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1135 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 32 optimal weight: 0.9980 chunk 169 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 268 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN D 190 HIS ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 GLN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS D 547 ASN D 550 GLN D 580 ASN D 746 ASN D 849 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1094 ASN ** D1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS B 456 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS B 911 GLN C 190 HIS ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C 540 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN C 911 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.183126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125854 restraints weight = 45564.665| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.06 r_work: 0.3405 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 1.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 32544 Z= 0.231 Angle : 0.857 13.522 44116 Z= 0.445 Chirality : 0.049 0.224 5144 Planarity : 0.006 0.130 5616 Dihedral : 5.951 28.250 4440 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.30 % Favored : 91.67 % Rotamer: Outliers : 2.44 % Allowed : 15.41 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.12), residues: 4108 helix: -1.02 (0.10), residues: 2426 sheet: 0.87 (0.75), residues: 55 loop : -2.30 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B1036 TYR 0.031 0.002 TYR B 450 PHE 0.033 0.002 PHE B 261 TRP 0.058 0.003 TRP C 383 HIS 0.013 0.002 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00520 (32540) covalent geometry : angle 0.85685 (44108) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.67930 ( 8) hydrogen bonds : bond 0.05409 ( 1140) hydrogen bonds : angle 4.69926 ( 3276) *********************** 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 759 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 677 time to evaluate : 1.348 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 175 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.4083 (mpp) REVERT: A 241 MET cc_start: 0.1230 (mmt) cc_final: 0.0653 (mtm) REVERT: A 275 HIS cc_start: 0.8103 (m90) cc_final: 0.7785 (m-70) REVERT: A 428 GLN cc_start: 0.6947 (mp10) cc_final: 0.6388 (tp40) REVERT: A 450 TYR cc_start: 0.7976 (m-10) cc_final: 0.7743 (m-10) REVERT: A 458 ARG cc_start: 0.8640 (tpt-90) cc_final: 0.8415 (ttp-170) REVERT: A 578 ASP cc_start: 0.8313 (m-30) cc_final: 0.7352 (t0) REVERT: A 593 HIS cc_start: 0.8493 (t-90) cc_final: 0.8121 (m90) REVERT: A 620 TYR cc_start: 0.8587 (t80) cc_final: 0.8326 (t80) REVERT: A 646 ASP cc_start: 0.7989 (p0) cc_final: 0.6820 (m-30) REVERT: A 730 GLU cc_start: 0.8731 (pt0) cc_final: 0.8487 (pt0) REVERT: A 844 MET cc_start: 0.7140 (mmt) cc_final: 0.6674 (ppp) REVERT: A 849 GLN cc_start: 0.7299 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 984 ASP cc_start: 0.8339 (t0) cc_final: 0.7667 (t0) REVERT: A 992 THR cc_start: 0.8875 (t) cc_final: 0.8572 (p) REVERT: A 1015 MET cc_start: 0.8659 (mmp) cc_final: 0.8453 (mmm) REVERT: A 1032 GLU cc_start: 0.8040 (tp30) cc_final: 0.7717 (tp30) REVERT: A 1096 PHE cc_start: 0.8500 (m-80) cc_final: 0.7935 (m-80) REVERT: A 1131 MET cc_start: 0.4927 (ptm) cc_final: 0.4558 (ptp) REVERT: D 175 MET cc_start: 0.5673 (ptp) cc_final: 0.5075 (ptp) REVERT: D 245 PHE cc_start: 0.7434 (t80) cc_final: 0.7055 (t80) REVERT: D 338 MET cc_start: 0.2950 (tpp) cc_final: 0.1274 (mmt) REVERT: D 432 GLN cc_start: 0.4356 (tp-100) cc_final: 0.3795 (tm-30) REVERT: D 461 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6124 (mm-30) REVERT: D 470 ILE cc_start: 0.7619 (mm) cc_final: 0.7142 (mm) REVERT: D 593 HIS cc_start: 0.8621 (t-90) cc_final: 0.8253 (m90) REVERT: D 625 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7907 (mt-10) REVERT: D 678 LYS cc_start: 0.7708 (mmtm) cc_final: 0.7202 (tmtt) REVERT: D 845 ARG cc_start: 0.5954 (mtp-110) cc_final: 0.4840 (mtt-85) REVERT: D 992 THR cc_start: 0.8642 (t) cc_final: 0.8429 (t) REVERT: D 1032 GLU cc_start: 0.8280 (tp30) cc_final: 0.7695 (tp30) REVERT: D 1131 MET cc_start: 0.5412 (ttt) cc_final: 0.4804 (tpt) REVERT: B 297 HIS cc_start: 0.7769 (m170) cc_final: 0.7370 (m170) REVERT: B 321 MET cc_start: 0.6553 (mmt) cc_final: 0.6023 (mmt) REVERT: B 355 TYR cc_start: 0.7032 (t80) cc_final: 0.6821 (t80) REVERT: B 593 HIS cc_start: 0.8677 (t-90) cc_final: 0.8390 (m-70) REVERT: B 677 LYS cc_start: 0.7889 (mppt) cc_final: 0.7272 (mtpt) REVERT: B 760 TYR cc_start: 0.7863 (t80) cc_final: 0.6994 (t80) REVERT: B 984 ASP cc_start: 0.8394 (t0) cc_final: 0.8105 (t0) REVERT: B 997 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7700 (mt0) REVERT: B 1015 MET cc_start: 0.8505 (tpt) cc_final: 0.8231 (tpt) REVERT: B 1032 GLU cc_start: 0.8455 (tp30) cc_final: 0.7992 (tp30) REVERT: B 1048 VAL cc_start: 0.8404 (p) cc_final: 0.8122 (m) REVERT: B 1064 ARG cc_start: 0.7924 (tpt90) cc_final: 0.7207 (ptm160) REVERT: B 1146 MET cc_start: 0.6080 (mmm) cc_final: 0.4685 (ppp) REVERT: C 154 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 237 SER cc_start: 0.7969 (m) cc_final: 0.7196 (p) REVERT: C 275 HIS cc_start: 0.8792 (m-70) cc_final: 0.8587 (m-70) REVERT: C 369 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7861 (tm-30) REVERT: C 388 LEU cc_start: 0.8090 (tp) cc_final: 0.7808 (tp) REVERT: C 494 ARG cc_start: 0.8407 (tpt-90) cc_final: 0.8207 (tmm-80) REVERT: C 562 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8345 (mt-10) REVERT: C 625 GLU cc_start: 0.7965 (tt0) cc_final: 0.7609 (pt0) REVERT: C 635 GLU cc_start: 0.8449 (tp30) cc_final: 0.8164 (tt0) REVERT: C 681 LYS cc_start: 0.8416 (ptpp) cc_final: 0.7599 (tppt) REVERT: C 760 TYR cc_start: 0.8001 (t80) cc_final: 0.7757 (t80) REVERT: C 820 GLU cc_start: 0.6815 (tt0) cc_final: 0.6603 (tt0) REVERT: C 829 LEU cc_start: 0.7891 (tp) cc_final: 0.7686 (tp) REVERT: C 844 MET cc_start: 0.6995 (tmm) cc_final: 0.6129 (mmt) REVERT: C 905 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8258 (tpt90) REVERT: C 996 ASP cc_start: 0.8278 (t70) cc_final: 0.7779 (t0) REVERT: C 1045 MET cc_start: 0.7694 (ptt) cc_final: 0.7175 (ttp) REVERT: C 1048 VAL cc_start: 0.8399 (p) cc_final: 0.8104 (m) REVERT: C 1135 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5542 (mm-40) REVERT: C 1146 MET cc_start: 0.1309 (mmm) cc_final: 0.1024 (mmt) outliers start: 82 outliers final: 25 residues processed: 723 average time/residue: 0.1907 time to fit residues: 222.4580 Evaluate side-chains 477 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 449 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 978 MET Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 963 LEU 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 429 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 856 HIS Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 540 HIS Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain C residue 905 ARG Chi-restraints excluded: chain C residue 1054 GLU Chi-restraints excluded: chain C residue 1135 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 212 optimal weight: 30.0000 chunk 375 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 206 optimal weight: 50.0000 chunk 245 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 296 GLN A 426 ASN A 491 ASN A 495 GLN A 540 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 856 HIS A 882 GLN ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A 997 GLN D 342 HIS ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 HIS D 495 GLN D 777 ASN D 962 HIS ** D1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 387 HIS ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS B 543 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 534 ASN C 565 HIS C 580 ASN C 590 ASN C 608 ASN C 734 HIS C 911 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119857 restraints weight = 45343.569| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.01 r_work: 0.3390 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 1.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32544 Z= 0.117 Angle : 0.642 11.957 44116 Z= 0.328 Chirality : 0.042 0.263 5144 Planarity : 0.004 0.065 5616 Dihedral : 4.869 20.943 4440 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.46 % Allowed : 18.36 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.13), residues: 4108 helix: -0.32 (0.10), residues: 2464 sheet: 1.39 (0.76), residues: 55 loop : -2.10 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 821 TYR 0.024 0.001 TYR C 620 PHE 0.027 0.001 PHE B 261 TRP 0.023 0.001 TRP B1091 HIS 0.020 0.001 HIS C 540 Details of bonding type rmsd covalent geometry : bond 0.00259 (32540) covalent geometry : angle 0.64214 (44108) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.99646 ( 8) hydrogen bonds : bond 0.03297 ( 1140) hydrogen bonds : angle 3.98780 ( 3276) *********************** 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 611 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 562 time to evaluate : 1.286 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 175 MET cc_start: 0.3995 (mtm) cc_final: 0.3637 (mpp) REVERT: A 196 HIS cc_start: 0.4054 (m90) cc_final: 0.3533 (m90) REVERT: A 227 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.4230 (t80) REVERT: A 275 HIS cc_start: 0.8249 (m90) cc_final: 0.7709 (m-70) REVERT: A 278 ASP cc_start: 0.6269 (t0) cc_final: 0.6038 (t0) REVERT: A 324 MET cc_start: 0.6416 (mmp) cc_final: 0.6204 (mmt) REVERT: A 417 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7234 (tt) REVERT: A 428 GLN cc_start: 0.7060 (mp10) cc_final: 0.6608 (tp40) REVERT: A 450 TYR cc_start: 0.7798 (m-10) cc_final: 0.7386 (m-10) REVERT: A 593 HIS cc_start: 0.8617 (t-90) cc_final: 0.8269 (m90) REVERT: A 616 ASP cc_start: 0.8380 (m-30) cc_final: 0.8141 (m-30) REVERT: A 620 TYR cc_start: 0.8696 (t80) cc_final: 0.8450 (t80) REVERT: A 646 ASP cc_start: 0.8128 (p0) cc_final: 0.6933 (m-30) REVERT: A 677 LYS cc_start: 0.6899 (mtpt) cc_final: 0.6618 (ttpt) REVERT: A 730 GLU cc_start: 0.8771 (pt0) cc_final: 0.8492 (pt0) REVERT: A 853 GLN cc_start: 0.6130 (tp-100) cc_final: 0.5681 (tm-30) REVERT: A 984 ASP cc_start: 0.8218 (t0) cc_final: 0.7613 (t0) REVERT: A 1032 GLU cc_start: 0.8164 (tp30) cc_final: 0.7879 (tp30) REVERT: A 1096 PHE cc_start: 0.8349 (m-80) cc_final: 0.8107 (m-80) REVERT: A 1131 MET cc_start: 0.5235 (ptm) cc_final: 0.4852 (ptp) REVERT: D 175 MET cc_start: 0.5623 (ptp) cc_final: 0.5191 (ptm) REVERT: D 241 MET cc_start: 0.6243 (ppp) cc_final: 0.5797 (ptm) REVERT: D 318 MET cc_start: 0.7570 (ttp) cc_final: 0.7217 (ptm) REVERT: D 432 GLN cc_start: 0.5387 (tp-100) cc_final: 0.4841 (tm-30) REVERT: D 457 ILE cc_start: 0.6995 (mt) cc_final: 0.6621 (mt) REVERT: D 470 ILE cc_start: 0.7889 (mm) cc_final: 0.7508 (mm) REVERT: D 590 ASN cc_start: 0.8266 (t0) cc_final: 0.8011 (t0) REVERT: D 593 HIS cc_start: 0.8558 (t-90) cc_final: 0.8230 (m90) REVERT: D 611 ASP cc_start: 0.8698 (m-30) cc_final: 0.8463 (m-30) REVERT: D 677 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.5796 (mtpp) REVERT: D 723 MET cc_start: 0.8531 (mtt) cc_final: 0.8311 (mtt) REVERT: D 748 TYR cc_start: 0.7093 (p90) cc_final: 0.6710 (p90) REVERT: D 842 ASN cc_start: 0.6676 (t0) cc_final: 0.6464 (t0) REVERT: D 845 ARG cc_start: 0.6093 (mtp-110) cc_final: 0.5037 (mtt-85) REVERT: D 989 TYR cc_start: 0.8546 (m-80) cc_final: 0.8086 (m-80) REVERT: D 1032 GLU cc_start: 0.8254 (tp30) cc_final: 0.7703 (tp30) REVERT: B 297 HIS cc_start: 0.7969 (m170) cc_final: 0.7716 (m170) REVERT: B 321 MET cc_start: 0.6435 (mmt) cc_final: 0.5992 (mmt) REVERT: B 355 TYR cc_start: 0.6893 (t80) cc_final: 0.6667 (t80) REVERT: B 384 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8715 (mttt) REVERT: B 458 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8390 (mmp80) REVERT: B 593 HIS cc_start: 0.8821 (t-90) cc_final: 0.8468 (m90) REVERT: B 622 LYS cc_start: 0.8611 (tptp) cc_final: 0.8249 (mttm) REVERT: B 677 LYS cc_start: 0.7702 (mppt) cc_final: 0.7392 (mtpt) REVERT: B 730 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8337 (pt0) REVERT: B 760 TYR cc_start: 0.7864 (t80) cc_final: 0.7121 (t80) REVERT: B 922 MET cc_start: 0.8969 (mtt) cc_final: 0.8731 (mtt) REVERT: B 970 MET cc_start: 0.8854 (tpt) cc_final: 0.8602 (tpp) REVERT: B 984 ASP cc_start: 0.8263 (t0) cc_final: 0.7745 (t0) REVERT: B 989 TYR cc_start: 0.8558 (m-80) cc_final: 0.8225 (m-80) REVERT: B 997 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7815 (mt0) REVERT: B 1032 GLU cc_start: 0.8471 (tp30) cc_final: 0.7734 (tp30) REVERT: B 1064 ARG cc_start: 0.8130 (tpt90) cc_final: 0.7863 (tmm-80) REVERT: B 1146 MET cc_start: 0.5591 (mmm) cc_final: 0.4370 (ppp) REVERT: C 237 SER cc_start: 0.8117 (m) cc_final: 0.7367 (p) REVERT: C 450 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6869 (m-10) REVERT: C 578 ASP cc_start: 0.8524 (m-30) cc_final: 0.8198 (t0) REVERT: C 635 GLU cc_start: 0.8339 (tp30) cc_final: 0.7994 (tt0) REVERT: C 681 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8148 (tppt) REVERT: C 760 TYR cc_start: 0.8231 (t80) cc_final: 0.8018 (t80) REVERT: C 844 MET cc_start: 0.7086 (tmm) cc_final: 0.6599 (mmt) REVERT: C 996 ASP cc_start: 0.8259 (t70) cc_final: 0.7800 (t0) REVERT: C 1032 GLU cc_start: 0.8180 (tp30) cc_final: 0.7706 (tp30) REVERT: C 1045 MET cc_start: 0.7740 (ptt) cc_final: 0.7351 (ttp) REVERT: C 1048 VAL cc_start: 0.8428 (p) cc_final: 0.8112 (m) REVERT: C 1146 MET cc_start: 0.1177 (mmm) cc_final: 0.0919 (mmt) outliers start: 49 outliers final: 23 residues processed: 591 average time/residue: 0.1780 time to fit residues: 174.6480 Evaluate side-chains 487 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 460 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 417 LEU 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 539 LEU Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 659 MET Chi-restraints excluded: chain D residue 677 LYS 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 429 THR Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 842 ASN Chi-restraints excluded: chain C residue 1049 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 278 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 276 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 209 optimal weight: 40.0000 chunk 240 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 409 optimal weight: 5.9990 chunk 211 optimal weight: 30.0000 chunk 372 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 203 HIS A 224 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 777 ASN ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN D 267 ASN D 296 GLN D 309 GLN D 336 GLN D 349 HIS D 476 ASN D 525 HIS D 547 ASN ** D1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS B 235 ASN B 449 HIS B 540 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 HIS B 911 GLN B1135 GLN C 186 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 462 ASN C 540 HIS C 570 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 ASN C 777 ASN C 911 GLN C1050 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100065 restraints weight = 44498.518| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.78 r_work: 0.3050 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 1.9379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 32544 Z= 0.227 Angle : 0.812 14.974 44116 Z= 0.412 Chirality : 0.048 0.272 5144 Planarity : 0.005 0.069 5616 Dihedral : 5.608 32.584 4440 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.26 % Allowed : 19.07 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.12), residues: 4108 helix: -0.70 (0.10), residues: 2466 sheet: 1.30 (0.72), residues: 55 loop : -2.17 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1064 TYR 0.024 0.002 TYR C 770 PHE 0.038 0.002 PHE B 261 TRP 0.034 0.003 TRP C 383 HIS 0.016 0.002 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00528 (32540) covalent geometry : angle 0.81155 (44108) SS BOND : bond 0.00324 ( 4) SS BOND : angle 0.53086 ( 8) hydrogen bonds : bond 0.04831 ( 1140) hydrogen bonds : angle 4.40301 ( 3276) *********************** 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 612 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 536 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.5104 (mtm) cc_final: 0.4675 (mpp) REVERT: A 318 MET cc_start: 0.6682 (mmm) cc_final: 0.6154 (mmm) REVERT: A 384 LYS cc_start: 0.8967 (tptp) cc_final: 0.8766 (ttmt) REVERT: A 390 ILE cc_start: 0.8710 (mt) cc_final: 0.8467 (pt) REVERT: A 554 MET cc_start: 0.8941 (ttp) cc_final: 0.8601 (ttp) REVERT: A 593 HIS cc_start: 0.8660 (t-90) cc_final: 0.8257 (m90) REVERT: A 625 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8220 (mt-10) REVERT: A 864 LEU cc_start: 0.8205 (mp) cc_final: 0.7854 (tp) REVERT: A 1032 GLU cc_start: 0.7993 (tp30) cc_final: 0.7688 (tp30) REVERT: A 1063 GLN cc_start: 0.8425 (tp40) cc_final: 0.8213 (tp40) REVERT: A 1096 PHE cc_start: 0.8575 (m-80) cc_final: 0.8315 (m-80) REVERT: A 1131 MET cc_start: 0.4590 (ptm) cc_final: 0.4158 (ptp) REVERT: D 175 MET cc_start: 0.6414 (ptp) cc_final: 0.5996 (ptm) REVERT: D 206 CYS cc_start: 0.7034 (m) cc_final: 0.5977 (t) REVERT: D 223 ASN cc_start: 0.8813 (m-40) cc_final: 0.8584 (m110) REVERT: D 450 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6094 (m-10) REVERT: D 458 ARG cc_start: 0.8637 (ttt90) cc_final: 0.8275 (ttp80) REVERT: D 593 HIS cc_start: 0.8803 (t-90) cc_final: 0.8453 (m90) REVERT: D 748 TYR cc_start: 0.8347 (p90) cc_final: 0.8113 (p90) REVERT: D 842 ASN cc_start: 0.7546 (t0) cc_final: 0.7335 (t0) REVERT: D 845 ARG cc_start: 0.6414 (mtp-110) cc_final: 0.5485 (mtt-85) REVERT: D 935 MET cc_start: 0.8545 (ttp) cc_final: 0.8282 (mtp) REVERT: D 970 MET cc_start: 0.8937 (tpt) cc_final: 0.8735 (tpp) REVERT: D 1032 GLU cc_start: 0.8181 (tp30) cc_final: 0.7740 (tp30) REVERT: D 1054 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: D 1131 MET cc_start: 0.5484 (ttt) cc_final: 0.4925 (tpt) REVERT: D 1140 ARG cc_start: 0.6661 (ttp-110) cc_final: 0.5743 (tpp-160) REVERT: B 156 LYS cc_start: 0.6243 (mtpm) cc_final: 0.5975 (mppt) REVERT: B 219 ARG cc_start: 0.8529 (mtm180) cc_final: 0.8189 (mtt90) REVERT: B 321 MET cc_start: 0.6565 (mmt) cc_final: 0.6252 (mmt) REVERT: B 355 TYR cc_start: 0.7390 (t80) cc_final: 0.6931 (t80) REVERT: B 369 GLU cc_start: 0.7910 (pt0) cc_final: 0.7298 (pp20) REVERT: B 501 LYS cc_start: 0.7390 (mttm) cc_final: 0.7135 (mtmt) REVERT: B 523 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8340 (mm-40) REVERT: B 593 HIS cc_start: 0.8788 (t-90) cc_final: 0.8519 (m90) REVERT: B 620 TYR cc_start: 0.8747 (t80) cc_final: 0.8464 (t80) REVERT: B 677 LYS cc_start: 0.7992 (mppt) cc_final: 0.7668 (ttpp) REVERT: B 730 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8507 (pt0) REVERT: B 746 ASN cc_start: 0.8537 (t0) cc_final: 0.8328 (m-40) REVERT: B 997 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7637 (mt0) REVERT: B 1032 GLU cc_start: 0.8401 (tp30) cc_final: 0.7808 (tp30) REVERT: B 1068 MET cc_start: 0.8008 (pmm) cc_final: 0.7785 (pmm) REVERT: B 1086 PHE cc_start: 0.7779 (t80) cc_final: 0.7460 (t80) REVERT: B 1146 MET cc_start: 0.5835 (mmm) cc_final: 0.4629 (ppp) REVERT: C 154 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7907 (tp30) REVERT: C 219 ARG cc_start: 0.8899 (mtm180) cc_final: 0.8292 (mtm-85) REVERT: C 345 SER cc_start: 0.8547 (t) cc_final: 0.8244 (p) REVERT: C 362 ASP cc_start: 0.7225 (t0) cc_final: 0.7012 (t0) REVERT: C 443 MET cc_start: 0.8825 (mmm) cc_final: 0.8613 (mmm) REVERT: C 458 ARG cc_start: 0.8352 (ttt90) cc_final: 0.7893 (ttp-110) REVERT: C 472 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 635 GLU cc_start: 0.8334 (tp30) cc_final: 0.8100 (tt0) REVERT: C 746 ASN cc_start: 0.8288 (t0) cc_final: 0.7856 (m-40) REVERT: C 844 MET cc_start: 0.7341 (tmm) cc_final: 0.6989 (mmt) REVERT: C 884 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7770 (p0) REVERT: C 1048 VAL cc_start: 0.8485 (p) cc_final: 0.8206 (p) REVERT: C 1064 ARG cc_start: 0.8336 (tmm-80) cc_final: 0.7779 (ppt170) REVERT: C 1146 MET cc_start: 0.2512 (mmm) cc_final: 0.2194 (mmt) outliers start: 76 outliers final: 32 residues processed: 586 average time/residue: 0.1923 time to fit residues: 184.9795 Evaluate side-chains 458 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 421 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 675 ASN Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 1054 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 523 GLN Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 1033 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 884 ASP Chi-restraints excluded: chain C residue 936 VAL Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 1054 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 209 optimal weight: 3.9990 chunk 272 optimal weight: 0.4980 chunk 356 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 245 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 284 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 309 GLN A 408 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS A 911 GLN ** A 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 ASN B 891 HIS C 157 GLN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 408 HIS C 432 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 GLN C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.162040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106675 restraints weight = 44199.366| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.65 r_work: 0.3212 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 1.9598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32544 Z= 0.115 Angle : 0.636 11.809 44116 Z= 0.320 Chirality : 0.041 0.246 5144 Planarity : 0.004 0.065 5616 Dihedral : 4.811 21.023 4440 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.07 % Allowed : 20.68 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.13), residues: 4108 helix: -0.22 (0.10), residues: 2545 sheet: 2.01 (0.75), residues: 55 loop : -2.06 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 208 TYR 0.017 0.001 TYR C 490 PHE 0.017 0.001 PHE B 261 TRP 0.015 0.001 TRP B 247 HIS 0.014 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00260 (32540) covalent geometry : angle 0.63617 (44108) SS BOND : bond 0.00345 ( 4) SS BOND : angle 0.77904 ( 8) hydrogen bonds : bond 0.03053 ( 1140) hydrogen bonds : angle 3.88406 ( 3276) *********************** 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 536 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 500 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 TYR cc_start: 0.7710 (t80) cc_final: 0.7344 (t80) REVERT: A 227 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5171 (t80) REVERT: A 391 ARG cc_start: 0.6844 (ttp80) cc_final: 0.6299 (ptp90) REVERT: A 501 LYS cc_start: 0.8290 (mttm) cc_final: 0.8067 (mtmt) REVERT: A 593 HIS cc_start: 0.8696 (t-90) cc_final: 0.8376 (m-70) REVERT: A 616 ASP cc_start: 0.8599 (m-30) cc_final: 0.8296 (m-30) REVERT: A 625 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8240 (mt-10) REVERT: A 641 MET cc_start: 0.8922 (mtp) cc_final: 0.8655 (mtp) REVERT: A 853 GLN cc_start: 0.6588 (tp-100) cc_final: 0.6256 (tm-30) REVERT: A 864 LEU cc_start: 0.8222 (mp) cc_final: 0.7784 (tp) REVERT: A 984 ASP cc_start: 0.8325 (t0) cc_final: 0.7741 (t0) REVERT: A 989 TYR cc_start: 0.8557 (m-80) cc_final: 0.8119 (m-80) REVERT: A 1032 GLU cc_start: 0.8328 (tp30) cc_final: 0.8105 (tp30) REVERT: A 1063 GLN cc_start: 0.8437 (tp40) cc_final: 0.8167 (tp40) REVERT: A 1131 MET cc_start: 0.5138 (ptm) cc_final: 0.4905 (ptp) REVERT: D 175 MET cc_start: 0.6364 (ptp) cc_final: 0.6045 (ptm) REVERT: D 324 MET cc_start: 0.7418 (mmp) cc_final: 0.7087 (tpp) REVERT: D 422 GLU cc_start: 0.7973 (tp30) cc_final: 0.7681 (tp30) REVERT: D 450 TYR cc_start: 0.7293 (m-10) cc_final: 0.7073 (m-10) REVERT: D 458 ARG cc_start: 0.8670 (ttt90) cc_final: 0.8430 (ttp80) REVERT: D 578 ASP cc_start: 0.8185 (m-30) cc_final: 0.7827 (t0) REVERT: D 593 HIS cc_start: 0.8634 (t-90) cc_final: 0.8413 (m-70) REVERT: D 723 MET cc_start: 0.8696 (mtt) cc_final: 0.8486 (mtp) REVERT: D 842 ASN cc_start: 0.7625 (t0) cc_final: 0.7184 (t0) REVERT: D 845 ARG cc_start: 0.6695 (mtp-110) cc_final: 0.5829 (mtt180) REVERT: D 1032 GLU cc_start: 0.8482 (tp30) cc_final: 0.7923 (tp30) REVERT: D 1054 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: D 1067 LYS cc_start: 0.7161 (tppt) cc_final: 0.6916 (mmtm) REVERT: D 1092 PHE cc_start: 0.7952 (m-80) cc_final: 0.7427 (t80) REVERT: D 1131 MET cc_start: 0.5879 (ttt) cc_final: 0.5261 (tpt) REVERT: D 1140 ARG cc_start: 0.6730 (ttp-110) cc_final: 0.5839 (tpp-160) REVERT: B 156 LYS cc_start: 0.6904 (mtpm) cc_final: 0.6578 (mppt) REVERT: B 219 ARG cc_start: 0.8364 (mtm180) cc_final: 0.8082 (mtt90) REVERT: B 257 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7316 (pt0) REVERT: B 324 MET cc_start: 0.7867 (mmt) cc_final: 0.7541 (mmp) REVERT: B 355 TYR cc_start: 0.7515 (t80) cc_final: 0.7152 (t80) REVERT: B 388 LEU cc_start: 0.8339 (mp) cc_final: 0.7893 (tp) REVERT: B 412 MET cc_start: 0.9105 (ptm) cc_final: 0.8807 (ptt) REVERT: B 501 LYS cc_start: 0.7556 (mttm) cc_final: 0.7296 (mtmt) REVERT: B 593 HIS cc_start: 0.8779 (t-90) cc_final: 0.8428 (m90) REVERT: B 760 TYR cc_start: 0.8372 (t80) cc_final: 0.7710 (t80) REVERT: B 970 MET cc_start: 0.8893 (tpt) cc_final: 0.8687 (tpp) REVERT: B 984 ASP cc_start: 0.8383 (t0) cc_final: 0.7871 (t0) REVERT: B 989 TYR cc_start: 0.8592 (m-80) cc_final: 0.8332 (m-80) REVERT: B 997 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7765 (mt0) REVERT: B 1032 GLU cc_start: 0.8633 (tp30) cc_final: 0.8129 (tp30) REVERT: B 1068 MET cc_start: 0.7884 (pmm) cc_final: 0.7667 (pmm) REVERT: B 1146 MET cc_start: 0.5686 (mmm) cc_final: 0.4522 (ppp) REVERT: C 154 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7871 (tp30) REVERT: C 219 ARG cc_start: 0.8780 (mtm180) cc_final: 0.8508 (mtm-85) REVERT: C 458 ARG cc_start: 0.8336 (ttt90) cc_final: 0.8093 (mpt180) REVERT: C 578 ASP cc_start: 0.8583 (m-30) cc_final: 0.8320 (t0) REVERT: C 746 ASN cc_start: 0.8076 (t0) cc_final: 0.7828 (m-40) REVERT: C 842 ASN cc_start: 0.7928 (m-40) cc_final: 0.7265 (t0) REVERT: C 844 MET cc_start: 0.7299 (tmm) cc_final: 0.7028 (mmt) REVERT: C 872 SER cc_start: 0.8850 (m) cc_final: 0.8283 (p) REVERT: C 982 GLU cc_start: 0.8280 (pm20) cc_final: 0.7911 (pt0) REVERT: C 989 TYR cc_start: 0.8495 (m-80) cc_final: 0.8092 (m-80) REVERT: C 996 ASP cc_start: 0.8339 (t0) cc_final: 0.7953 (t0) REVERT: C 1032 GLU cc_start: 0.8304 (tp30) cc_final: 0.8007 (tp30) REVERT: C 1048 VAL cc_start: 0.8723 (p) cc_final: 0.8461 (m) REVERT: C 1064 ARG cc_start: 0.8419 (tmm-80) cc_final: 0.8049 (ptt90) REVERT: C 1146 MET cc_start: 0.2546 (mmm) cc_final: 0.2178 (mmt) outliers start: 36 outliers final: 17 residues processed: 521 average time/residue: 0.1822 time to fit residues: 155.9619 Evaluate side-chains 453 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 434 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 1054 GLU Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 540 HIS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 348 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 0.0270 chunk 290 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 chunk 248 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 127 optimal weight: 0.0040 chunk 327 optimal weight: 0.8980 overall best weight: 0.4650 ------------------------------------------------------------------------------- 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 349 HIS A 426 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 ASN D 574 GLN ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1134 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 230 HIS ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.162266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107597 restraints weight = 44544.132| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.67 r_work: 0.3225 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 1.9738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32544 Z= 0.107 Angle : 0.616 13.066 44116 Z= 0.307 Chirality : 0.040 0.231 5144 Planarity : 0.004 0.067 5616 Dihedral : 4.457 20.585 4440 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.80 % Allowed : 21.51 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.13), residues: 4108 helix: 0.12 (0.11), residues: 2528 sheet: 2.26 (0.74), residues: 55 loop : -1.93 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 208 TYR 0.025 0.001 TYR A 262 PHE 0.017 0.001 PHE C 245 TRP 0.015 0.001 TRP B 247 HIS 0.007 0.001 HIS C 856 Details of bonding type rmsd covalent geometry : bond 0.00241 (32540) covalent geometry : angle 0.61617 (44108) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.67011 ( 8) hydrogen bonds : bond 0.02898 ( 1140) hydrogen bonds : angle 3.73157 ( 3276) ********************** 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 498 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 471 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.4765 (mtm) cc_final: 0.4334 (mpp) REVERT: A 220 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7625 (mtmt) REVERT: A 227 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5301 (t80) REVERT: A 501 LYS cc_start: 0.8250 (mttm) cc_final: 0.8002 (mtmt) REVERT: A 593 HIS cc_start: 0.8693 (t-90) cc_final: 0.8387 (m-70) REVERT: A 616 ASP cc_start: 0.8591 (m-30) cc_final: 0.8186 (m-30) REVERT: A 625 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8227 (mt-10) REVERT: A 853 GLN cc_start: 0.6595 (tp-100) cc_final: 0.6183 (tm-30) REVERT: A 864 LEU cc_start: 0.8197 (mp) cc_final: 0.7779 (tp) REVERT: A 984 ASP cc_start: 0.8358 (t0) cc_final: 0.7864 (t0) REVERT: A 989 TYR cc_start: 0.8562 (m-80) cc_final: 0.8021 (m-80) REVERT: A 1032 GLU cc_start: 0.8249 (tp30) cc_final: 0.7783 (tp30) REVERT: A 1131 MET cc_start: 0.5143 (ptm) cc_final: 0.4935 (ptp) REVERT: D 175 MET cc_start: 0.6369 (ptp) cc_final: 0.5953 (ptm) REVERT: D 324 MET cc_start: 0.7372 (mmp) cc_final: 0.7059 (tpp) REVERT: D 450 TYR cc_start: 0.8089 (m-10) cc_final: 0.7772 (m-10) REVERT: D 458 ARG cc_start: 0.8756 (ttt90) cc_final: 0.8523 (ttp80) REVERT: D 495 GLN cc_start: 0.8454 (tp40) cc_final: 0.8176 (tp40) REVERT: D 500 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7313 (mm-30) REVERT: D 578 ASP cc_start: 0.8134 (m-30) cc_final: 0.7850 (t0) REVERT: D 593 HIS cc_start: 0.8703 (t-90) cc_final: 0.8497 (m90) REVERT: D 723 MET cc_start: 0.8633 (mtt) cc_final: 0.8418 (mtp) REVERT: D 842 ASN cc_start: 0.7572 (t0) cc_final: 0.7204 (t0) REVERT: D 845 ARG cc_start: 0.6706 (mtp-110) cc_final: 0.5839 (mtt180) REVERT: D 912 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7639 (mtt-85) REVERT: D 1032 GLU cc_start: 0.8441 (tp30) cc_final: 0.7857 (tp30) REVERT: D 1054 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: D 1067 LYS cc_start: 0.7263 (tppt) cc_final: 0.7011 (mmtm) REVERT: D 1092 PHE cc_start: 0.8020 (m-80) cc_final: 0.7391 (t80) REVERT: D 1131 MET cc_start: 0.5953 (ttt) cc_final: 0.5389 (tpt) REVERT: D 1140 ARG cc_start: 0.6851 (ttp-110) cc_final: 0.5987 (tpp-160) REVERT: B 156 LYS cc_start: 0.6855 (mtpm) cc_final: 0.6595 (mppt) REVERT: B 219 ARG cc_start: 0.8372 (mtm180) cc_final: 0.8069 (mtt90) REVERT: B 257 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7299 (pt0) REVERT: B 355 TYR cc_start: 0.7508 (t80) cc_final: 0.7159 (t80) REVERT: B 369 GLU cc_start: 0.7590 (pt0) cc_final: 0.7201 (pp20) REVERT: B 388 LEU cc_start: 0.8316 (mp) cc_final: 0.7749 (tp) REVERT: B 501 LYS cc_start: 0.7590 (mttm) cc_final: 0.7311 (mtmt) REVERT: B 593 HIS cc_start: 0.8728 (t-90) cc_final: 0.8489 (m90) REVERT: B 760 TYR cc_start: 0.8361 (t80) cc_final: 0.7753 (t80) REVERT: B 872 SER cc_start: 0.8914 (m) cc_final: 0.8318 (p) REVERT: B 970 MET cc_start: 0.8852 (tpt) cc_final: 0.8651 (tpp) REVERT: B 997 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7887 (mt0) REVERT: B 1032 GLU cc_start: 0.8656 (tp30) cc_final: 0.8039 (tp30) REVERT: B 1068 MET cc_start: 0.7853 (pmm) cc_final: 0.7632 (pmm) REVERT: B 1131 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.5160 (tmm) REVERT: C 154 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7839 (tp30) REVERT: C 219 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8467 (mtm-85) REVERT: C 245 PHE cc_start: 0.7686 (m-10) cc_final: 0.7480 (m-10) REVERT: C 246 GLN cc_start: 0.7723 (mt0) cc_final: 0.7516 (mp10) REVERT: C 450 TYR cc_start: 0.8475 (m-10) cc_final: 0.7963 (m-80) REVERT: C 458 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8031 (ttp-170) REVERT: C 589 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: C 746 ASN cc_start: 0.8148 (t0) cc_final: 0.7926 (m-40) REVERT: C 842 ASN cc_start: 0.7984 (m-40) cc_final: 0.7341 (t0) REVERT: C 872 SER cc_start: 0.8873 (m) cc_final: 0.8294 (p) REVERT: C 982 GLU cc_start: 0.8182 (pm20) cc_final: 0.7883 (pt0) REVERT: C 996 ASP cc_start: 0.8267 (t0) cc_final: 0.7890 (t0) REVERT: C 1032 GLU cc_start: 0.8240 (tp30) cc_final: 0.7955 (tp30) REVERT: C 1048 VAL cc_start: 0.8741 (p) cc_final: 0.8494 (m) REVERT: C 1138 LEU cc_start: 0.4881 (tp) cc_final: 0.4008 (pp) outliers start: 27 outliers final: 13 residues processed: 487 average time/residue: 0.1761 time to fit residues: 142.8290 Evaluate side-chains 455 residues out of total 3616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 438 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 1054 GLU Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 589 GLU Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 302 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 344 optimal weight: 0.0770 chunk 58 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 46 optimal weight: 5.9990 chunk 209 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- 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 349 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 HIS C 223 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.157336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100934 restraints weight = 43938.900| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.82 r_work: 0.3094 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 2.0046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32544 Z= 0.123 Angle : 0.633 13.004 44116 Z= 0.318 Chirality : 0.041 0.219 5144 Planarity : 0.004 0.066 5616 Dihedral : 4.543 20.754 4440 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.92 % Allowed : 21.93 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.13), residues: 4108 helix: 0.11 (0.11), residues: 2550 sheet: 2.25 (0.73), residues: 55 loop : -1.92 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 465 TYR 0.024 0.001 TYR A 262 PHE 0.017 0.001 PHE C 830 TRP 0.014 0.001 TRP C 383 HIS 0.011 0.001 HIS C 856 Details of bonding type rmsd covalent geometry : bond 0.00293 (32540) covalent geometry : angle 0.63346 (44108) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.62011 ( 8) hydrogen bonds : bond 0.03278 ( 1140) hydrogen bonds : angle 3.79084 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8567.14 seconds wall clock time: 147 minutes 10.74 seconds (8830.74 seconds total)