Starting phenix.real_space_refine on Fri Feb 6 03:03:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9li6_63112/02_2026/9li6_63112_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9li6_63112/02_2026/9li6_63112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9li6_63112/02_2026/9li6_63112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9li6_63112/02_2026/9li6_63112.map" model { file = "/net/cci-nas-00/data/ceres_data/9li6_63112/02_2026/9li6_63112_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9li6_63112/02_2026/9li6_63112_neut_trim.cif" } resolution = 3.49 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= 0.004 sd= 0.042 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 106 5.16 5 C 14036 2.51 5 N 3664 2.21 5 O 3882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21688 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 10812 Classifications: {'peptide': 1366} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1309} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GDN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 13.37, per 1000 atoms: 0.62 Number of scatterers: 21688 At special positions: 0 Unit cell: (170.5, 111.1, 147.4, 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 106 16.00 O 3882 8.00 N 3664 7.00 C 14036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " distance=2.02 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 32 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 923.9 milliseconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 57.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.731A pdb=" N TRP A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.746A pdb=" N VAL A 45 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 74 through 93 removed outlier: 3.527A pdb=" N ALA A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 107 through 132 removed outlier: 3.527A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET A 125 " --> pdb=" O TRP A 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 removed outlier: 3.912A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 6.004A pdb=" N GLU A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 168 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 192 removed outlier: 3.668A pdb=" N GLY A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.696A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.677A pdb=" N THR A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.683A pdb=" N LYS A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 267 through 273 removed outlier: 4.054A pdb=" N THR A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.543A pdb=" N MET A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.610A pdb=" N GLY A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR A 360 " --> pdb=" O CYS A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.630A pdb=" N ARG A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 408 through 416 removed outlier: 3.839A pdb=" N ILE A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 Proline residue: A 424 - end of helix removed outlier: 3.625A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 3.770A pdb=" N ILE A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.824A pdb=" N LYS A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.561A pdb=" N GLY A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.543A pdb=" N VAL A 504 " --> pdb=" O PHE A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.668A pdb=" N LYS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 518 " --> pdb=" O TRP A 514 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 560 through 565 removed outlier: 3.520A pdb=" N ALA A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 565' Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.727A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 596 removed outlier: 3.516A pdb=" N VAL A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 removed outlier: 3.501A pdb=" N ILE A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 removed outlier: 3.527A pdb=" N ASN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 4.137A pdb=" N ALA A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.966A pdb=" N LEU A 722 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 723 " --> pdb=" O HIS A 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 719 through 723' Processing helix chain 'A' and resid 741 through 757 removed outlier: 3.607A pdb=" N ARG A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 754 " --> pdb=" O MET A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 782 Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.712A pdb=" N SER A 803 " --> pdb=" O HIS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 removed outlier: 3.778A pdb=" N SER A 827 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 828 " --> pdb=" O LEU A 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 824 through 828' Processing helix chain 'A' and resid 906 through 916 removed outlier: 3.777A pdb=" N TYR A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.854A pdb=" N GLU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 939 " --> pdb=" O ARG A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 945 Processing helix chain 'A' and resid 957 through 981 removed outlier: 3.666A pdb=" N ILE A 962 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 973 " --> pdb=" O GLY A 969 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 980 " --> pdb=" O THR A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 removed outlier: 3.917A pdb=" N TYR A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1011 removed outlier: 3.931A pdb=" N PHE A1008 " --> pdb=" O PRO A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1022 removed outlier: 3.637A pdb=" N PHE A1020 " --> pdb=" O ILE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 3.613A pdb=" N VAL A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A1041 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A1048 " --> pdb=" O GLN A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 removed outlier: 3.554A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1082 removed outlier: 3.910A pdb=" N TYR A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A1077 " --> pdb=" O ALA A1073 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR A1080 " --> pdb=" O TYR A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1091 removed outlier: 3.610A pdb=" N SER A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1102 removed outlier: 4.244A pdb=" N GLN A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE A1099 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1127 removed outlier: 3.981A pdb=" N ASN A1122 " --> pdb=" O MET A1118 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A1126 " --> pdb=" O ASN A1122 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1129 No H-bonds generated for 'chain 'A' and resid 1128 through 1129' Processing helix chain 'A' and resid 1130 through 1133 Processing helix chain 'A' and resid 1134 through 1147 removed outlier: 3.981A pdb=" N ASN A1140 " --> pdb=" O ASN A1136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1166 removed outlier: 4.422A pdb=" N VAL A1163 " --> pdb=" O ALA A1159 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET A1164 " --> pdb=" O SER A1160 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A1166 " --> pdb=" O ALA A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1187 removed outlier: 3.646A pdb=" N SER A1184 " --> pdb=" O GLY A1180 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A1185 " --> pdb=" O LEU A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1207 removed outlier: 3.813A pdb=" N LEU A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1204 " --> pdb=" O ALA A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1216 removed outlier: 3.890A pdb=" N ASN A1215 " --> pdb=" O ARG A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1290 removed outlier: 3.551A pdb=" N ASN A1287 " --> pdb=" O SER A1283 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1317 Processing helix chain 'A' and resid 1344 through 1355 removed outlier: 3.627A pdb=" N LEU A1348 " --> pdb=" O ASN A1344 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP A1349 " --> pdb=" O ASP A1345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A1350 " --> pdb=" O ALA A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1363 removed outlier: 3.660A pdb=" N ILE A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1395 removed outlier: 3.510A pdb=" N GLN A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1386 " --> pdb=" O GLY A1382 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A1387 " --> pdb=" O GLN A1383 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A1388 " --> pdb=" O ARG A1384 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1389 " --> pdb=" O GLN A1385 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A1393 " --> pdb=" O LEU A1389 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1425 removed outlier: 3.951A pdb=" N GLN A1418 " --> pdb=" O ASP A1414 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A1420 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 4.592A pdb=" N ASP A1442 " --> pdb=" O THR A1439 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A1443 " --> pdb=" O ILE A1440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1439 through 1443' Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.746A pdb=" N VAL B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 74 through 93 removed outlier: 3.526A pdb=" N ALA B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 107 through 132 removed outlier: 3.527A pdb=" N GLY B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET B 125 " --> pdb=" O TRP B 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 removed outlier: 3.912A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 removed outlier: 6.004A pdb=" N GLU B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 168 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 192 removed outlier: 3.667A pdb=" N GLY B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.696A pdb=" N PHE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.677A pdb=" N THR B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.683A pdb=" N LYS B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 267 through 273 removed outlier: 4.053A pdb=" N THR B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.543A pdb=" N MET B 338 " --> pdb=" O PRO B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 362 removed outlier: 3.610A pdb=" N GLY B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR B 360 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 373 removed outlier: 3.631A pdb=" N ARG B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.839A pdb=" N ILE B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 416 " --> pdb=" O GLN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 439 Proline residue: B 424 - end of helix removed outlier: 3.625A pdb=" N ILE B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 446 removed outlier: 3.770A pdb=" N ILE B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.824A pdb=" N LYS B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.560A pdb=" N GLY B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 Processing helix chain 'B' and resid 498 through 512 removed outlier: 3.542A pdb=" N VAL B 504 " --> pdb=" O PHE B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.668A pdb=" N LYS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 518 " --> pdb=" O TRP B 514 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET B 526 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 560 through 565 removed outlier: 3.519A pdb=" N ALA B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 565' Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 572 through 581 removed outlier: 3.727A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 3.516A pdb=" N VAL B 585 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B 590 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 664 removed outlier: 3.502A pdb=" N ILE B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 removed outlier: 3.528A pdb=" N ASN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 717 removed outlier: 4.138A pdb=" N ALA B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 723 removed outlier: 3.966A pdb=" N LEU B 722 " --> pdb=" O LYS B 719 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU B 723 " --> pdb=" O HIS B 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 719 through 723' Processing helix chain 'B' and resid 741 through 757 removed outlier: 3.607A pdb=" N ARG B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 754 " --> pdb=" O MET B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 Processing helix chain 'B' and resid 799 through 804 removed outlier: 3.712A pdb=" N SER B 803 " --> pdb=" O HIS B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 828 removed outlier: 3.779A pdb=" N SER B 827 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 828 " --> pdb=" O LEU B 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 824 through 828' Processing helix chain 'B' and resid 906 through 916 removed outlier: 3.777A pdb=" N TYR B 911 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 Processing helix chain 'B' and resid 928 through 940 removed outlier: 3.854A pdb=" N GLU B 932 " --> pdb=" O TYR B 928 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 957 through 981 removed outlier: 3.666A pdb=" N ILE B 962 " --> pdb=" O PHE B 958 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 970 " --> pdb=" O LEU B 966 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 973 " --> pdb=" O GLY B 969 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 974 " --> pdb=" O GLN B 970 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 978 " --> pdb=" O THR B 974 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 980 " --> pdb=" O THR B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1001 removed outlier: 3.916A pdb=" N TYR B 987 " --> pdb=" O MET B 983 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 990 " --> pdb=" O LEU B 986 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1011 removed outlier: 3.930A pdb=" N PHE B1008 " --> pdb=" O PRO B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1022 removed outlier: 3.637A pdb=" N PHE B1020 " --> pdb=" O ILE B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1056 removed outlier: 3.613A pdb=" N VAL B1035 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B1041 " --> pdb=" O MET B1037 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B1044 " --> pdb=" O GLY B1040 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B1048 " --> pdb=" O GLN B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1064 removed outlier: 3.553A pdb=" N LEU B1060 " --> pdb=" O SER B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1082 removed outlier: 3.910A pdb=" N TYR B1074 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1075 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B1076 " --> pdb=" O GLY B1072 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR B1077 " --> pdb=" O ALA B1073 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR B1080 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1091 removed outlier: 3.611A pdb=" N SER B1089 " --> pdb=" O LYS B1085 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B1090 " --> pdb=" O ARG B1086 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B1091 " --> pdb=" O MET B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1102 removed outlier: 4.245A pdb=" N GLN B1098 " --> pdb=" O PRO B1094 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE B1099 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY B1100 " --> pdb=" O TYR B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1127 removed outlier: 3.981A pdb=" N ASN B1122 " --> pdb=" O MET B1118 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B1126 " --> pdb=" O ASN B1122 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B1127 " --> pdb=" O GLY B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1129 No H-bonds generated for 'chain 'B' and resid 1128 through 1129' Processing helix chain 'B' and resid 1130 through 1133 Processing helix chain 'B' and resid 1134 through 1147 removed outlier: 3.981A pdb=" N ASN B1140 " --> pdb=" O ASN B1136 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG B1141 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP B1142 " --> pdb=" O GLY B1138 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B1143 " --> pdb=" O ALA B1139 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1166 removed outlier: 4.422A pdb=" N VAL B1163 " --> pdb=" O ALA B1159 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B1164 " --> pdb=" O SER B1160 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B1165 " --> pdb=" O PHE B1161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B1166 " --> pdb=" O ALA B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1187 removed outlier: 3.645A pdb=" N SER B1184 " --> pdb=" O GLY B1180 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B1185 " --> pdb=" O LEU B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1207 removed outlier: 3.813A pdb=" N LEU B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B1199 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B1202 " --> pdb=" O ARG B1198 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B1204 " --> pdb=" O ALA B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1212 through 1216 removed outlier: 3.890A pdb=" N ASN B1215 " --> pdb=" O ARG B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1290 removed outlier: 3.551A pdb=" N ASN B1287 " --> pdb=" O SER B1283 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B1289 " --> pdb=" O LEU B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1317 Processing helix chain 'B' and resid 1344 through 1355 removed outlier: 3.628A pdb=" N LEU B1348 " --> pdb=" O ASN B1344 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP B1349 " --> pdb=" O ASP B1345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B1350 " --> pdb=" O ALA B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1363 removed outlier: 3.660A pdb=" N ILE B1361 " --> pdb=" O LEU B1357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B1363 " --> pdb=" O ASP B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1395 removed outlier: 3.510A pdb=" N GLN B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1386 " --> pdb=" O GLY B1382 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B1387 " --> pdb=" O GLN B1383 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B1388 " --> pdb=" O ARG B1384 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B1389 " --> pdb=" O GLN B1385 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B1392 " --> pdb=" O SER B1388 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B1393 " --> pdb=" O LEU B1389 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B1395 " --> pdb=" O ARG B1391 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1425 removed outlier: 3.951A pdb=" N GLN B1418 " --> pdb=" O ASP B1414 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B1419 " --> pdb=" O ALA B1415 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B1420 " --> pdb=" O LEU B1416 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B1422 " --> pdb=" O GLN B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1443 removed outlier: 4.592A pdb=" N ASP B1442 " --> pdb=" O THR B1439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B1443 " --> pdb=" O ILE B1440 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1439 through 1443' Processing sheet with id=AA1, first strand: chain 'A' and resid 636 through 639 removed outlier: 3.829A pdb=" N LEU A 637 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 614 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 680 through 683 removed outlier: 3.586A pdb=" N ILE A 762 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR A 761 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 795 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE A 763 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 647 " --> pdb=" O LEU A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1259 through 1262 removed outlier: 6.268A pdb=" N HIS A1260 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A1249 " --> pdb=" O HIS A1260 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A1262 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A1299 " --> pdb=" O GLU A1245 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A1247 " --> pdb=" O LYS A1297 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS A1297 " --> pdb=" O VAL A1247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1271 through 1274 removed outlier: 3.578A pdb=" N LEU A1402 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A1433 " --> pdb=" O LEU A1402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 636 through 639 removed outlier: 3.828A pdb=" N LEU B 637 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 614 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 680 through 683 removed outlier: 3.586A pdb=" N ILE B 762 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR B 761 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 795 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N PHE B 763 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 647 " --> pdb=" O LEU B 794 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1259 through 1262 removed outlier: 6.268A pdb=" N HIS B1260 " --> pdb=" O LEU B1249 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B1249 " --> pdb=" O HIS B1260 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B1262 " --> pdb=" O VAL B1247 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B1299 " --> pdb=" O GLU B1245 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B1247 " --> pdb=" O LYS B1297 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B1297 " --> pdb=" O VAL B1247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1271 through 1274 removed outlier: 3.577A pdb=" N LEU B1402 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B1433 " --> pdb=" O LEU B1402 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3466 1.30 - 1.43: 5855 1.43 - 1.56: 12665 1.56 - 1.69: 2 1.69 - 1.82: 184 Bond restraints: 22172 Sorted by residual: bond pdb=" C2 GDN A1701 " pdb=" N3 GDN A1701 " ideal model delta sigma weight residual 1.336 1.444 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C2 GDN B1701 " pdb=" N3 GDN B1701 " ideal model delta sigma weight residual 1.336 1.444 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CD1 GDN B1701 " pdb=" N2 GDN B1701 " ideal model delta sigma weight residual 1.345 1.438 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" CD1 GDN A1701 " pdb=" N2 GDN A1701 " ideal model delta sigma weight residual 1.345 1.437 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" SG2 GDN A1701 " pdb=" C1' GDN A1701 " ideal model delta sigma weight residual 1.748 1.820 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 22167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.46: 30066 7.46 - 14.92: 38 14.92 - 22.38: 0 22.38 - 29.84: 0 29.84 - 37.30: 2 Bond angle restraints: 30106 Sorted by residual: angle pdb=" C LEU A 601 " pdb=" CA LEU A 601 " pdb=" CB LEU A 601 " ideal model delta sigma weight residual 110.16 72.86 37.30 1.44e+00 4.82e-01 6.71e+02 angle pdb=" C LEU B 601 " pdb=" CA LEU B 601 " pdb=" CB LEU B 601 " ideal model delta sigma weight residual 110.16 72.87 37.29 1.44e+00 4.82e-01 6.71e+02 angle pdb=" N LEU B 602 " pdb=" CA LEU B 602 " pdb=" C LEU B 602 " ideal model delta sigma weight residual 108.85 95.70 13.15 1.88e+00 2.83e-01 4.89e+01 angle pdb=" N LEU A 602 " pdb=" CA LEU A 602 " pdb=" C LEU A 602 " ideal model delta sigma weight residual 108.85 95.76 13.09 1.88e+00 2.83e-01 4.85e+01 angle pdb=" N VAL A 536 " pdb=" CA VAL A 536 " pdb=" C VAL A 536 " ideal model delta sigma weight residual 112.96 107.07 5.89 1.00e+00 1.00e+00 3.47e+01 ... (remaining 30101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 12502 16.60 - 33.20: 530 33.20 - 49.80: 138 49.80 - 66.40: 6 66.40 - 83.00: 8 Dihedral angle restraints: 13184 sinusoidal: 5280 harmonic: 7904 Sorted by residual: dihedral pdb=" C LEU A 601 " pdb=" N LEU A 601 " pdb=" CA LEU A 601 " pdb=" CB LEU A 601 " ideal model delta harmonic sigma weight residual -122.60 -79.35 -43.25 0 2.50e+00 1.60e-01 2.99e+02 dihedral pdb=" C LEU B 601 " pdb=" N LEU B 601 " pdb=" CA LEU B 601 " pdb=" CB LEU B 601 " ideal model delta harmonic sigma weight residual -122.60 -79.37 -43.23 0 2.50e+00 1.60e-01 2.99e+02 dihedral pdb=" N LEU A 601 " pdb=" C LEU A 601 " pdb=" CA LEU A 601 " pdb=" CB LEU A 601 " ideal model delta harmonic sigma weight residual 122.80 101.66 21.14 0 2.50e+00 1.60e-01 7.15e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 3387 0.135 - 0.270: 57 0.270 - 0.405: 4 0.405 - 0.540: 2 0.540 - 0.675: 2 Chirality restraints: 3452 Sorted by residual: chirality pdb=" CA LEU B 602 " pdb=" N LEU B 602 " pdb=" C LEU B 602 " pdb=" CB LEU B 602 " both_signs ideal model delta sigma weight residual False 2.51 3.19 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU A 602 " pdb=" N LEU A 602 " pdb=" C LEU A 602 " pdb=" CB LEU A 602 " both_signs ideal model delta sigma weight residual False 2.51 3.19 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU A 601 " pdb=" N LEU A 601 " pdb=" C LEU A 601 " pdb=" CB LEU A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 3449 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" SG2 GDN A1701 " -0.183 2.00e-02 2.50e+03 1.72e-01 6.66e+02 pdb=" C1' GDN A1701 " -0.040 2.00e-02 2.50e+03 pdb=" C2' GDN A1701 " 0.014 2.00e-02 2.50e+03 pdb=" C3' GDN A1701 " 0.328 2.00e-02 2.50e+03 pdb=" C4' GDN A1701 " -0.114 2.00e-02 2.50e+03 pdb=" C5' GDN A1701 " 0.170 2.00e-02 2.50e+03 pdb=" C6' GDN A1701 " 0.105 2.00e-02 2.50e+03 pdb=" N2' GDN A1701 " -0.016 2.00e-02 2.50e+03 pdb=" N4' GDN A1701 " -0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" SG2 GDN B1701 " 0.183 2.00e-02 2.50e+03 1.72e-01 6.66e+02 pdb=" C1' GDN B1701 " 0.040 2.00e-02 2.50e+03 pdb=" C2' GDN B1701 " -0.014 2.00e-02 2.50e+03 pdb=" C3' GDN B1701 " -0.328 2.00e-02 2.50e+03 pdb=" C4' GDN B1701 " 0.113 2.00e-02 2.50e+03 pdb=" C5' GDN B1701 " -0.170 2.00e-02 2.50e+03 pdb=" C6' GDN B1701 " -0.105 2.00e-02 2.50e+03 pdb=" N2' GDN B1701 " 0.016 2.00e-02 2.50e+03 pdb=" N4' GDN B1701 " 0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 423 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO A 424 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " 0.044 5.00e-02 4.00e+02 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 68 2.51 - 3.11: 14456 3.11 - 3.70: 31295 3.70 - 4.30: 43607 4.30 - 4.90: 71631 Nonbonded interactions: 161057 Sorted by model distance: nonbonded pdb=" O LEU B 601 " pdb=" CB LEU B 601 " model vdw 1.912 2.752 nonbonded pdb=" O LEU A 601 " pdb=" CB LEU A 601 " model vdw 1.912 2.752 nonbonded pdb=" OE1 GLU B1148 " pdb=" OG1 THR B1190 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU A1148 " pdb=" OG1 THR A1190 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR B 405 " pdb=" OG SER B 586 " model vdw 2.336 3.040 ... (remaining 161052 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.110 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.510 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 0.108 22174 Z= 0.341 Angle : 1.046 37.296 30110 Z= 0.565 Chirality : 0.061 0.675 3452 Planarity : 0.008 0.172 3792 Dihedral : 10.518 82.996 8086 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -6.31 (0.10), residues: 2720 helix: -4.78 (0.04), residues: 1598 sheet: -1.90 (0.46), residues: 122 loop : -3.05 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1391 TYR 0.019 0.002 TYR A1076 PHE 0.027 0.002 PHE B 934 TRP 0.045 0.003 TRP A 945 HIS 0.007 0.001 HIS B 993 Details of bonding type rmsd covalent geometry : bond 0.00778 (22172) covalent geometry : angle 1.04634 (30106) SS BOND : bond 0.00727 ( 2) SS BOND : angle 0.99934 ( 4) hydrogen bonds : bond 0.34796 ( 706) hydrogen bonds : angle 10.01008 ( 2010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8491 (pt0) cc_final: 0.8145 (pt0) REVERT: A 257 LYS cc_start: 0.8928 (mttt) cc_final: 0.8511 (mtmm) REVERT: A 592 GLU cc_start: 0.7518 (pp20) cc_final: 0.7239 (pp20) REVERT: A 685 GLN cc_start: 0.8212 (tt0) cc_final: 0.7089 (tp-100) REVERT: A 690 PHE cc_start: 0.7861 (m-80) cc_final: 0.7587 (m-80) REVERT: A 708 LYS cc_start: 0.8309 (ptmm) cc_final: 0.7987 (mmmm) REVERT: A 755 TYR cc_start: 0.7690 (t80) cc_final: 0.7413 (t80) REVERT: A 764 ASP cc_start: 0.8288 (t0) cc_final: 0.7992 (t0) REVERT: A 1284 SER cc_start: 0.9152 (m) cc_final: 0.8739 (p) REVERT: A 1324 GLN cc_start: 0.7730 (tp40) cc_final: 0.7001 (tp40) REVERT: A 1403 ASP cc_start: 0.8368 (t0) cc_final: 0.7890 (t0) REVERT: A 1443 CYS cc_start: 0.7914 (m) cc_final: 0.7613 (m) REVERT: A 1444 ASP cc_start: 0.8006 (m-30) cc_final: 0.7789 (t70) REVERT: B 6 ILE cc_start: 0.8828 (mm) cc_final: 0.8595 (tt) REVERT: B 128 ILE cc_start: 0.8840 (mm) cc_final: 0.8640 (tp) REVERT: B 179 GLU cc_start: 0.8341 (pt0) cc_final: 0.8076 (pt0) REVERT: B 257 LYS cc_start: 0.9040 (mttt) cc_final: 0.8521 (mtmm) REVERT: B 412 GLN cc_start: 0.8699 (tp40) cc_final: 0.8301 (tm-30) REVERT: B 685 GLN cc_start: 0.8365 (tt0) cc_final: 0.7172 (tp-100) REVERT: B 693 THR cc_start: 0.8229 (p) cc_final: 0.8027 (t) REVERT: B 764 ASP cc_start: 0.8294 (t0) cc_final: 0.7989 (t0) REVERT: B 1284 SER cc_start: 0.8893 (m) cc_final: 0.8574 (p) REVERT: B 1324 GLN cc_start: 0.7738 (tp40) cc_final: 0.7003 (tp40) REVERT: B 1371 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 1403 ASP cc_start: 0.8503 (t0) cc_final: 0.7941 (t0) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1773 time to fit residues: 105.8763 Evaluate side-chains 288 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 395 GLN A 800 HIS A1324 GLN A1378 ASN B 74 ASN B 395 GLN B 697 ASN B 800 HIS B1267 HIS B1324 GLN B1378 ASN B1383 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102960 restraints weight = 31900.357| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.03 r_work: 0.3072 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22174 Z= 0.133 Angle : 0.629 7.757 30110 Z= 0.329 Chirality : 0.044 0.186 3452 Planarity : 0.005 0.053 3792 Dihedral : 6.261 45.902 3006 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.89 % Allowed : 6.69 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -4.58 (0.13), residues: 2720 helix: -3.28 (0.09), residues: 1558 sheet: -1.75 (0.44), residues: 142 loop : -2.50 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1002 TYR 0.021 0.002 TYR B 261 PHE 0.016 0.001 PHE B 571 TRP 0.022 0.001 TRP B 945 HIS 0.002 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00285 (22172) covalent geometry : angle 0.62861 (30106) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.37258 ( 4) hydrogen bonds : bond 0.05849 ( 706) hydrogen bonds : angle 5.34637 ( 2010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 THR cc_start: 0.8291 (t) cc_final: 0.8012 (t) REVERT: A 257 LYS cc_start: 0.9039 (mttt) cc_final: 0.8508 (mtmm) REVERT: A 265 TRP cc_start: 0.7132 (m100) cc_final: 0.6766 (m100) REVERT: A 385 ARG cc_start: 0.6948 (tpp-160) cc_final: 0.6715 (tpp-160) REVERT: A 403 MET cc_start: 0.8176 (mmp) cc_final: 0.7956 (tmm) REVERT: A 572 MET cc_start: 0.8263 (tpp) cc_final: 0.8052 (tpp) REVERT: A 685 GLN cc_start: 0.8158 (tt0) cc_final: 0.7049 (tp-100) REVERT: A 690 PHE cc_start: 0.7686 (m-80) cc_final: 0.6964 (m-80) REVERT: A 755 TYR cc_start: 0.8524 (t80) cc_final: 0.7834 (t80) REVERT: A 764 ASP cc_start: 0.8159 (t0) cc_final: 0.7615 (t0) REVERT: A 1284 SER cc_start: 0.9003 (m) cc_final: 0.8652 (p) REVERT: A 1363 ARG cc_start: 0.8179 (ptp-110) cc_final: 0.7918 (ptp90) REVERT: A 1371 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 1443 CYS cc_start: 0.7783 (m) cc_final: 0.7172 (m) REVERT: A 1444 ASP cc_start: 0.8064 (m-30) cc_final: 0.7640 (t70) REVERT: B 177 THR cc_start: 0.8396 (t) cc_final: 0.8142 (t) REVERT: B 257 LYS cc_start: 0.9202 (mttt) cc_final: 0.8617 (mtmm) REVERT: B 265 TRP cc_start: 0.7067 (m100) cc_final: 0.6614 (m100) REVERT: B 288 PRO cc_start: 0.5975 (Cg_exo) cc_final: 0.5629 (Cg_endo) REVERT: B 385 ARG cc_start: 0.6847 (tpp-160) cc_final: 0.6586 (tpp-160) REVERT: B 403 MET cc_start: 0.8147 (mmp) cc_final: 0.7791 (tmm) REVERT: B 572 MET cc_start: 0.8270 (tpp) cc_final: 0.7933 (tpp) REVERT: B 683 VAL cc_start: 0.7876 (t) cc_final: 0.7669 (m) REVERT: B 685 GLN cc_start: 0.8185 (tt0) cc_final: 0.7223 (tp-100) REVERT: B 690 PHE cc_start: 0.7795 (m-80) cc_final: 0.7384 (m-80) REVERT: B 746 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7876 (mm-40) REVERT: B 755 TYR cc_start: 0.7817 (t80) cc_final: 0.7487 (t80) REVERT: B 764 ASP cc_start: 0.7994 (t0) cc_final: 0.7327 (t0) REVERT: B 1245 GLU cc_start: 0.6362 (pm20) cc_final: 0.6065 (pm20) REVERT: B 1284 SER cc_start: 0.8730 (m) cc_final: 0.8451 (p) REVERT: B 1324 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7544 (tp40) REVERT: B 1371 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 1443 CYS cc_start: 0.7933 (m) cc_final: 0.7197 (m) outliers start: 21 outliers final: 16 residues processed: 342 average time/residue: 0.1606 time to fit residues: 85.3975 Evaluate side-chains 296 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 1242 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 11 optimal weight: 8.9990 chunk 71 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 40.0000 chunk 198 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 HIS A1267 HIS A1324 GLN B 183 GLN B 312 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092315 restraints weight = 32291.839| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.50 r_work: 0.2983 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22174 Z= 0.268 Angle : 0.698 8.708 30110 Z= 0.360 Chirality : 0.048 0.162 3452 Planarity : 0.005 0.053 3792 Dihedral : 6.244 42.678 3006 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.82 % Allowed : 9.53 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.88 (0.14), residues: 2720 helix: -2.68 (0.11), residues: 1582 sheet: -1.66 (0.44), residues: 142 loop : -2.21 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 370 TYR 0.025 0.002 TYR A 171 PHE 0.021 0.002 PHE A 571 TRP 0.019 0.002 TRP A 945 HIS 0.009 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00638 (22172) covalent geometry : angle 0.69789 (30106) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.49338 ( 4) hydrogen bonds : bond 0.06242 ( 706) hydrogen bonds : angle 5.09788 ( 2010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8821 (tpp) cc_final: 0.8524 (tpp) REVERT: A 242 MET cc_start: 0.8636 (mtm) cc_final: 0.8405 (mtm) REVERT: A 257 LYS cc_start: 0.9220 (mttt) cc_final: 0.8715 (mtmm) REVERT: A 403 MET cc_start: 0.8487 (mmp) cc_final: 0.8072 (tmm) REVERT: A 412 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 572 MET cc_start: 0.8584 (tpp) cc_final: 0.8241 (tpp) REVERT: A 685 GLN cc_start: 0.8241 (tt0) cc_final: 0.7316 (tp-100) REVERT: A 750 MET cc_start: 0.9066 (tpt) cc_final: 0.8591 (tmm) REVERT: A 755 TYR cc_start: 0.8592 (t80) cc_final: 0.7967 (t80) REVERT: A 758 SER cc_start: 0.8249 (m) cc_final: 0.7415 (p) REVERT: A 763 PHE cc_start: 0.8233 (m-10) cc_final: 0.7870 (m-80) REVERT: A 1284 SER cc_start: 0.9142 (m) cc_final: 0.8777 (p) REVERT: A 1371 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 1443 CYS cc_start: 0.8005 (m) cc_final: 0.7468 (m) REVERT: B 257 LYS cc_start: 0.9235 (mttt) cc_final: 0.8730 (mtmm) REVERT: B 403 MET cc_start: 0.8455 (mmp) cc_final: 0.8065 (tmm) REVERT: B 412 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 571 PHE cc_start: 0.8487 (t80) cc_final: 0.8257 (t80) REVERT: B 572 MET cc_start: 0.8566 (tpp) cc_final: 0.8160 (tpp) REVERT: B 655 LYS cc_start: 0.7310 (mtmp) cc_final: 0.6707 (tptt) REVERT: B 660 SER cc_start: 0.9160 (m) cc_final: 0.8956 (p) REVERT: B 690 PHE cc_start: 0.7595 (m-80) cc_final: 0.7071 (m-80) REVERT: B 735 GLU cc_start: 0.6568 (mp0) cc_final: 0.4478 (tt0) REVERT: B 755 TYR cc_start: 0.8048 (t80) cc_final: 0.7690 (t80) REVERT: B 763 PHE cc_start: 0.7917 (m-80) cc_final: 0.7683 (m-80) REVERT: B 1245 GLU cc_start: 0.6874 (pm20) cc_final: 0.6456 (pm20) REVERT: B 1284 SER cc_start: 0.9070 (m) cc_final: 0.8726 (p) REVERT: B 1324 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7530 (tp40) REVERT: B 1371 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7687 (mm-30) REVERT: B 1443 CYS cc_start: 0.8018 (m) cc_final: 0.7298 (m) outliers start: 43 outliers final: 23 residues processed: 308 average time/residue: 0.1609 time to fit residues: 76.5042 Evaluate side-chains 297 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1397 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 800 HIS A1324 GLN ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100419 restraints weight = 31953.953| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.11 r_work: 0.3048 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22174 Z= 0.108 Angle : 0.553 8.392 30110 Z= 0.285 Chirality : 0.042 0.163 3452 Planarity : 0.004 0.048 3792 Dihedral : 5.631 39.863 3006 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.44 % Allowed : 10.93 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.21 (0.15), residues: 2720 helix: -2.05 (0.12), residues: 1538 sheet: -0.95 (0.48), residues: 142 loop : -2.19 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.020 0.001 TYR A 171 PHE 0.022 0.001 PHE A 571 TRP 0.012 0.001 TRP A 945 HIS 0.002 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00239 (22172) covalent geometry : angle 0.55339 (30106) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.20820 ( 4) hydrogen bonds : bond 0.04353 ( 706) hydrogen bonds : angle 4.51557 ( 2010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8034 (m-80) cc_final: 0.7790 (m-80) REVERT: A 125 MET cc_start: 0.9004 (tpp) cc_final: 0.8689 (tpp) REVERT: A 257 LYS cc_start: 0.9172 (mttt) cc_final: 0.8642 (mtmm) REVERT: A 403 MET cc_start: 0.8270 (mmp) cc_final: 0.7985 (tmm) REVERT: A 412 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 572 MET cc_start: 0.8371 (tpp) cc_final: 0.7982 (tpt) REVERT: A 685 GLN cc_start: 0.8184 (tt0) cc_final: 0.7311 (tp40) REVERT: A 750 MET cc_start: 0.9091 (tpt) cc_final: 0.8726 (tmm) REVERT: A 755 TYR cc_start: 0.8537 (t80) cc_final: 0.7894 (t80) REVERT: A 758 SER cc_start: 0.8058 (m) cc_final: 0.7338 (p) REVERT: A 763 PHE cc_start: 0.8240 (m-10) cc_final: 0.7985 (m-10) REVERT: A 1087 MET cc_start: 0.9039 (mtm) cc_final: 0.8649 (mtp) REVERT: A 1284 SER cc_start: 0.8951 (m) cc_final: 0.8587 (p) REVERT: A 1371 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 1443 CYS cc_start: 0.7826 (m) cc_final: 0.7316 (m) REVERT: B 112 PHE cc_start: 0.8056 (m-80) cc_final: 0.7826 (m-80) REVERT: B 125 MET cc_start: 0.8980 (tpp) cc_final: 0.8699 (tpp) REVERT: B 257 LYS cc_start: 0.9175 (mttt) cc_final: 0.8674 (mtmm) REVERT: B 357 GLU cc_start: 0.8489 (tt0) cc_final: 0.8278 (tt0) REVERT: B 403 MET cc_start: 0.8270 (mmp) cc_final: 0.7909 (tmm) REVERT: B 412 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 572 MET cc_start: 0.8322 (tpp) cc_final: 0.8009 (tpp) REVERT: B 690 PHE cc_start: 0.7529 (m-80) cc_final: 0.6641 (m-80) REVERT: B 755 TYR cc_start: 0.7993 (t80) cc_final: 0.7596 (t80) REVERT: B 1101 GLU cc_start: 0.7680 (tp30) cc_final: 0.6754 (tm-30) REVERT: B 1284 SER cc_start: 0.8802 (m) cc_final: 0.8458 (p) REVERT: B 1324 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7707 (tp40) REVERT: B 1371 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 1443 CYS cc_start: 0.7899 (m) cc_final: 0.7347 (m) outliers start: 34 outliers final: 20 residues processed: 304 average time/residue: 0.1438 time to fit residues: 67.9916 Evaluate side-chains 289 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1397 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 128 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 170 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 HIS A1324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100277 restraints weight = 31873.074| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.35 r_work: 0.3024 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22174 Z= 0.134 Angle : 0.556 8.743 30110 Z= 0.285 Chirality : 0.043 0.156 3452 Planarity : 0.004 0.050 3792 Dihedral : 5.530 40.082 3006 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.23 % Allowed : 12.33 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.91 (0.16), residues: 2720 helix: -1.79 (0.12), residues: 1546 sheet: -0.85 (0.48), residues: 142 loop : -2.09 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 589 TYR 0.020 0.001 TYR A 171 PHE 0.026 0.001 PHE A 571 TRP 0.011 0.001 TRP A 945 HIS 0.006 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00313 (22172) covalent geometry : angle 0.55591 (30106) SS BOND : bond 0.00013 ( 2) SS BOND : angle 0.21170 ( 4) hydrogen bonds : bond 0.04331 ( 706) hydrogen bonds : angle 4.39900 ( 2010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8052 (m-80) cc_final: 0.7817 (m-80) REVERT: A 125 MET cc_start: 0.8967 (tpp) cc_final: 0.8384 (tpp) REVERT: A 257 LYS cc_start: 0.9177 (mttt) cc_final: 0.8654 (mtmm) REVERT: A 403 MET cc_start: 0.8214 (mmp) cc_final: 0.7993 (tmm) REVERT: A 412 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 572 MET cc_start: 0.8371 (tpp) cc_final: 0.8107 (tpp) REVERT: A 685 GLN cc_start: 0.8167 (tt0) cc_final: 0.7276 (tp40) REVERT: A 750 MET cc_start: 0.9063 (tpt) cc_final: 0.8711 (tmm) REVERT: A 755 TYR cc_start: 0.8624 (t80) cc_final: 0.8010 (t80) REVERT: A 758 SER cc_start: 0.8078 (m) cc_final: 0.7327 (p) REVERT: A 763 PHE cc_start: 0.8209 (m-10) cc_final: 0.7967 (m-10) REVERT: A 1087 MET cc_start: 0.9036 (mtm) cc_final: 0.8661 (mtp) REVERT: A 1284 SER cc_start: 0.8937 (m) cc_final: 0.8569 (p) REVERT: A 1371 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 1443 CYS cc_start: 0.7808 (m) cc_final: 0.7329 (m) REVERT: B 125 MET cc_start: 0.9025 (tpp) cc_final: 0.8736 (tpp) REVERT: B 257 LYS cc_start: 0.9160 (mttt) cc_final: 0.8658 (mtmm) REVERT: B 403 MET cc_start: 0.8248 (mmp) cc_final: 0.7951 (tmm) REVERT: B 572 MET cc_start: 0.8391 (tpp) cc_final: 0.8075 (tpp) REVERT: B 755 TYR cc_start: 0.8006 (t80) cc_final: 0.7547 (t80) REVERT: B 1284 SER cc_start: 0.8878 (m) cc_final: 0.8542 (p) REVERT: B 1324 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7708 (tp40) REVERT: B 1371 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7568 (mm-30) REVERT: B 1443 CYS cc_start: 0.7869 (m) cc_final: 0.7247 (m) outliers start: 29 outliers final: 24 residues processed: 286 average time/residue: 0.1567 time to fit residues: 69.8732 Evaluate side-chains 291 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1446 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 1301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 239 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN A 800 HIS A1324 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.153381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094600 restraints weight = 32091.053| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.53 r_work: 0.3018 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22174 Z= 0.170 Angle : 0.579 7.828 30110 Z= 0.294 Chirality : 0.044 0.152 3452 Planarity : 0.004 0.049 3792 Dihedral : 5.513 38.867 3006 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.82 % Allowed : 12.29 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.79 (0.16), residues: 2720 helix: -1.68 (0.12), residues: 1572 sheet: -0.79 (0.49), residues: 142 loop : -2.07 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.018 0.001 TYR A 171 PHE 0.027 0.001 PHE A 571 TRP 0.011 0.001 TRP B 265 HIS 0.020 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00403 (22172) covalent geometry : angle 0.57875 (30106) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.26082 ( 4) hydrogen bonds : bond 0.04522 ( 706) hydrogen bonds : angle 4.39425 ( 2010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8083 (m-80) cc_final: 0.7860 (m-80) REVERT: A 125 MET cc_start: 0.8972 (tpp) cc_final: 0.8422 (tpp) REVERT: A 257 LYS cc_start: 0.9226 (mttt) cc_final: 0.8693 (mtmm) REVERT: A 385 ARG cc_start: 0.6981 (tpp-160) cc_final: 0.6617 (tpp-160) REVERT: A 403 MET cc_start: 0.8417 (mmp) cc_final: 0.7916 (tmm) REVERT: A 412 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 572 MET cc_start: 0.8566 (tpp) cc_final: 0.8260 (tpp) REVERT: A 750 MET cc_start: 0.9066 (tpt) cc_final: 0.8642 (tmm) REVERT: A 755 TYR cc_start: 0.8676 (t80) cc_final: 0.8110 (t80) REVERT: A 758 SER cc_start: 0.8178 (m) cc_final: 0.7380 (p) REVERT: A 1284 SER cc_start: 0.8970 (m) cc_final: 0.8587 (p) REVERT: A 1371 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 1443 CYS cc_start: 0.7907 (m) cc_final: 0.7399 (m) REVERT: B 125 MET cc_start: 0.9015 (tpp) cc_final: 0.8485 (tpp) REVERT: B 257 LYS cc_start: 0.9181 (mttt) cc_final: 0.8699 (mtmm) REVERT: B 403 MET cc_start: 0.8455 (mmp) cc_final: 0.7875 (tmm) REVERT: B 412 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8610 (tm-30) REVERT: B 572 MET cc_start: 0.8562 (tpp) cc_final: 0.8233 (tpp) REVERT: B 690 PHE cc_start: 0.7658 (m-80) cc_final: 0.6973 (m-80) REVERT: B 755 TYR cc_start: 0.8037 (t80) cc_final: 0.7600 (t80) REVERT: B 1284 SER cc_start: 0.8888 (m) cc_final: 0.8517 (p) REVERT: B 1371 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 1443 CYS cc_start: 0.7877 (m) cc_final: 0.7312 (m) outliers start: 43 outliers final: 29 residues processed: 292 average time/residue: 0.1545 time to fit residues: 70.5195 Evaluate side-chains 286 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1446 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1397 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 74 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098802 restraints weight = 31806.371| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.94 r_work: 0.3026 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22174 Z= 0.134 Angle : 0.561 9.125 30110 Z= 0.284 Chirality : 0.043 0.147 3452 Planarity : 0.004 0.050 3792 Dihedral : 5.400 38.024 3006 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.91 % Allowed : 12.63 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.56 (0.16), residues: 2720 helix: -1.48 (0.13), residues: 1560 sheet: -0.78 (0.48), residues: 142 loop : -1.97 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.017 0.001 TYR A 171 PHE 0.028 0.001 PHE A 571 TRP 0.013 0.001 TRP B 265 HIS 0.014 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00315 (22172) covalent geometry : angle 0.56057 (30106) SS BOND : bond 0.00011 ( 2) SS BOND : angle 0.21389 ( 4) hydrogen bonds : bond 0.04252 ( 706) hydrogen bonds : angle 4.29019 ( 2010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8077 (m-80) cc_final: 0.7869 (m-80) REVERT: A 125 MET cc_start: 0.8998 (tpp) cc_final: 0.8453 (tpp) REVERT: A 257 LYS cc_start: 0.9221 (mttt) cc_final: 0.8673 (mtmm) REVERT: A 403 MET cc_start: 0.8405 (mmp) cc_final: 0.7939 (tmm) REVERT: A 572 MET cc_start: 0.8567 (tpp) cc_final: 0.8279 (tpp) REVERT: A 683 VAL cc_start: 0.7801 (t) cc_final: 0.7591 (m) REVERT: A 750 MET cc_start: 0.9108 (tpt) cc_final: 0.8702 (tmm) REVERT: A 758 SER cc_start: 0.8197 (m) cc_final: 0.7406 (p) REVERT: A 1284 SER cc_start: 0.8959 (m) cc_final: 0.8571 (p) REVERT: A 1371 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 1399 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 125 MET cc_start: 0.8983 (tpp) cc_final: 0.8449 (tpp) REVERT: B 257 LYS cc_start: 0.9134 (mttt) cc_final: 0.8634 (mtmm) REVERT: B 403 MET cc_start: 0.8405 (mmp) cc_final: 0.7883 (tmm) REVERT: B 412 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 572 MET cc_start: 0.8562 (tpp) cc_final: 0.8217 (tpp) REVERT: B 690 PHE cc_start: 0.7662 (m-80) cc_final: 0.6942 (m-80) REVERT: B 755 TYR cc_start: 0.8001 (t80) cc_final: 0.7534 (t80) REVERT: B 1275 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8407 (m) REVERT: B 1284 SER cc_start: 0.8902 (m) cc_final: 0.8531 (p) REVERT: B 1371 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7608 (mm-30) outliers start: 45 outliers final: 37 residues processed: 282 average time/residue: 0.1550 time to fit residues: 67.6523 Evaluate side-chains 291 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1446 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1275 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1397 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 176 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 211 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097557 restraints weight = 32106.380| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.10 r_work: 0.2953 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22174 Z= 0.221 Angle : 0.630 9.385 30110 Z= 0.317 Chirality : 0.046 0.147 3452 Planarity : 0.004 0.050 3792 Dihedral : 5.543 38.377 3006 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.37 % Allowed : 12.33 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.56 (0.16), residues: 2720 helix: -1.53 (0.13), residues: 1574 sheet: -0.77 (0.48), residues: 142 loop : -1.87 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 426 TYR 0.020 0.001 TYR A 369 PHE 0.029 0.002 PHE A 571 TRP 0.015 0.001 TRP B 265 HIS 0.018 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00528 (22172) covalent geometry : angle 0.63028 (30106) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.26166 ( 4) hydrogen bonds : bond 0.04854 ( 706) hydrogen bonds : angle 4.48292 ( 2010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 254 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.8114 (m-80) cc_final: 0.7914 (m-80) REVERT: A 125 MET cc_start: 0.9015 (tpp) cc_final: 0.8413 (tpp) REVERT: A 257 LYS cc_start: 0.9102 (mttt) cc_final: 0.8530 (mtmm) REVERT: A 403 MET cc_start: 0.8253 (mmp) cc_final: 0.8019 (tmm) REVERT: A 412 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 572 MET cc_start: 0.8444 (tpp) cc_final: 0.8099 (tpp) REVERT: A 750 MET cc_start: 0.9162 (tpt) cc_final: 0.8707 (tmm) REVERT: A 758 SER cc_start: 0.8348 (m) cc_final: 0.7576 (p) REVERT: A 1284 SER cc_start: 0.9026 (m) cc_final: 0.8655 (p) REVERT: A 1324 GLN cc_start: 0.7660 (tp40) cc_final: 0.7131 (tp40) REVERT: A 1371 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 1399 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8485 (mt) REVERT: B 125 MET cc_start: 0.9012 (tpp) cc_final: 0.8490 (tpp) REVERT: B 257 LYS cc_start: 0.9084 (mttt) cc_final: 0.8587 (mtmm) REVERT: B 403 MET cc_start: 0.8333 (mmp) cc_final: 0.8054 (tmm) REVERT: B 412 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8710 (tm-30) REVERT: B 572 MET cc_start: 0.8464 (tpp) cc_final: 0.8101 (tpp) REVERT: B 690 PHE cc_start: 0.7640 (m-80) cc_final: 0.6904 (m-80) REVERT: B 755 TYR cc_start: 0.8049 (t80) cc_final: 0.7604 (t80) REVERT: B 1275 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8516 (m) REVERT: B 1284 SER cc_start: 0.8919 (m) cc_final: 0.8527 (p) REVERT: B 1371 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 1403 ASP cc_start: 0.8568 (t0) cc_final: 0.8082 (t0) outliers start: 56 outliers final: 41 residues processed: 294 average time/residue: 0.1474 time to fit residues: 67.7205 Evaluate side-chains 296 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1446 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1275 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1397 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 118 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN ** B1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098227 restraints weight = 32102.797| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.17 r_work: 0.2976 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22174 Z= 0.195 Angle : 0.624 10.864 30110 Z= 0.312 Chirality : 0.045 0.161 3452 Planarity : 0.004 0.074 3792 Dihedral : 5.536 40.607 3006 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.29 % Allowed : 12.67 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.50 (0.16), residues: 2720 helix: -1.46 (0.13), residues: 1570 sheet: -0.87 (0.51), residues: 122 loop : -1.85 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 426 TYR 0.017 0.001 TYR A 369 PHE 0.030 0.001 PHE A 571 TRP 0.018 0.001 TRP A 265 HIS 0.006 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00467 (22172) covalent geometry : angle 0.62360 (30106) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.25164 ( 4) hydrogen bonds : bond 0.04761 ( 706) hydrogen bonds : angle 4.45889 ( 2010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9018 (tpp) cc_final: 0.8421 (tpp) REVERT: A 257 LYS cc_start: 0.9098 (mttt) cc_final: 0.8527 (mtmm) REVERT: A 403 MET cc_start: 0.8230 (mmp) cc_final: 0.8026 (tmm) REVERT: A 412 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8619 (tm-30) REVERT: A 572 MET cc_start: 0.8431 (tpp) cc_final: 0.8096 (tpp) REVERT: A 750 MET cc_start: 0.9150 (tpt) cc_final: 0.8658 (tmm) REVERT: A 755 TYR cc_start: 0.8536 (t80) cc_final: 0.8121 (t80) REVERT: A 758 SER cc_start: 0.8353 (m) cc_final: 0.7579 (p) REVERT: A 1284 SER cc_start: 0.9004 (m) cc_final: 0.8636 (p) REVERT: A 1324 GLN cc_start: 0.7611 (tp40) cc_final: 0.7136 (tp40) REVERT: A 1371 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 1399 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8588 (mt) REVERT: B 125 MET cc_start: 0.9017 (tpp) cc_final: 0.8447 (tpp) REVERT: B 403 MET cc_start: 0.8309 (mmp) cc_final: 0.8063 (tmm) REVERT: B 412 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8752 (tm-30) REVERT: B 572 MET cc_start: 0.8436 (tpp) cc_final: 0.8070 (tpp) REVERT: B 690 PHE cc_start: 0.7631 (m-80) cc_final: 0.6897 (m-80) REVERT: B 755 TYR cc_start: 0.8106 (t80) cc_final: 0.7773 (t80) REVERT: B 1284 SER cc_start: 0.8923 (m) cc_final: 0.8533 (p) REVERT: B 1350 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8724 (tm-30) REVERT: B 1371 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7623 (mm-30) REVERT: B 1403 ASP cc_start: 0.8566 (t0) cc_final: 0.8188 (t0) outliers start: 54 outliers final: 43 residues processed: 296 average time/residue: 0.1492 time to fit residues: 68.6030 Evaluate side-chains 294 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain A residue 1446 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain B residue 1397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 chunk 245 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 800 HIS ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101587 restraints weight = 31556.222| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.02 r_work: 0.3060 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22174 Z= 0.101 Angle : 0.579 12.349 30110 Z= 0.286 Chirality : 0.042 0.190 3452 Planarity : 0.004 0.045 3792 Dihedral : 5.290 40.517 3006 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.57 % Allowed : 13.18 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.19 (0.16), residues: 2720 helix: -1.16 (0.13), residues: 1558 sheet: -0.83 (0.51), residues: 122 loop : -1.80 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 677 TYR 0.017 0.001 TYR A 171 PHE 0.029 0.001 PHE A 571 TRP 0.023 0.001 TRP B 265 HIS 0.012 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00223 (22172) covalent geometry : angle 0.57938 (30106) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.19860 ( 4) hydrogen bonds : bond 0.03960 ( 706) hydrogen bonds : angle 4.15070 ( 2010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9043 (tpp) cc_final: 0.8833 (tpp) REVERT: A 257 LYS cc_start: 0.9163 (mttt) cc_final: 0.8595 (mtmm) REVERT: A 403 MET cc_start: 0.8215 (mmp) cc_final: 0.7945 (tmm) REVERT: A 750 MET cc_start: 0.9023 (tpt) cc_final: 0.8612 (tmm) REVERT: A 755 TYR cc_start: 0.8566 (t80) cc_final: 0.8142 (t80) REVERT: A 758 SER cc_start: 0.8198 (m) cc_final: 0.7425 (p) REVERT: A 1284 SER cc_start: 0.8924 (m) cc_final: 0.8565 (p) REVERT: A 1324 GLN cc_start: 0.7625 (tp40) cc_final: 0.7186 (tp40) REVERT: A 1371 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 125 MET cc_start: 0.9031 (tpp) cc_final: 0.8443 (tpp) REVERT: B 392 ARG cc_start: 0.7050 (mmt180) cc_final: 0.6743 (mtt-85) REVERT: B 403 MET cc_start: 0.8222 (mmp) cc_final: 0.7907 (tmm) REVERT: B 690 PHE cc_start: 0.7579 (m-80) cc_final: 0.6793 (m-80) REVERT: B 755 TYR cc_start: 0.8150 (t80) cc_final: 0.7872 (t80) REVERT: B 1284 SER cc_start: 0.8838 (m) cc_final: 0.8457 (p) REVERT: B 1371 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 1399 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 1403 ASP cc_start: 0.8448 (t0) cc_final: 0.8145 (t0) outliers start: 37 outliers final: 30 residues processed: 287 average time/residue: 0.1475 time to fit residues: 66.4142 Evaluate side-chains 281 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 777 GLN Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1444 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1399 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 164 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 57 optimal weight: 0.0570 chunk 161 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 244 optimal weight: 0.0570 chunk 96 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.156041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102466 restraints weight = 31497.281| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.97 r_work: 0.3063 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22174 Z= 0.097 Angle : 0.572 12.663 30110 Z= 0.280 Chirality : 0.042 0.182 3452 Planarity : 0.004 0.046 3792 Dihedral : 5.136 40.746 3006 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.40 % Allowed : 13.52 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -1.96 (0.16), residues: 2720 helix: -0.93 (0.13), residues: 1544 sheet: -0.77 (0.50), residues: 122 loop : -1.76 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 677 TYR 0.015 0.001 TYR A 171 PHE 0.027 0.001 PHE B 571 TRP 0.019 0.001 TRP B 265 HIS 0.013 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00214 (22172) covalent geometry : angle 0.57246 (30106) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.14347 ( 4) hydrogen bonds : bond 0.03631 ( 706) hydrogen bonds : angle 4.01563 ( 2010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4889.34 seconds wall clock time: 84 minutes 21.88 seconds (5061.88 seconds total)