Starting phenix.real_space_refine on Thu Sep 18 21:04:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d5m_46579/09_2025/9d5m_46579.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d5m_46579/09_2025/9d5m_46579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d5m_46579/09_2025/9d5m_46579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d5m_46579/09_2025/9d5m_46579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d5m_46579/09_2025/9d5m_46579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d5m_46579/09_2025/9d5m_46579.map" } resolution = 3.05 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= 0.000 sd= 0.017 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 86 5.16 5 C 12810 2.51 5 N 3374 2.21 5 O 3761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20031 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 9784 Classifications: {'peptide': 1201} Link IDs: {'PTRANS': 72, 'TRANS': 1128} Chain: "B" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1199, 9773 Classifications: {'peptide': 1199} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1126} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.58, per 1000 atoms: 0.23 Number of scatterers: 20031 At special positions: 0 Unit cell: (105.728, 137.942, 158.592, 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 86 16.00 O 3761 8.00 N 3374 7.00 C 12810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A1114 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 728 " - pdb=" SG CYS B 734 " distance=2.03 Simple disulfide: pdb=" SG CYS B 928 " - pdb=" SG CYS B 946 " distance=2.02 Simple disulfide: pdb=" SG CYS B1114 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG F 1 " - " FUC F 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 9 " " NAG A1302 " - " ASN A 648 " " NAG A1303 " - " ASN A 666 " " NAG B1301 " - " ASN B 9 " " NAG B1302 " - " ASN B 82 " " NAG B1303 " - " ASN B 666 " " NAG D 1 " - " ASN A 25 " " NAG F 1 " - " ASN A 117 " " NAG G 1 " - " ASN A 289 " " NAG H 1 " - " ASN A 416 " " NAG I 1 " - " ASN A 480 " " NAG L 1 " - " ASN A 685 " " NAG N 1 " - " ASN B 25 " " NAG P 1 " - " ASN B 117 " " NAG Q 1 " - " ASN B 289 " " NAG R 1 " - " ASN B 416 " " NAG S 1 " - " ASN B 480 " " NAG U 1 " - " ASN B 685 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 902.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 8 sheets defined 67.7% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.610A pdb=" N ASN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 removed outlier: 4.198A pdb=" N ALA A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 removed outlier: 3.585A pdb=" N THR A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.926A pdb=" N ASN A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 171 through 190 Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.522A pdb=" N TYR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.745A pdb=" N VAL A 268 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.780A pdb=" N PHE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.934A pdb=" N GLU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 372 Processing helix chain 'A' and resid 386 through 400 removed outlier: 3.820A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 417 through 433 removed outlier: 3.845A pdb=" N ASP A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 451 removed outlier: 3.622A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 498 through 520 removed outlier: 4.151A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.601A pdb=" N GLN A 527 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.507A pdb=" N GLY A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 616 through 648 removed outlier: 3.610A pdb=" N VAL A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 676 removed outlier: 3.602A pdb=" N SER A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 4.134A pdb=" N ASP A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 724 Processing helix chain 'A' and resid 740 through 747 Processing helix chain 'A' and resid 750 through 771 removed outlier: 4.251A pdb=" N GLN A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 804 through 836 Proline residue: A 818 - end of helix Processing helix chain 'A' and resid 876 through 884 removed outlier: 3.739A pdb=" N LEU A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 903 removed outlier: 3.727A pdb=" N GLY A 903 " --> pdb=" O PHE A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.263A pdb=" N ASN A 913 " --> pdb=" O PRO A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.921A pdb=" N TYR A 970 " --> pdb=" O TYR A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 998 removed outlier: 3.664A pdb=" N HIS A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 994 " --> pdb=" O GLY A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1011 through 1014 Processing helix chain 'A' and resid 1015 through 1029 removed outlier: 3.802A pdb=" N ASP A1029 " --> pdb=" O LYS A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1049 removed outlier: 4.037A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1055 No H-bonds generated for 'chain 'A' and resid 1053 through 1055' Processing helix chain 'A' and resid 1056 through 1068 Processing helix chain 'A' and resid 1082 through 1087 removed outlier: 3.536A pdb=" N LYS A1087 " --> pdb=" O PRO A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1117 removed outlier: 3.877A pdb=" N PHE A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A1108 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.681A pdb=" N ALA A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 4.241A pdb=" N ARG A1148 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1158 removed outlier: 3.807A pdb=" N ALA A1153 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'A' and resid 1172 through 1187 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.692A pdb=" N GLN B 6 " --> pdb=" O PRO B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 removed outlier: 3.901A pdb=" N PHE B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 75 Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.564A pdb=" N PHE B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.714A pdb=" N ALA B 101 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.543A pdb=" N ASN B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 171 through 190 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.787A pdb=" N TRP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 218 through 238 Processing helix chain 'B' and resid 261 through 268 removed outlier: 4.121A pdb=" N ASP B 266 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 4.136A pdb=" N LEU B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 304 removed outlier: 3.833A pdb=" N ARG B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 removed outlier: 4.557A pdb=" N TRP B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 372 removed outlier: 3.850A pdb=" N TYR B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.736A pdb=" N ARG B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 386 through 400 removed outlier: 3.849A pdb=" N LEU B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 408 Processing helix chain 'B' and resid 417 through 433 removed outlier: 4.332A pdb=" N GLU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 451 removed outlier: 3.633A pdb=" N TYR B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.548A pdb=" N ALA B 488 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 489 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 519 removed outlier: 4.161A pdb=" N PHE B 502 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.534A pdb=" N GLN B 527 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 546 removed outlier: 4.079A pdb=" N ALA B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 616 through 647 removed outlier: 3.915A pdb=" N VAL B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.701A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 704 through 724 Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'B' and resid 750 through 771 removed outlier: 4.305A pdb=" N GLN B 771 " --> pdb=" O ARG B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 788 Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 804 through 836 Proline residue: B 818 - end of helix Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 859 through 867 removed outlier: 4.634A pdb=" N ASP B 864 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 867 " --> pdb=" O ASP B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 883 removed outlier: 4.321A pdb=" N GLU B 879 " --> pdb=" O MET B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 903 removed outlier: 3.926A pdb=" N ALA B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 Processing helix chain 'B' and resid 950 through 970 removed outlier: 3.547A pdb=" N LEU B 954 " --> pdb=" O ASN B 950 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B 970 " --> pdb=" O TYR B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 998 removed outlier: 4.105A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 993 " --> pdb=" O ILE B 989 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 996 " --> pdb=" O VAL B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1005 Processing helix chain 'B' and resid 1015 through 1031 Processing helix chain 'B' and resid 1032 through 1049 removed outlier: 4.394A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1055 No H-bonds generated for 'chain 'B' and resid 1053 through 1055' Processing helix chain 'B' and resid 1056 through 1068 removed outlier: 3.588A pdb=" N GLU B1060 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B1061 " --> pdb=" O TYR B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1087 removed outlier: 3.503A pdb=" N LYS B1087 " --> pdb=" O PRO B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1093 removed outlier: 3.714A pdb=" N SER B1092 " --> pdb=" O HIS B1089 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B1093 " --> pdb=" O ILE B1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1089 through 1093' Processing helix chain 'B' and resid 1096 through 1118 removed outlier: 3.832A pdb=" N PHE B1100 " --> pdb=" O TYR B1096 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE B1107 " --> pdb=" O PHE B1103 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1126 removed outlier: 3.552A pdb=" N LYS B1125 " --> pdb=" O PRO B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1143 Processing helix chain 'B' and resid 1149 through 1158 removed outlier: 3.676A pdb=" N ALA B1153 " --> pdb=" O PRO B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1172 Processing helix chain 'B' and resid 1172 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.131A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AA3, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.254A pdb=" N ILE A 846 " --> pdb=" O CYS A1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 249 removed outlier: 6.337A pdb=" N ILE B 248 " --> pdb=" O CYS B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 333 through 334 removed outlier: 3.527A pdb=" N SER B 333 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 727 through 728 Processing sheet with id=AA7, first strand: chain 'B' and resid 846 through 847 removed outlier: 6.597A pdb=" N ILE B 846 " --> pdb=" O CYS B1072 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 931 through 935 removed outlier: 4.181A pdb=" N ASP B 940 " --> pdb=" O PHE B 935 " (cutoff:3.500A) 1074 hydrogen bonds defined for protein. 3135 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: 3.16 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5717 1.33 - 1.46: 4276 1.46 - 1.58: 10494 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 20631 Sorted by residual: bond pdb=" N GLU B 77 " pdb=" CA GLU B 77 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.02e+01 bond pdb=" N GLN B 736 " pdb=" CA GLN B 736 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.14e-02 7.69e+03 8.51e+00 bond pdb=" N VAL A1040 " pdb=" CA VAL A1040 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.37e+00 bond pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.35e+00 bond pdb=" N VAL B 727 " pdb=" CA VAL B 727 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.32e-02 5.74e+03 7.61e+00 ... (remaining 20626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27245 1.88 - 3.76: 706 3.76 - 5.63: 115 5.63 - 7.51: 20 7.51 - 9.39: 9 Bond angle restraints: 28095 Sorted by residual: angle pdb=" N PHE A1033 " pdb=" CA PHE A1033 " pdb=" C PHE A1033 " ideal model delta sigma weight residual 113.12 107.63 5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" N ILE B 530 " pdb=" CA ILE B 530 " pdb=" C ILE B 530 " ideal model delta sigma weight residual 111.77 107.83 3.94 1.04e+00 9.25e-01 1.44e+01 angle pdb=" N GLU B 74 " pdb=" CA GLU B 74 " pdb=" C GLU B 74 " ideal model delta sigma weight residual 114.12 109.00 5.12 1.39e+00 5.18e-01 1.36e+01 angle pdb=" N ILE A 46 " pdb=" CA ILE A 46 " pdb=" CB ILE A 46 " ideal model delta sigma weight residual 111.23 105.51 5.72 1.65e+00 3.67e-01 1.20e+01 angle pdb=" CA ASP B 529 " pdb=" C ASP B 529 " pdb=" O ASP B 529 " ideal model delta sigma weight residual 121.94 118.26 3.68 1.15e+00 7.56e-01 1.02e+01 ... (remaining 28090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10686 17.85 - 35.70: 1349 35.70 - 53.56: 449 53.56 - 71.41: 111 71.41 - 89.26: 28 Dihedral angle restraints: 12623 sinusoidal: 5569 harmonic: 7054 Sorted by residual: dihedral pdb=" CB CYS B 330 " pdb=" SG CYS B 330 " pdb=" SG CYS B 348 " pdb=" CB CYS B 348 " ideal model delta sinusoidal sigma weight residual 93.00 16.50 76.50 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 19.85 73.15 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS A 330 " pdb=" SG CYS A 330 " pdb=" SG CYS A 348 " pdb=" CB CYS A 348 " ideal model delta sinusoidal sigma weight residual -86.00 -141.28 55.28 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 12620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2770 0.083 - 0.167: 240 0.167 - 0.250: 11 0.250 - 0.333: 1 0.333 - 0.417: 3 Chirality restraints: 3025 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 289 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 25 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 25 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 3022 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.027 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP B 40 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 907 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 908 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 635 " -0.012 2.00e-02 2.50e+03 1.21e-02 3.68e+00 pdb=" CG TRP B 635 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 635 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 635 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 635 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 635 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 635 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 635 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 635 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 635 " -0.001 2.00e-02 2.50e+03 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2927 2.75 - 3.29: 19569 3.29 - 3.82: 35040 3.82 - 4.36: 40069 4.36 - 4.90: 69889 Nonbonded interactions: 167494 Sorted by model distance: nonbonded pdb=" O PHE A 313 " pdb=" OG SER A 317 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP B 342 " pdb=" NH2 ARG B 344 " model vdw 2.223 3.120 nonbonded pdb=" NZ LYS B 694 " pdb=" OE1 GLU B 979 " model vdw 2.231 3.120 nonbonded pdb=" O ARG B 236 " pdb=" NE2 GLN B 684 " model vdw 2.261 3.120 nonbonded pdb=" OG1 THR A 650 " pdb=" OG1 THR A 653 " model vdw 2.265 3.040 ... (remaining 167489 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 1200 or resid 1301 through 1303)) selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.410 Find NCS groups from input model: 0.470 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.006 0.059 20677 Z= 0.275 Angle : 0.749 12.386 28222 Z= 0.389 Chirality : 0.049 0.417 3025 Planarity : 0.005 0.062 3602 Dihedral : 18.013 89.260 8046 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.43 % Allowed : 27.95 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2396 helix: 1.09 (0.13), residues: 1477 sheet: -2.05 (0.94), residues: 32 loop : -1.77 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.021 0.002 TYR B 671 PHE 0.025 0.002 PHE B 64 TRP 0.059 0.002 TRP B 40 HIS 0.007 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00595 (20631) covalent geometry : angle 0.72406 (28095) SS BOND : bond 0.00433 ( 11) SS BOND : angle 0.82990 ( 22) hydrogen bonds : bond 0.12911 ( 1074) hydrogen bonds : angle 5.30525 ( 3135) link_BETA1-4 : bond 0.00802 ( 16) link_BETA1-4 : angle 3.01563 ( 48) link_BETA1-6 : bond 0.00720 ( 1) link_BETA1-6 : angle 1.24445 ( 3) link_NAG-ASN : bond 0.00989 ( 18) link_NAG-ASN : angle 3.43540 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 223 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 6 GLN cc_start: 0.5789 (mp10) cc_final: 0.5348 (mp10) REVERT: A 35 SER cc_start: 0.8730 (t) cc_final: 0.8320 (m) REVERT: A 49 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6938 (mp0) REVERT: A 53 ARG cc_start: 0.7618 (mpt-90) cc_final: 0.7346 (mpt-90) REVERT: A 210 ASP cc_start: 0.7959 (m-30) cc_final: 0.7579 (m-30) REVERT: A 342 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: A 640 GLU cc_start: 0.5762 (mm-30) cc_final: 0.5185 (mt-10) REVERT: A 723 SER cc_start: 0.8703 (t) cc_final: 0.8228 (p) REVERT: A 859 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.6725 (p90) REVERT: A 979 GLU cc_start: 0.7675 (pt0) cc_final: 0.7350 (mm-30) REVERT: A 1018 HIS cc_start: 0.5951 (t-90) cc_final: 0.5621 (t-170) REVERT: A 1077 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7709 (mmp-170) REVERT: A 1119 HIS cc_start: 0.3963 (OUTLIER) cc_final: 0.3347 (p90) REVERT: A 1147 SER cc_start: 0.8893 (t) cc_final: 0.8627 (p) REVERT: B 55 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7264 (tp30) REVERT: B 83 PHE cc_start: 0.4844 (OUTLIER) cc_final: 0.4205 (m-10) REVERT: B 89 ARG cc_start: 0.7613 (tpt170) cc_final: 0.6684 (mtm180) REVERT: B 235 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7429 (mtm110) REVERT: B 283 MET cc_start: 0.5646 (mpp) cc_final: 0.4242 (mpp) REVERT: B 406 HIS cc_start: 0.7077 (t70) cc_final: 0.6868 (t-90) REVERT: B 432 LYS cc_start: 0.7770 (mmtm) cc_final: 0.6257 (tptp) REVERT: B 521 TYR cc_start: 0.7449 (t80) cc_final: 0.7045 (t80) REVERT: B 640 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6368 (tt0) REVERT: B 649 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7238 (mm) REVERT: B 655 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7760 (mtmt) REVERT: B 674 GLN cc_start: 0.7730 (tt0) cc_final: 0.7263 (mt0) REVERT: B 707 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 811 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7203 (mtm110) REVERT: B 881 MET cc_start: 0.7007 (ttm) cc_final: 0.6669 (tpt) REVERT: B 916 MET cc_start: 0.4693 (pmm) cc_final: 0.4173 (ptp) REVERT: B 952 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5532 (tm-30) REVERT: B 1029 ASP cc_start: 0.8167 (m-30) cc_final: 0.7862 (m-30) REVERT: B 1041 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8397 (t0) REVERT: B 1044 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.6842 (mtm-85) REVERT: B 1160 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6617 (pm20) outliers start: 92 outliers final: 62 residues processed: 300 average time/residue: 0.1591 time to fit residues: 73.8032 Evaluate side-chains 290 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 217 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1054 LYS Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 ARG Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 894 GLU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1137 ARG Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1160 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 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 = 0.3977 r_free = 0.3977 target = 0.165678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113378 restraints weight = 26360.466| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.08 r_work: 0.3195 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20677 Z= 0.168 Angle : 0.661 12.877 28222 Z= 0.317 Chirality : 0.045 0.425 3025 Planarity : 0.005 0.061 3602 Dihedral : 9.374 75.062 3496 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.25 % Allowed : 25.01 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.17), residues: 2396 helix: 1.24 (0.13), residues: 1494 sheet: -2.12 (0.92), residues: 32 loop : -1.71 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 978 TYR 0.018 0.002 TYR B 671 PHE 0.018 0.001 PHE A 502 TRP 0.037 0.001 TRP B 40 HIS 0.007 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00394 (20631) covalent geometry : angle 0.63121 (28095) SS BOND : bond 0.00445 ( 11) SS BOND : angle 1.08987 ( 22) hydrogen bonds : bond 0.04792 ( 1074) hydrogen bonds : angle 4.38253 ( 3135) link_BETA1-4 : bond 0.00761 ( 16) link_BETA1-4 : angle 3.05740 ( 48) link_BETA1-6 : bond 0.00745 ( 1) link_BETA1-6 : angle 1.19136 ( 3) link_NAG-ASN : bond 0.00870 ( 18) link_NAG-ASN : angle 3.45867 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 223 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6007 (mp10) cc_final: 0.5584 (mp10) REVERT: A 49 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6894 (mp0) REVERT: A 53 ARG cc_start: 0.7764 (mpt-90) cc_final: 0.7388 (mpp80) REVERT: A 63 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7570 (mt-10) REVERT: A 210 ASP cc_start: 0.8007 (m-30) cc_final: 0.7663 (m-30) REVERT: A 342 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: A 353 MET cc_start: 0.7730 (mmm) cc_final: 0.7097 (mtm) REVERT: A 413 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.4884 (mmm160) REVERT: A 554 GLU cc_start: 0.8049 (tp30) cc_final: 0.7840 (tp30) REVERT: A 640 GLU cc_start: 0.5775 (mm-30) cc_final: 0.5194 (mt-10) REVERT: A 699 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.4914 (pm20) REVERT: A 723 SER cc_start: 0.8744 (t) cc_final: 0.8356 (p) REVERT: A 736 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6904 (mt0) REVERT: A 745 MET cc_start: 0.8723 (tpt) cc_final: 0.8404 (tpt) REVERT: A 859 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.6864 (p-90) REVERT: A 891 MET cc_start: 0.5088 (ptt) cc_final: 0.4773 (ptt) REVERT: A 963 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.6286 (m-70) REVERT: A 1018 HIS cc_start: 0.6140 (t-90) cc_final: 0.5757 (t-170) REVERT: A 1147 SER cc_start: 0.8813 (t) cc_final: 0.8455 (p) REVERT: A 1156 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6730 (tp) REVERT: A 1164 SER cc_start: 0.8812 (t) cc_final: 0.8505 (m) REVERT: B 55 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7353 (tp30) REVERT: B 235 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7603 (mtm110) REVERT: B 256 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7739 (ttp) REVERT: B 283 MET cc_start: 0.5798 (mpp) cc_final: 0.4330 (mpp) REVERT: B 432 LYS cc_start: 0.7510 (mmtm) cc_final: 0.6428 (tmtt) REVERT: B 521 TYR cc_start: 0.7495 (t80) cc_final: 0.7066 (t80) REVERT: B 640 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6593 (tt0) REVERT: B 674 GLN cc_start: 0.7906 (tt0) cc_final: 0.7466 (mt0) REVERT: B 811 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7392 (mtm110) REVERT: B 846 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7464 (mt) REVERT: B 881 MET cc_start: 0.7001 (ttm) cc_final: 0.6720 (tpt) REVERT: B 916 MET cc_start: 0.4405 (pmm) cc_final: 0.4040 (ptm) REVERT: B 1024 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7811 (tpp) REVERT: B 1029 ASP cc_start: 0.8258 (m-30) cc_final: 0.7871 (m-30) REVERT: B 1041 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8340 (t0) REVERT: B 1168 MET cc_start: 0.8875 (ttt) cc_final: 0.8571 (ttt) REVERT: B 1188 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7716 (mt-10) outliers start: 130 outliers final: 78 residues processed: 319 average time/residue: 0.1485 time to fit residues: 74.4161 Evaluate side-chains 302 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 212 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 HIS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 894 GLU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1056 ASN Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1157 ILE Chi-restraints excluded: chain B residue 1188 GLU Chi-restraints excluded: chain B residue 1189 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 234 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 969 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 = 0.3965 r_free = 0.3965 target = 0.164353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113615 restraints weight = 26471.949| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.31 r_work: 0.3150 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20677 Z= 0.197 Angle : 0.680 12.833 28222 Z= 0.325 Chirality : 0.046 0.425 3025 Planarity : 0.005 0.061 3602 Dihedral : 8.868 75.642 3438 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 7.17 % Allowed : 24.10 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2396 helix: 1.24 (0.13), residues: 1494 sheet: -2.02 (0.95), residues: 32 loop : -1.73 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 629 TYR 0.018 0.002 TYR A 215 PHE 0.029 0.002 PHE B 83 TRP 0.029 0.001 TRP B 40 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00476 (20631) covalent geometry : angle 0.64638 (28095) SS BOND : bond 0.00478 ( 11) SS BOND : angle 1.58412 ( 22) hydrogen bonds : bond 0.04888 ( 1074) hydrogen bonds : angle 4.29461 ( 3135) link_BETA1-4 : bond 0.00780 ( 16) link_BETA1-4 : angle 3.03115 ( 48) link_BETA1-6 : bond 0.00731 ( 1) link_BETA1-6 : angle 1.21168 ( 3) link_NAG-ASN : bond 0.00917 ( 18) link_NAG-ASN : angle 3.85572 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 226 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6055 (mp10) cc_final: 0.5615 (mp10) REVERT: A 35 SER cc_start: 0.8798 (t) cc_final: 0.8365 (m) REVERT: A 53 ARG cc_start: 0.7755 (mpt-90) cc_final: 0.7345 (mpp80) REVERT: A 210 ASP cc_start: 0.8149 (m-30) cc_final: 0.7805 (m-30) REVERT: A 353 MET cc_start: 0.7713 (mmm) cc_final: 0.7063 (mtm) REVERT: A 413 ARG cc_start: 0.5536 (OUTLIER) cc_final: 0.4758 (mmm160) REVERT: A 565 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 640 GLU cc_start: 0.5893 (mm-30) cc_final: 0.5302 (mt-10) REVERT: A 723 SER cc_start: 0.8765 (t) cc_final: 0.8401 (p) REVERT: A 736 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: A 859 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.6928 (p-90) REVERT: A 891 MET cc_start: 0.5119 (ptt) cc_final: 0.4901 (ptt) REVERT: A 914 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.6255 (tttm) REVERT: A 961 MET cc_start: 0.7358 (mmm) cc_final: 0.7142 (mmm) REVERT: A 979 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6826 (mm-30) REVERT: A 1007 ASN cc_start: 0.3401 (OUTLIER) cc_final: 0.3083 (p0) REVERT: A 1018 HIS cc_start: 0.6148 (t-90) cc_final: 0.5752 (t-170) REVERT: A 1119 HIS cc_start: 0.4034 (OUTLIER) cc_final: 0.3417 (p90) REVERT: A 1147 SER cc_start: 0.8841 (t) cc_final: 0.8461 (p) REVERT: A 1156 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6773 (tp) REVERT: B 55 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7217 (tp30) REVERT: B 74 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 235 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7603 (mtm110) REVERT: B 283 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.4531 (mpp) REVERT: B 432 LYS cc_start: 0.7540 (mmtm) cc_final: 0.6326 (tptp) REVERT: B 443 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: B 521 TYR cc_start: 0.7501 (t80) cc_final: 0.7012 (t80) REVERT: B 594 TRP cc_start: 0.7734 (OUTLIER) cc_final: 0.6525 (p-90) REVERT: B 640 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6700 (tt0) REVERT: B 662 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7606 (mpp) REVERT: B 674 GLN cc_start: 0.7962 (tt0) cc_final: 0.7512 (mt0) REVERT: B 811 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7459 (mtm110) REVERT: B 846 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7485 (mt) REVERT: B 881 MET cc_start: 0.6950 (ttm) cc_final: 0.6659 (tpt) REVERT: B 916 MET cc_start: 0.4393 (pmm) cc_final: 0.3930 (ttm) REVERT: B 931 SER cc_start: 0.7821 (t) cc_final: 0.7204 (p) REVERT: B 942 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7247 (ptt180) REVERT: B 979 GLU cc_start: 0.8224 (mp0) cc_final: 0.7935 (mp0) REVERT: B 1016 ASP cc_start: 0.7639 (m-30) cc_final: 0.7299 (p0) REVERT: B 1024 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: B 1029 ASP cc_start: 0.8298 (m-30) cc_final: 0.7907 (m-30) REVERT: B 1188 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7762 (mt-10) outliers start: 149 outliers final: 107 residues processed: 335 average time/residue: 0.1314 time to fit residues: 69.6478 Evaluate side-chains 338 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 215 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 894 GLU Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 935 PHE Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1157 ILE Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1188 GLU Chi-restraints excluded: chain B residue 1189 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 86 optimal weight: 0.0170 chunk 68 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 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 = 0.3993 r_free = 0.3993 target = 0.167083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115070 restraints weight = 26358.754| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.08 r_work: 0.3227 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20677 Z= 0.127 Angle : 0.638 12.500 28222 Z= 0.302 Chirality : 0.044 0.473 3025 Planarity : 0.004 0.060 3602 Dihedral : 8.569 75.299 3431 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 6.35 % Allowed : 24.96 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2396 helix: 1.43 (0.13), residues: 1487 sheet: -1.97 (0.93), residues: 32 loop : -1.65 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 978 TYR 0.022 0.001 TYR B 970 PHE 0.015 0.001 PHE A 502 TRP 0.028 0.001 TRP B 40 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00281 (20631) covalent geometry : angle 0.59926 (28095) SS BOND : bond 0.00389 ( 11) SS BOND : angle 2.19023 ( 22) hydrogen bonds : bond 0.04094 ( 1074) hydrogen bonds : angle 4.13440 ( 3135) link_BETA1-4 : bond 0.00796 ( 16) link_BETA1-4 : angle 3.06104 ( 48) link_BETA1-6 : bond 0.00687 ( 1) link_BETA1-6 : angle 1.16296 ( 3) link_NAG-ASN : bond 0.00899 ( 18) link_NAG-ASN : angle 3.96121 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 226 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6079 (mp10) cc_final: 0.5693 (mp10) REVERT: A 49 GLU cc_start: 0.7034 (mp0) cc_final: 0.6825 (mp0) REVERT: A 53 ARG cc_start: 0.7851 (mpt-90) cc_final: 0.7453 (mpp80) REVERT: A 63 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7589 (mt-10) REVERT: A 353 MET cc_start: 0.7659 (mmm) cc_final: 0.7030 (mtm) REVERT: A 354 ASP cc_start: 0.6876 (p0) cc_final: 0.6660 (p0) REVERT: A 387 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: A 413 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.4801 (mmm160) REVERT: A 544 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7329 (tt) REVERT: A 640 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5272 (mt-10) REVERT: A 699 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.5055 (pm20) REVERT: A 723 SER cc_start: 0.8719 (t) cc_final: 0.8365 (p) REVERT: A 736 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6861 (mt0) REVERT: A 859 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.6539 (p90) REVERT: A 914 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6133 (tmtt) REVERT: A 961 MET cc_start: 0.7315 (mmm) cc_final: 0.7010 (mmm) REVERT: A 979 GLU cc_start: 0.7000 (tm-30) cc_final: 0.6672 (mm-30) REVERT: A 1007 ASN cc_start: 0.3294 (OUTLIER) cc_final: 0.3021 (p0) REVERT: A 1012 GLU cc_start: 0.1428 (OUTLIER) cc_final: -0.0550 (tm-30) REVERT: A 1018 HIS cc_start: 0.6080 (t-90) cc_final: 0.5699 (t-170) REVERT: A 1119 HIS cc_start: 0.3965 (OUTLIER) cc_final: 0.3360 (p90) REVERT: A 1130 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: A 1156 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6881 (tp) REVERT: A 1164 SER cc_start: 0.8704 (t) cc_final: 0.8423 (m) REVERT: B 55 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7329 (tp30) REVERT: B 89 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6351 (mtm180) REVERT: B 235 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7554 (mtm110) REVERT: B 256 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7776 (ttp) REVERT: B 293 MET cc_start: 0.7517 (mtp) cc_final: 0.7291 (mtm) REVERT: B 393 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7681 (t0) REVERT: B 411 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6797 (tm) REVERT: B 432 LYS cc_start: 0.7474 (mmtm) cc_final: 0.6405 (tmtt) REVERT: B 521 TYR cc_start: 0.7452 (t80) cc_final: 0.7000 (t80) REVERT: B 554 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8100 (mp0) REVERT: B 594 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.6741 (p-90) REVERT: B 662 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7559 (mpp) REVERT: B 674 GLN cc_start: 0.7903 (tt0) cc_final: 0.7483 (mt0) REVERT: B 707 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: B 710 GLU cc_start: 0.8124 (tp30) cc_final: 0.7827 (tt0) REVERT: B 811 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7401 (mtm110) REVERT: B 875 MET cc_start: 0.5731 (tpp) cc_final: 0.5219 (tpp) REVERT: B 881 MET cc_start: 0.6818 (ttm) cc_final: 0.6552 (tpt) REVERT: B 931 SER cc_start: 0.7729 (t) cc_final: 0.7094 (p) REVERT: B 942 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7157 (ptt180) REVERT: B 979 GLU cc_start: 0.8054 (mp0) cc_final: 0.7761 (mp0) REVERT: B 1016 ASP cc_start: 0.7557 (m-30) cc_final: 0.7269 (p0) REVERT: B 1024 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7798 (tpp) REVERT: B 1029 ASP cc_start: 0.8231 (m-30) cc_final: 0.7812 (m-30) REVERT: B 1188 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7427 (mt-10) outliers start: 132 outliers final: 82 residues processed: 320 average time/residue: 0.1350 time to fit residues: 68.2814 Evaluate side-chains 318 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 215 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 729 HIS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1157 ILE Chi-restraints excluded: chain B residue 1188 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 216 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 168 optimal weight: 0.3980 chunk 144 optimal weight: 0.0270 chunk 195 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114108 restraints weight = 26270.363| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.38 r_work: 0.3194 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20677 Z= 0.151 Angle : 0.656 14.715 28222 Z= 0.310 Chirality : 0.045 0.422 3025 Planarity : 0.004 0.060 3602 Dihedral : 8.354 73.961 3419 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 7.17 % Allowed : 24.05 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2396 helix: 1.49 (0.13), residues: 1487 sheet: -1.90 (0.93), residues: 32 loop : -1.63 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 629 TYR 0.020 0.002 TYR B 24 PHE 0.016 0.001 PHE A 502 TRP 0.027 0.001 TRP B 40 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00354 (20631) covalent geometry : angle 0.61228 (28095) SS BOND : bond 0.00646 ( 11) SS BOND : angle 2.57161 ( 22) hydrogen bonds : bond 0.04262 ( 1074) hydrogen bonds : angle 4.10948 ( 3135) link_BETA1-4 : bond 0.00759 ( 16) link_BETA1-4 : angle 3.10350 ( 48) link_BETA1-6 : bond 0.00661 ( 1) link_BETA1-6 : angle 1.17259 ( 3) link_NAG-ASN : bond 0.00847 ( 18) link_NAG-ASN : angle 4.26753 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 219 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6096 (mp10) cc_final: 0.5689 (mp10) REVERT: A 63 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7578 (mt-10) REVERT: A 98 LEU cc_start: 0.8644 (mt) cc_final: 0.8299 (mp) REVERT: A 210 ASP cc_start: 0.8104 (m-30) cc_final: 0.7716 (m-30) REVERT: A 353 MET cc_start: 0.7742 (mmm) cc_final: 0.7083 (mtm) REVERT: A 354 ASP cc_start: 0.6870 (p0) cc_final: 0.6621 (p0) REVERT: A 387 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: A 413 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.4835 (mmm160) REVERT: A 544 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7326 (tt) REVERT: A 625 GLU cc_start: 0.7444 (tp30) cc_final: 0.7144 (tp30) REVERT: A 640 GLU cc_start: 0.5840 (mm-30) cc_final: 0.5258 (mt-10) REVERT: A 699 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5037 (pm20) REVERT: A 723 SER cc_start: 0.8741 (t) cc_final: 0.8383 (p) REVERT: A 859 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.6435 (p90) REVERT: A 914 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6238 (tttm) REVERT: A 961 MET cc_start: 0.7306 (mmm) cc_final: 0.6942 (mmm) REVERT: A 979 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6694 (mm-30) REVERT: A 1007 ASN cc_start: 0.3329 (OUTLIER) cc_final: 0.3114 (p0) REVERT: A 1012 GLU cc_start: 0.1436 (OUTLIER) cc_final: -0.0615 (tm-30) REVERT: A 1018 HIS cc_start: 0.6085 (t-90) cc_final: 0.5734 (t-170) REVERT: A 1119 HIS cc_start: 0.4073 (OUTLIER) cc_final: 0.3459 (p90) REVERT: A 1147 SER cc_start: 0.8799 (t) cc_final: 0.8425 (p) REVERT: A 1156 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6819 (tp) REVERT: B 26 SER cc_start: 0.8011 (OUTLIER) cc_final: 0.7753 (p) REVERT: B 55 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7321 (tp30) REVERT: B 235 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7573 (mtm110) REVERT: B 393 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7682 (t0) REVERT: B 411 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6768 (tm) REVERT: B 432 LYS cc_start: 0.7515 (mmtm) cc_final: 0.6429 (tmtt) REVERT: B 521 TYR cc_start: 0.7366 (t80) cc_final: 0.6891 (t80) REVERT: B 554 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8125 (mp0) REVERT: B 594 TRP cc_start: 0.7673 (OUTLIER) cc_final: 0.6725 (p-90) REVERT: B 640 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6544 (tt0) REVERT: B 662 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7496 (mpp) REVERT: B 674 GLN cc_start: 0.7914 (tt0) cc_final: 0.7488 (mt0) REVERT: B 707 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: B 710 GLU cc_start: 0.8091 (tp30) cc_final: 0.7811 (tt0) REVERT: B 811 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7354 (mtm110) REVERT: B 894 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 916 MET cc_start: 0.3836 (pmm) cc_final: 0.3591 (ptp) REVERT: B 952 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.5472 (tm-30) REVERT: B 979 GLU cc_start: 0.8082 (mp0) cc_final: 0.7761 (mp0) REVERT: B 1016 ASP cc_start: 0.7562 (m-30) cc_final: 0.7267 (p0) REVERT: B 1024 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7785 (tpp) REVERT: B 1029 ASP cc_start: 0.8269 (m-30) cc_final: 0.7821 (m-30) REVERT: B 1160 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: B 1188 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7739 (mt-10) outliers start: 149 outliers final: 100 residues processed: 331 average time/residue: 0.1339 time to fit residues: 70.3651 Evaluate side-chains 337 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 217 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1157 ILE Chi-restraints excluded: chain B residue 1160 GLN Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1188 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.168246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118938 restraints weight = 26118.941| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.37 r_work: 0.3257 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20677 Z= 0.169 Angle : 0.663 12.657 28222 Z= 0.316 Chirality : 0.045 0.400 3025 Planarity : 0.004 0.060 3602 Dihedral : 8.458 73.829 3419 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 7.50 % Allowed : 23.47 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2396 helix: 1.47 (0.13), residues: 1490 sheet: -1.67 (0.94), residues: 32 loop : -1.63 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 629 TYR 0.018 0.002 TYR B 970 PHE 0.018 0.001 PHE A 502 TRP 0.019 0.001 TRP B 40 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00403 (20631) covalent geometry : angle 0.62585 (28095) SS BOND : bond 0.00737 ( 11) SS BOND : angle 2.74387 ( 22) hydrogen bonds : bond 0.04391 ( 1074) hydrogen bonds : angle 4.12445 ( 3135) link_BETA1-4 : bond 0.00782 ( 16) link_BETA1-4 : angle 3.10404 ( 48) link_BETA1-6 : bond 0.00662 ( 1) link_BETA1-6 : angle 1.17989 ( 3) link_NAG-ASN : bond 0.00844 ( 18) link_NAG-ASN : angle 3.74283 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 223 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6007 (mp10) cc_final: 0.5628 (mp10) REVERT: A 63 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7586 (mt-10) REVERT: A 98 LEU cc_start: 0.8655 (mt) cc_final: 0.8343 (mp) REVERT: A 210 ASP cc_start: 0.7757 (m-30) cc_final: 0.7442 (m-30) REVERT: A 353 MET cc_start: 0.7713 (mmm) cc_final: 0.7103 (mtm) REVERT: A 354 ASP cc_start: 0.6828 (p0) cc_final: 0.6620 (p0) REVERT: A 387 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: A 413 ARG cc_start: 0.5631 (OUTLIER) cc_final: 0.4880 (mmm160) REVERT: A 530 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 544 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7283 (tt) REVERT: A 625 GLU cc_start: 0.7466 (tp30) cc_final: 0.7182 (tp30) REVERT: A 640 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5303 (mt-10) REVERT: A 699 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.5079 (pm20) REVERT: A 723 SER cc_start: 0.8780 (t) cc_final: 0.8463 (p) REVERT: A 736 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: A 859 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.6459 (p90) REVERT: A 914 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.5831 (tmtm) REVERT: A 961 MET cc_start: 0.7261 (mmm) cc_final: 0.6856 (mmm) REVERT: A 979 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6748 (mm-30) REVERT: A 1007 ASN cc_start: 0.3059 (OUTLIER) cc_final: 0.2825 (p0) REVERT: A 1012 GLU cc_start: 0.1655 (OUTLIER) cc_final: -0.0402 (tm-30) REVERT: A 1018 HIS cc_start: 0.6097 (t-90) cc_final: 0.5743 (t-170) REVERT: A 1119 HIS cc_start: 0.4052 (OUTLIER) cc_final: 0.3483 (p90) REVERT: A 1130 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: A 1147 SER cc_start: 0.8754 (t) cc_final: 0.8420 (p) REVERT: A 1156 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6881 (tp) REVERT: B 26 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7766 (p) REVERT: B 55 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7343 (tp30) REVERT: B 89 ARG cc_start: 0.7204 (tpt170) cc_final: 0.6281 (mtm180) REVERT: B 363 MET cc_start: 0.8496 (ttp) cc_final: 0.8171 (ttp) REVERT: B 393 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7486 (t0) REVERT: B 411 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6796 (tm) REVERT: B 432 LYS cc_start: 0.7430 (mmtm) cc_final: 0.6455 (tmtt) REVERT: B 554 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7988 (mp0) REVERT: B 594 TRP cc_start: 0.7446 (OUTLIER) cc_final: 0.6721 (p-90) REVERT: B 640 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6630 (tt0) REVERT: B 662 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: B 674 GLN cc_start: 0.7870 (tt0) cc_final: 0.7458 (mt0) REVERT: B 707 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: B 811 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7521 (mtm110) REVERT: B 875 MET cc_start: 0.5798 (tpp) cc_final: 0.5328 (tpp) REVERT: B 918 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6429 (pp20) REVERT: B 952 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5581 (tm-30) REVERT: B 979 GLU cc_start: 0.8074 (mp0) cc_final: 0.7196 (mp0) REVERT: B 1016 ASP cc_start: 0.7588 (m-30) cc_final: 0.7328 (p0) REVERT: B 1024 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7729 (tpp) REVERT: B 1029 ASP cc_start: 0.8128 (m-30) cc_final: 0.7720 (m-30) REVERT: B 1041 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: B 1160 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: B 1188 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7682 (mt-10) outliers start: 156 outliers final: 110 residues processed: 342 average time/residue: 0.1315 time to fit residues: 72.1056 Evaluate side-chains 353 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 218 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1129 TYR Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1157 ILE Chi-restraints excluded: chain B residue 1160 GLN Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1188 GLU Chi-restraints excluded: chain B residue 1189 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 23 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 179 optimal weight: 0.0570 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 132 optimal weight: 0.0030 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS ** B 969 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 = 0.4090 r_free = 0.4090 target = 0.171464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125615 restraints weight = 26145.736| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.37 r_work: 0.3305 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20677 Z= 0.115 Angle : 0.629 15.360 28222 Z= 0.296 Chirality : 0.043 0.413 3025 Planarity : 0.004 0.059 3602 Dihedral : 8.185 73.747 3419 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.72 % Allowed : 25.25 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.18), residues: 2396 helix: 1.62 (0.13), residues: 1490 sheet: -1.72 (0.92), residues: 32 loop : -1.59 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 629 TYR 0.016 0.001 TYR B 970 PHE 0.013 0.001 PHE A 502 TRP 0.019 0.001 TRP B 40 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00247 (20631) covalent geometry : angle 0.59307 (28095) SS BOND : bond 0.00640 ( 11) SS BOND : angle 2.91327 ( 22) hydrogen bonds : bond 0.03717 ( 1074) hydrogen bonds : angle 3.99334 ( 3135) link_BETA1-4 : bond 0.00779 ( 16) link_BETA1-4 : angle 3.02215 ( 48) link_BETA1-6 : bond 0.00608 ( 1) link_BETA1-6 : angle 1.13379 ( 3) link_NAG-ASN : bond 0.00841 ( 18) link_NAG-ASN : angle 3.47446 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 234 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6065 (mp10) cc_final: 0.5677 (mp10) REVERT: A 22 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: A 63 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7615 (mt-10) REVERT: A 98 LEU cc_start: 0.8613 (mt) cc_final: 0.8305 (mp) REVERT: A 353 MET cc_start: 0.7667 (mmm) cc_final: 0.7060 (mtm) REVERT: A 354 ASP cc_start: 0.6782 (p0) cc_final: 0.6561 (p0) REVERT: A 387 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: A 388 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: A 530 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 625 GLU cc_start: 0.7445 (tp30) cc_final: 0.7176 (tp30) REVERT: A 640 GLU cc_start: 0.5792 (mm-30) cc_final: 0.5255 (mt-10) REVERT: A 699 GLU cc_start: 0.5385 (OUTLIER) cc_final: 0.5177 (pm20) REVERT: A 723 SER cc_start: 0.8788 (t) cc_final: 0.8481 (p) REVERT: A 736 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6828 (mt0) REVERT: A 859 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.6017 (p90) REVERT: A 914 LYS cc_start: 0.6371 (OUTLIER) cc_final: 0.5759 (tmtm) REVERT: A 961 MET cc_start: 0.7257 (mmm) cc_final: 0.6835 (mmm) REVERT: A 979 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6682 (mm-30) REVERT: A 1012 GLU cc_start: 0.1507 (OUTLIER) cc_final: -0.0546 (tm-30) REVERT: A 1018 HIS cc_start: 0.6063 (t-90) cc_final: 0.5710 (t-170) REVERT: A 1119 HIS cc_start: 0.4014 (OUTLIER) cc_final: 0.3487 (p90) REVERT: A 1130 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: A 1156 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6976 (tp) REVERT: A 1164 SER cc_start: 0.8526 (t) cc_final: 0.8277 (m) REVERT: B 55 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7351 (tp30) REVERT: B 89 ARG cc_start: 0.7160 (tpt170) cc_final: 0.6329 (mtm180) REVERT: B 96 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7696 (tmm-80) REVERT: B 370 LEU cc_start: 0.8419 (tm) cc_final: 0.7715 (mm) REVERT: B 393 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: B 411 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6797 (tm) REVERT: B 554 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7932 (mp0) REVERT: B 594 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.6684 (p-90) REVERT: B 662 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7399 (mpp) REVERT: B 674 GLN cc_start: 0.7867 (tt0) cc_final: 0.7450 (mt0) REVERT: B 707 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: B 801 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: B 811 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7488 (mtm110) REVERT: B 875 MET cc_start: 0.5808 (tpp) cc_final: 0.5322 (tpp) REVERT: B 894 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7813 (mm-30) REVERT: B 952 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5447 (tm-30) REVERT: B 1016 ASP cc_start: 0.7529 (m-30) cc_final: 0.7295 (p0) REVERT: B 1024 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7799 (tpp) REVERT: B 1029 ASP cc_start: 0.8119 (m-30) cc_final: 0.7670 (m-30) REVERT: B 1041 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8022 (t0) outliers start: 119 outliers final: 77 residues processed: 321 average time/residue: 0.1312 time to fit residues: 67.6131 Evaluate side-chains 316 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1130 GLN Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1090 ILE Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1185 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 112 optimal weight: 6.9990 chunk 147 optimal weight: 0.0570 chunk 115 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.170865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121814 restraints weight = 26129.806| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.30 r_work: 0.3319 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20677 Z= 0.125 Angle : 0.643 19.180 28222 Z= 0.303 Chirality : 0.044 0.546 3025 Planarity : 0.004 0.059 3602 Dihedral : 7.933 73.005 3404 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.39 % Allowed : 25.54 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2396 helix: 1.67 (0.13), residues: 1490 sheet: -1.87 (0.90), residues: 32 loop : -1.58 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 629 TYR 0.027 0.001 TYR A 372 PHE 0.027 0.001 PHE B 898 TRP 0.033 0.001 TRP B 40 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00281 (20631) covalent geometry : angle 0.60746 (28095) SS BOND : bond 0.00914 ( 11) SS BOND : angle 3.15374 ( 22) hydrogen bonds : bond 0.03812 ( 1074) hydrogen bonds : angle 3.95171 ( 3135) link_BETA1-4 : bond 0.00790 ( 16) link_BETA1-4 : angle 2.94939 ( 48) link_BETA1-6 : bond 0.00585 ( 1) link_BETA1-6 : angle 1.13559 ( 3) link_NAG-ASN : bond 0.00970 ( 18) link_NAG-ASN : angle 3.49593 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 223 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6150 (mp10) cc_final: 0.5737 (mp10) REVERT: A 63 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7681 (mt-10) REVERT: A 98 LEU cc_start: 0.8693 (mt) cc_final: 0.8363 (mp) REVERT: A 353 MET cc_start: 0.7706 (mmm) cc_final: 0.7090 (mtm) REVERT: A 354 ASP cc_start: 0.6908 (p0) cc_final: 0.6671 (p0) REVERT: A 387 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: A 388 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8168 (m-70) REVERT: A 413 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.4871 (mmm160) REVERT: A 530 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8279 (mp) REVERT: A 625 GLU cc_start: 0.7480 (tp30) cc_final: 0.7188 (tp30) REVERT: A 640 GLU cc_start: 0.5889 (mm-30) cc_final: 0.5324 (mt-10) REVERT: A 699 GLU cc_start: 0.5496 (OUTLIER) cc_final: 0.5246 (pm20) REVERT: A 723 SER cc_start: 0.8806 (t) cc_final: 0.8491 (p) REVERT: A 736 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6940 (mt0) REVERT: A 811 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7064 (ttp80) REVERT: A 859 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.6295 (p90) REVERT: A 961 MET cc_start: 0.7481 (mmm) cc_final: 0.7041 (mmm) REVERT: A 979 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6749 (mm-30) REVERT: A 1012 GLU cc_start: 0.1492 (OUTLIER) cc_final: -0.0649 (tm-30) REVERT: A 1018 HIS cc_start: 0.6099 (t-90) cc_final: 0.5752 (t-170) REVERT: A 1119 HIS cc_start: 0.4077 (OUTLIER) cc_final: 0.3538 (p90) REVERT: A 1147 SER cc_start: 0.8730 (t) cc_final: 0.8407 (p) REVERT: A 1156 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6988 (tp) REVERT: A 1164 SER cc_start: 0.8602 (t) cc_final: 0.8358 (m) REVERT: B 55 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7336 (tp30) REVERT: B 89 ARG cc_start: 0.7239 (tpt170) cc_final: 0.6430 (mtm180) REVERT: B 96 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7796 (tmm-80) REVERT: B 363 MET cc_start: 0.8625 (ttp) cc_final: 0.8363 (ttp) REVERT: B 393 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7718 (t0) REVERT: B 554 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8088 (mp0) REVERT: B 594 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.6764 (p-90) REVERT: B 674 GLN cc_start: 0.7967 (tt0) cc_final: 0.7535 (mt0) REVERT: B 801 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: B 811 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7513 (mtm110) REVERT: B 875 MET cc_start: 0.5813 (tpp) cc_final: 0.5329 (tpp) REVERT: B 894 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7833 (mm-30) REVERT: B 952 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5511 (tm-30) REVERT: B 1016 ASP cc_start: 0.7589 (m-30) cc_final: 0.7323 (p0) REVERT: B 1029 ASP cc_start: 0.8293 (m-30) cc_final: 0.7817 (m-30) REVERT: B 1055 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8367 (mp0) outliers start: 112 outliers final: 82 residues processed: 304 average time/residue: 0.1447 time to fit residues: 70.0189 Evaluate side-chains 316 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1055 GLU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1189 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 70 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS ** B 965 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 = 0.4082 r_free = 0.4082 target = 0.170741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124546 restraints weight = 26036.820| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.23 r_work: 0.3308 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20677 Z= 0.132 Angle : 0.646 17.551 28222 Z= 0.305 Chirality : 0.044 0.527 3025 Planarity : 0.004 0.059 3602 Dihedral : 7.821 72.927 3398 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.72 % Allowed : 24.92 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2396 helix: 1.68 (0.13), residues: 1490 sheet: -1.85 (0.91), residues: 32 loop : -1.58 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 629 TYR 0.025 0.001 TYR A 372 PHE 0.022 0.001 PHE B 898 TRP 0.029 0.001 TRP B 635 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00301 (20631) covalent geometry : angle 0.61106 (28095) SS BOND : bond 0.00591 ( 11) SS BOND : angle 3.14024 ( 22) hydrogen bonds : bond 0.03877 ( 1074) hydrogen bonds : angle 3.94493 ( 3135) link_BETA1-4 : bond 0.00773 ( 16) link_BETA1-4 : angle 2.93082 ( 48) link_BETA1-6 : bond 0.00579 ( 1) link_BETA1-6 : angle 1.13965 ( 3) link_NAG-ASN : bond 0.00886 ( 18) link_NAG-ASN : angle 3.44173 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 222 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6183 (mp10) cc_final: 0.5759 (mp10) REVERT: A 22 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7131 (mp10) REVERT: A 63 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7679 (mt-10) REVERT: A 98 LEU cc_start: 0.8702 (mt) cc_final: 0.8371 (mp) REVERT: A 353 MET cc_start: 0.7725 (mmm) cc_final: 0.7115 (mtm) REVERT: A 354 ASP cc_start: 0.6926 (p0) cc_final: 0.6689 (p0) REVERT: A 387 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: A 388 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.8176 (m-70) REVERT: A 413 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.4873 (mmm160) REVERT: A 530 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 625 GLU cc_start: 0.7489 (tp30) cc_final: 0.7205 (tp30) REVERT: A 640 GLU cc_start: 0.5820 (mm-30) cc_final: 0.5295 (mt-10) REVERT: A 699 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.5230 (pm20) REVERT: A 723 SER cc_start: 0.8830 (t) cc_final: 0.8526 (p) REVERT: A 736 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.6953 (mt0) REVERT: A 811 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7086 (ttp80) REVERT: A 859 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.6458 (p90) REVERT: A 914 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5861 (tmtm) REVERT: A 961 MET cc_start: 0.7506 (mmm) cc_final: 0.7055 (mmm) REVERT: A 979 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6705 (mm-30) REVERT: A 1012 GLU cc_start: 0.1557 (OUTLIER) cc_final: -0.0538 (tm-30) REVERT: A 1018 HIS cc_start: 0.6133 (t-90) cc_final: 0.5783 (t-170) REVERT: A 1119 HIS cc_start: 0.4102 (OUTLIER) cc_final: 0.3588 (p90) REVERT: A 1147 SER cc_start: 0.8749 (t) cc_final: 0.8426 (p) REVERT: A 1156 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7004 (tp) REVERT: A 1164 SER cc_start: 0.8628 (t) cc_final: 0.8394 (m) REVERT: B 55 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7332 (tp30) REVERT: B 89 ARG cc_start: 0.7323 (tpt170) cc_final: 0.6538 (mtm180) REVERT: B 96 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (tmm-80) REVERT: B 363 MET cc_start: 0.8618 (ttp) cc_final: 0.8369 (ttp) REVERT: B 393 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7745 (t0) REVERT: B 411 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6886 (tm) REVERT: B 554 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8118 (mp0) REVERT: B 594 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.6800 (p-90) REVERT: B 674 GLN cc_start: 0.7994 (tt0) cc_final: 0.7559 (mt0) REVERT: B 801 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: B 811 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7541 (mtm110) REVERT: B 875 MET cc_start: 0.5646 (tpp) cc_final: 0.5156 (tpp) REVERT: B 894 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 952 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5505 (tm-30) REVERT: B 1016 ASP cc_start: 0.7613 (m-30) cc_final: 0.7339 (p0) REVERT: B 1024 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: B 1029 ASP cc_start: 0.8321 (m-30) cc_final: 0.7872 (m-30) REVERT: B 1055 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8445 (mp0) outliers start: 119 outliers final: 93 residues processed: 309 average time/residue: 0.1443 time to fit residues: 71.2804 Evaluate side-chains 331 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 218 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 859 TRP Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1055 GLU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 200 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 180 optimal weight: 0.0170 chunk 224 optimal weight: 0.0980 chunk 218 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.171134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125667 restraints weight = 26107.823| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.37 r_work: 0.3328 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20677 Z= 0.128 Angle : 0.645 16.305 28222 Z= 0.306 Chirality : 0.044 0.501 3025 Planarity : 0.004 0.059 3602 Dihedral : 7.729 72.732 3398 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.53 % Allowed : 24.92 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2396 helix: 1.71 (0.13), residues: 1482 sheet: -1.85 (0.90), residues: 32 loop : -1.58 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 629 TYR 0.025 0.001 TYR A 372 PHE 0.023 0.001 PHE B 898 TRP 0.031 0.001 TRP B 635 HIS 0.010 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00289 (20631) covalent geometry : angle 0.61112 (28095) SS BOND : bond 0.00516 ( 11) SS BOND : angle 3.18195 ( 22) hydrogen bonds : bond 0.03825 ( 1074) hydrogen bonds : angle 3.93791 ( 3135) link_BETA1-4 : bond 0.00769 ( 16) link_BETA1-4 : angle 2.89730 ( 48) link_BETA1-6 : bond 0.00568 ( 1) link_BETA1-6 : angle 1.13414 ( 3) link_NAG-ASN : bond 0.00880 ( 18) link_NAG-ASN : angle 3.39329 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 221 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.6276 (mp10) cc_final: 0.5839 (mp10) REVERT: A 22 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: A 63 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7666 (mt-10) REVERT: A 98 LEU cc_start: 0.8687 (mt) cc_final: 0.8356 (mp) REVERT: A 283 MET cc_start: 0.4909 (pmm) cc_final: 0.4133 (mtt) REVERT: A 353 MET cc_start: 0.7727 (mmm) cc_final: 0.7135 (mtm) REVERT: A 354 ASP cc_start: 0.6929 (p0) cc_final: 0.6685 (p0) REVERT: A 387 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: A 388 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8121 (m-70) REVERT: A 413 ARG cc_start: 0.5528 (OUTLIER) cc_final: 0.4869 (mmm160) REVERT: A 530 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 625 GLU cc_start: 0.7445 (tp30) cc_final: 0.7182 (tp30) REVERT: A 640 GLU cc_start: 0.5811 (mm-30) cc_final: 0.5300 (mt-10) REVERT: A 699 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.5218 (pm20) REVERT: A 723 SER cc_start: 0.8820 (t) cc_final: 0.8512 (p) REVERT: A 736 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: A 811 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7067 (ttp80) REVERT: A 914 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5865 (tmtm) REVERT: A 961 MET cc_start: 0.7486 (mmm) cc_final: 0.7028 (mmm) REVERT: A 979 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6673 (mm-30) REVERT: A 1012 GLU cc_start: 0.1597 (OUTLIER) cc_final: -0.0545 (tm-30) REVERT: A 1018 HIS cc_start: 0.6124 (t-90) cc_final: 0.5765 (t-170) REVERT: A 1119 HIS cc_start: 0.4107 (OUTLIER) cc_final: 0.3606 (p90) REVERT: A 1147 SER cc_start: 0.8747 (t) cc_final: 0.8404 (p) REVERT: A 1156 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6988 (tp) REVERT: A 1164 SER cc_start: 0.8619 (t) cc_final: 0.8389 (m) REVERT: B 55 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7342 (tp30) REVERT: B 89 ARG cc_start: 0.7298 (tpt170) cc_final: 0.6498 (mtm180) REVERT: B 96 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7782 (tmm-80) REVERT: B 363 MET cc_start: 0.8607 (ttp) cc_final: 0.8356 (ttp) REVERT: B 393 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7713 (t0) REVERT: B 411 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6837 (tm) REVERT: B 554 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8102 (mp0) REVERT: B 594 TRP cc_start: 0.7439 (OUTLIER) cc_final: 0.6857 (p-90) REVERT: B 674 GLN cc_start: 0.7994 (tt0) cc_final: 0.7553 (mt0) REVERT: B 801 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: B 811 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7516 (mtm110) REVERT: B 875 MET cc_start: 0.5640 (tpp) cc_final: 0.5161 (tpp) REVERT: B 894 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 952 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5496 (tm-30) REVERT: B 1016 ASP cc_start: 0.7584 (m-30) cc_final: 0.7319 (p0) REVERT: B 1024 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7830 (tpp) REVERT: B 1029 ASP cc_start: 0.8321 (m-30) cc_final: 0.7868 (m-30) REVERT: B 1055 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8525 (mp0) outliers start: 115 outliers final: 88 residues processed: 306 average time/residue: 0.1431 time to fit residues: 68.7770 Evaluate side-chains 322 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 215 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 707 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1015 SER Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1056 ASN Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1150 TRP Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 TRP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 801 GLU Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 902 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 LEU Chi-restraints excluded: chain B residue 931 SER Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1024 MET Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1044 ARG Chi-restraints excluded: chain B residue 1055 GLU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1150 TRP Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 181 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN ** B 965 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 = 0.4077 r_free = 0.4077 target = 0.170209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123770 restraints weight = 26257.901| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.21 r_work: 0.3305 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20677 Z= 0.141 Angle : 0.647 15.242 28222 Z= 0.308 Chirality : 0.044 0.487 3025 Planarity : 0.004 0.059 3602 Dihedral : 7.700 72.822 3396 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.87 % Allowed : 24.72 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.18), residues: 2396 helix: 1.71 (0.13), residues: 1484 sheet: -1.93 (0.89), residues: 32 loop : -1.60 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 629 TYR 0.034 0.002 TYR A 531 PHE 0.020 0.001 PHE B 898 TRP 0.033 0.001 TRP B 635 HIS 0.008 0.001 HIS A 834 Details of bonding type rmsd covalent geometry : bond 0.00327 (20631) covalent geometry : angle 0.61299 (28095) SS BOND : bond 0.00481 ( 11) SS BOND : angle 3.16855 ( 22) hydrogen bonds : bond 0.04001 ( 1074) hydrogen bonds : angle 3.95187 ( 3135) link_BETA1-4 : bond 0.00772 ( 16) link_BETA1-4 : angle 2.88378 ( 48) link_BETA1-6 : bond 0.00567 ( 1) link_BETA1-6 : angle 1.14756 ( 3) link_NAG-ASN : bond 0.00870 ( 18) link_NAG-ASN : angle 3.38925 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.10 seconds wall clock time: 110 minutes 54.78 seconds (6654.78 seconds total)