Starting phenix.real_space_refine on Mon Sep 14 00:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xo3_67068/09_2026/9xo3_67068.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xo3_67068/09_2026/9xo3_67068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xo3_67068/09_2026/9xo3_67068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xo3_67068/09_2026/9xo3_67068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xo3_67068/09_2026/9xo3_67068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xo3_67068/09_2026/9xo3_67068.map" } resolution = 3.8 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= 0.002 sd= 0.033 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 125 5.16 5 C 16417 2.51 5 N 4151 2.21 5 O 5144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25837 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7555 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 37, 'TRANS': 947} Chain breaks: 16 Chain: "B" Number of atoms: 8748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 8748 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 41, 'TRANS': 1096} Chain breaks: 10 Chain: "C" Number of atoms: 8763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8763 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 41, 'TRANS': 1099} Chain breaks: 9 Chain: "D" 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: "E" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.10, per 1000 atoms: 0.24 Number of scatterers: 25837 At special positions: 0 Unit cell: (157.08, 165, 167.64, 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 125 16.00 O 5144 8.00 N 4151 7.00 C 16417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.04 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.04 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1401 " - " ASN A 216 " " NAG A1402 " - " ASN A 344 " " NAG A1403 " - " ASN A 726 " " NAG A1404 " - " ASN A 781 " " NAG A1405 " - " ASN A 514 " " NAG A1406 " - " ASN A 743 " " NAG A1407 " - " ASN A 787 " " NAG A1408 " - " ASN A 873 " " NAG B1401 " - " ASN B 324 " " NAG B1402 " - " ASN B 216 " " NAG B1403 " - " ASN B 514 " " NAG B1404 " - " ASN B 726 " " NAG B1405 " - " ASN B 781 " " NAG B1406 " - " ASN B 743 " " NAG B1407 " - " ASN B 787 " " NAG B1408 " - " ASN B 873 " " NAG B1409 " - " ASN B1232 " " NAG B1410 " - " ASN B 344 " " NAG B1411 " - " ASN B 351 " " NAG C1401 " - " ASN C 324 " " NAG C1402 " - " ASN C 216 " " NAG C1403 " - " ASN C 514 " " NAG C1404 " - " ASN C 726 " " NAG C1405 " - " ASN C 781 " " NAG C1406 " - " ASN C 743 " " NAG C1407 " - " ASN C 787 " " NAG C1408 " - " ASN C 873 " " NAG C1409 " - " ASN C1232 " " NAG C1410 " - " ASN C 344 " " NAG C1411 " - " ASN C 351 " " NAG D 1 " - " ASN A 324 " " NAG E 1 " - " ASN A 688 " " NAG F 1 " - " ASN A 264 " " NAG G 1 " - " ASN B 264 " " NAG H 1 " - " ASN B 688 " " NAG I 1 " - " ASN B 425 " " NAG J 1 " - " ASN C 264 " " NAG K 1 " - " ASN C 688 " " NAG L 1 " - " ASN C 425 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6058 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 53 sheets defined 22.1% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.704A pdb=" N SER A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.612A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 807 through 813 removed outlier: 3.950A pdb=" N TYR A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.961A pdb=" N LEU A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 removed outlier: 3.768A pdb=" N GLN A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.583A pdb=" N LEU A 878 " --> pdb=" O THR A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 917 through 922 removed outlier: 4.031A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 917 through 922' Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 959 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.833A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1030 through 1045 Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1066 through 1074 removed outlier: 3.703A pdb=" N LEU A1074 " --> pdb=" O ILE A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.663A pdb=" N ALA A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A1084 " --> pdb=" O ASP A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.685A pdb=" N LYS B 38 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 39 " --> pdb=" O PHE B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 39' Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.856A pdb=" N GLY B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 225 " --> pdb=" O GLU B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.555A pdb=" N VAL B 328 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 330 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.568A pdb=" N LEU B 357 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 358' Processing helix chain 'B' and resid 466 through 475 removed outlier: 3.707A pdb=" N LEU B 471 " --> pdb=" O PRO B 467 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 825 removed outlier: 4.174A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.548A pdb=" N THR B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.839A pdb=" N LEU B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.540A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 921 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 960 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.796A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1015 removed outlier: 3.565A pdb=" N GLU B1015 " --> pdb=" O THR B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1044 removed outlier: 3.514A pdb=" N ALA B1034 " --> pdb=" O THR B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1054 Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1077 through 1123 removed outlier: 4.397A pdb=" N VAL B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B1082 " --> pdb=" O SER B1078 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B1086 " --> pdb=" O GLN B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1234 through 1236 No H-bonds generated for 'chain 'B' and resid 1234 through 1236' Processing helix chain 'B' and resid 1237 through 1242 removed outlier: 3.861A pdb=" N VAL B1241 " --> pdb=" O GLN B1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 4.103A pdb=" N ILE C 225 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.515A pdb=" N VAL C 328 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 330 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 removed outlier: 3.568A pdb=" N GLN C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 580 removed outlier: 4.473A pdb=" N ASN C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.174A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.599A pdb=" N THR C 832 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 860 removed outlier: 3.794A pdb=" N GLN C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 918 through 923 removed outlier: 3.753A pdb=" N ASN C 922 " --> pdb=" O LYS C 918 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY C 923 " --> pdb=" O ARG C 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 923' Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 946 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 973 through 983 removed outlier: 3.808A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1014 removed outlier: 3.673A pdb=" N THR C1011 " --> pdb=" O ILE C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1044 Processing helix chain 'C' and resid 1046 through 1054 Processing helix chain 'C' and resid 1055 through 1058 removed outlier: 3.656A pdb=" N HIS C1058 " --> pdb=" O GLN C1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1055 through 1058' Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1123 removed outlier: 3.719A pdb=" N ASP C1080 " --> pdb=" O ILE C1076 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL C1081 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C1086 " --> pdb=" O GLN C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1242 removed outlier: 3.600A pdb=" N VAL C1241 " --> pdb=" O GLN C1237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 removed outlier: 3.611A pdb=" N VAL A 47 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.737A pdb=" N GLY A 165 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.579A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 444 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 7.579A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.893A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 424 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 334 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 350 removed outlier: 3.537A pdb=" N CYS A 373 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 389 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 4.261A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 531 through 536 removed outlier: 3.984A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 549 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 587 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 585 " --> pdb=" O GLY A 625 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 536 removed outlier: 3.984A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 549 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 650 through 654 removed outlier: 3.521A pdb=" N GLY A 659 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 685 " --> pdb=" O TYR A 676 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 786 removed outlier: 3.953A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A1189 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 798 removed outlier: 4.059A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1172 through 1174 removed outlier: 3.517A pdb=" N THR A1181 " --> pdb=" O VAL A1221 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.667A pdb=" N ALA B 45 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 47 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 215 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 213 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.979A pdb=" N GLY B 69 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 196 " --> pdb=" O GLY B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 180 through 184 removed outlier: 3.850A pdb=" N VAL B 175 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 165 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 79 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 81 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.503A pdb=" N PHE B 91 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 111 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 Processing sheet with id=AC4, first strand: chain 'B' and resid 270 through 278 removed outlier: 3.719A pdb=" N GLY B 271 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 453 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 449 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP B 448 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR B 463 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 450 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 461 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU B 452 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 457 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 288 removed outlier: 3.511A pdb=" N LEU B 285 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 440 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 408 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 293 through 296 removed outlier: 3.669A pdb=" N GLN B 295 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 379 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 382 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 483 through 488 removed outlier: 4.085A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 718 " --> pdb=" O PHE B 735 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 738 " --> pdb=" O SER B 727 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 533 through 536 removed outlier: 3.654A pdb=" N ILE B 515 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 517 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 558 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR B 619 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 590 " --> pdb=" O TYR B 619 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN B 621 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 588 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 623 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY B 625 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N SER B 584 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 533 through 536 removed outlier: 3.654A pdb=" N ILE B 515 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 517 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 558 " --> pdb=" O ALA B 519 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS B 614 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY B 605 " --> pdb=" O LYS B 614 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 616 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 567 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 649 through 654 Processing sheet with id=AD2, first strand: chain 'B' and resid 675 through 677 Processing sheet with id=AD3, first strand: chain 'B' and resid 749 through 751 removed outlier: 3.627A pdb=" N LEU B 749 " --> pdb=" O VAL B 756 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 780 through 797 removed outlier: 6.632A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN B 787 " --> pdb=" O GLY B1161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B1157 " --> pdb=" O SER B 791 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 780 through 797 removed outlier: 6.632A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN B 787 " --> pdb=" O GLY B1161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B1157 " --> pdb=" O SER B 791 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B1189 " --> pdb=" O ILE B1169 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD7, first strand: chain 'B' and resid 1179 through 1182 removed outlier: 4.365A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AE1, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.781A pdb=" N GLY C 69 " --> pdb=" O CYS C 196 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS C 196 " --> pdb=" O GLY C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AE3, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.528A pdb=" N VAL C 175 " --> pdb=" O TYR C 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'C' and resid 270 through 288 removed outlier: 5.613A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 401 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 270 through 288 removed outlier: 5.613A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP C 448 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR C 463 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C 450 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE C 461 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLU C 452 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 293 through 298 removed outlier: 3.514A pdb=" N GLN C 295 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 421 " --> pdb=" O HIS C 338 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 293 through 298 removed outlier: 3.514A pdb=" N GLN C 295 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 421 " --> pdb=" O HIS C 338 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 382 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 499 through 502 removed outlier: 3.538A pdb=" N GLY C 659 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 531 through 536 removed outlier: 3.631A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 520 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 550 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 517 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 549 " --> pdb=" O THR C 629 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 531 through 536 removed outlier: 3.631A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 520 " --> pdb=" O ALA C 531 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 550 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 517 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 549 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS C 587 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR C 616 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 567 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR C 606 " --> pdb=" O SER C 565 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 705 through 706 Processing sheet with id=AF4, first strand: chain 'C' and resid 747 through 751 Processing sheet with id=AF5, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.698A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF7, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.933A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C1178 " --> pdb=" O VAL C1174 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N CYS C1173 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1188 through 1190 938 hydrogen bonds defined for protein. 2589 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: 7.33 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8122 1.34 - 1.46: 6752 1.46 - 1.59: 11331 1.59 - 1.71: 0 1.71 - 1.83: 159 Bond restraints: 26364 Sorted by residual: bond pdb=" C ALA B 43 " pdb=" N PRO B 44 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" CA ILE C 530 " pdb=" C ILE C 530 " ideal model delta sigma weight residual 1.523 1.534 -0.011 9.60e-03 1.09e+04 1.27e+00 bond pdb=" C ALA A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.26e+00 bond pdb=" C ASP C 466 " pdb=" N PRO C 467 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.03e+00 bond pdb=" CA ASN A 233 " pdb=" CB ASN A 233 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.99e-01 ... (remaining 26359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 35501 2.33 - 4.66: 334 4.66 - 6.99: 19 6.99 - 9.32: 4 9.32 - 11.65: 2 Bond angle restraints: 35860 Sorted by residual: angle pdb=" N ILE B 530 " pdb=" CA ILE B 530 " pdb=" C ILE B 530 " ideal model delta sigma weight residual 111.48 107.65 3.83 9.40e-01 1.13e+00 1.66e+01 angle pdb=" C2 NAG B1409 " pdb=" N2 NAG B1409 " pdb=" C7 NAG B1409 " ideal model delta sigma weight residual 124.56 136.21 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C2 NAG C1409 " pdb=" N2 NAG C1409 " pdb=" C7 NAG C1409 " ideal model delta sigma weight residual 124.56 136.20 -11.64 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C ALA A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 121.54 128.91 -7.37 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C ILE A1223 " pdb=" N GLU A1224 " pdb=" CA GLU A1224 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 ... (remaining 35855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.01: 15620 24.01 - 48.02: 543 48.02 - 72.03: 95 72.03 - 96.04: 19 96.04 - 120.05: 6 Dihedral angle restraints: 16283 sinusoidal: 6842 harmonic: 9441 Sorted by residual: dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 700 " pdb=" CB CYS C 700 " ideal model delta sinusoidal sigma weight residual -86.00 -2.99 -83.01 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C 230 " pdb=" SG CYS C 230 " pdb=" SG CYS C 234 " pdb=" CB CYS C 234 " ideal model delta sinusoidal sigma weight residual 93.00 169.87 -76.87 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 757 " pdb=" CB CYS C 757 " ideal model delta sinusoidal sigma weight residual 93.00 17.01 75.99 1 1.00e+01 1.00e-02 7.28e+01 ... (remaining 16280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3617 0.060 - 0.119: 630 0.119 - 0.179: 66 0.179 - 0.238: 7 0.238 - 0.298: 2 Chirality restraints: 4322 Sorted by residual: chirality pdb=" C2 NAG B1409 " pdb=" C1 NAG B1409 " pdb=" C3 NAG B1409 " pdb=" N2 NAG B1409 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C2 NAG C1409 " pdb=" C1 NAG C1409 " pdb=" C3 NAG C1409 " pdb=" N2 NAG C1409 " both_signs ideal model delta sigma weight residual False -2.49 -2.21 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB ILE B1140 " pdb=" CA ILE B1140 " pdb=" CG1 ILE B1140 " pdb=" CG2 ILE B1140 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4319 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 277 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 278 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 392 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 393 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 393 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 393 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1147 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A1148 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1148 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1148 " 0.024 5.00e-02 4.00e+02 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9551 2.89 - 3.40: 22672 3.40 - 3.90: 41267 3.90 - 4.40: 44968 4.40 - 4.90: 78974 Nonbonded interactions: 197432 Sorted by model distance: nonbonded pdb=" O5 MAN G 4 " pdb=" O6 MAN G 4 " model vdw 2.392 2.432 nonbonded pdb=" O5 MAN J 4 " pdb=" O6 MAN J 4 " model vdw 2.394 2.432 nonbonded pdb=" C3 MAN J 5 " pdb=" O5 MAN J 5 " model vdw 2.568 2.776 nonbonded pdb=" C3 MAN G 5 " pdb=" O5 MAN G 5 " model vdw 2.568 2.776 nonbonded pdb=" O2 BMA G 3 " pdb=" O3 BMA G 3 " model vdw 2.590 2.432 ... (remaining 197427 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' selection = (chain 'B' and (resid 33 through 54 or resid 67 through 82 or resid 163 through \ 168 or resid 173 through 178 or resid 205 through 219 or resid 225 through 290 o \ r resid 294 through 355 or resid 369 through 426 or resid 437 through 880 or res \ id 894 through 904 or resid 915 through 970 or resid 972 through 989 or resid 99 \ 6 through 1014 or resid 1026 through 1231 or resid 1404 through 1411)) selection = (chain 'C' and (resid 33 through 54 or resid 67 through 73 or resid 77 through 8 \ 2 or resid 163 through 168 or resid 173 through 178 or resid 205 through 219 or \ resid 225 through 290 or resid 294 through 355 or resid 369 through 426 or resid \ 437 through 880 or resid 894 through 904 or resid 915 through 970 or resid 972 \ through 989 or resid 996 through 1014 or resid 1026 through 1231 or resid 1404 t \ hrough 1411)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 27.190 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.003 0.028 26466 Z= 0.125 Angle : 0.583 11.650 36121 Z= 0.298 Chirality : 0.045 0.298 4322 Planarity : 0.004 0.048 4521 Dihedral : 12.354 120.053 10090 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3188 helix: 0.59 (0.20), residues: 609 sheet: -0.40 (0.19), residues: 846 loop : -1.26 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 919 TYR 0.017 0.001 TYR A1071 PHE 0.019 0.001 PHE B 347 TRP 0.023 0.002 TRP A 259 HIS 0.006 0.001 HIS B 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (26364) covalent geometry : angle 0.57081 / 0.30 (35860) SS BOND : bond 0.00209 / 0.14 ( 45) SS BOND : angle 1.22539 / 0.88 ( 90) hydrogen bonds : bond 0.21045 / 13.40 ( 880) hydrogen bonds : angle 8.75356 / 6.00 ( 2589) link_ALPHA1-3 : bond 0.00820 / 0.41 ( 3) link_ALPHA1-3 : angle 1.68780 / 1.13 ( 9) link_ALPHA1-6 : bond 0.00846 / 0.44 ( 3) link_ALPHA1-6 : angle 1.44150 / 1.09 ( 9) link_BETA1-4 : bond 0.00298 / 0.21 ( 12) link_BETA1-4 : angle 1.66946 / 1.20 ( 36) link_NAG-ASN : bond 0.00209 / 0.14 ( 39) link_NAG-ASN : angle 1.62182 / 1.15 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 867 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.7836 (m110) cc_final: 0.7585 (m-40) REVERT: A 41 VAL cc_start: 0.8141 (t) cc_final: 0.7807 (p) REVERT: A 247 ASN cc_start: 0.7537 (p0) cc_final: 0.7260 (p0) REVERT: A 313 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7747 (mm110) REVERT: A 386 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7564 (mtpp) REVERT: A 391 LEU cc_start: 0.7901 (mp) cc_final: 0.7551 (mp) REVERT: A 397 GLU cc_start: 0.6967 (tt0) cc_final: 0.6414 (tt0) REVERT: A 398 ILE cc_start: 0.7917 (mt) cc_final: 0.7683 (mm) REVERT: A 481 ASP cc_start: 0.7509 (m-30) cc_final: 0.7239 (m-30) REVERT: A 507 PHE cc_start: 0.7866 (p90) cc_final: 0.7277 (p90) REVERT: A 508 ASN cc_start: 0.8009 (t0) cc_final: 0.7776 (t0) REVERT: A 539 PHE cc_start: 0.8058 (m-80) cc_final: 0.7852 (m-10) REVERT: A 593 SER cc_start: 0.7920 (m) cc_final: 0.7572 (p) REVERT: A 624 LYS cc_start: 0.7681 (tppp) cc_final: 0.7162 (tptp) REVERT: A 642 SER cc_start: 0.8650 (m) cc_final: 0.8374 (p) REVERT: A 651 LYS cc_start: 0.8128 (tttt) cc_final: 0.7897 (mtpp) REVERT: A 660 GLU cc_start: 0.6600 (mp0) cc_final: 0.6391 (mp0) REVERT: A 687 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8238 (tttt) REVERT: A 730 GLU cc_start: 0.7507 (tt0) cc_final: 0.7110 (tt0) REVERT: A 735 PHE cc_start: 0.8672 (m-80) cc_final: 0.7920 (m-10) REVERT: A 737 HIS cc_start: 0.8078 (m-70) cc_final: 0.7674 (m170) REVERT: A 738 SER cc_start: 0.8210 (p) cc_final: 0.7714 (m) REVERT: A 757 CYS cc_start: 0.6541 (t) cc_final: 0.6010 (t) REVERT: A 758 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8110 (ttmm) REVERT: A 773 LYS cc_start: 0.8246 (tttp) cc_final: 0.7706 (tttm) REVERT: A 782 ILE cc_start: 0.8801 (pt) cc_final: 0.8588 (pt) REVERT: A 795 GLU cc_start: 0.7756 (tt0) cc_final: 0.6767 (tt0) REVERT: A 801 ASN cc_start: 0.8090 (p0) cc_final: 0.7806 (p0) REVERT: A 820 LYS cc_start: 0.7613 (mtmt) cc_final: 0.7412 (mttp) REVERT: A 831 LYS cc_start: 0.6736 (tttt) cc_final: 0.6478 (ttpp) REVERT: A 844 GLU cc_start: 0.7664 (tp30) cc_final: 0.7283 (tp30) REVERT: A 853 THR cc_start: 0.7825 (p) cc_final: 0.7580 (p) REVERT: A 859 LEU cc_start: 0.8420 (tp) cc_final: 0.7995 (tp) REVERT: A 918 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7467 (mtmm) REVERT: A 949 LYS cc_start: 0.7517 (tttt) cc_final: 0.7192 (ttmm) REVERT: A 954 SER cc_start: 0.7900 (m) cc_final: 0.7359 (p) REVERT: A 978 VAL cc_start: 0.8084 (t) cc_final: 0.7775 (p) REVERT: A 1007 ILE cc_start: 0.8237 (tp) cc_final: 0.7941 (tp) REVERT: A 1011 THR cc_start: 0.8386 (m) cc_final: 0.8127 (p) REVERT: A 1040 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6686 (tm-30) REVERT: A 1069 ASP cc_start: 0.6833 (t0) cc_final: 0.6571 (t0) REVERT: A 1120 ASN cc_start: 0.7665 (m-40) cc_final: 0.7375 (m110) REVERT: A 1162 ASP cc_start: 0.6395 (t0) cc_final: 0.6087 (t0) REVERT: A 1167 ILE cc_start: 0.8183 (mm) cc_final: 0.7972 (mm) REVERT: A 1172 LEU cc_start: 0.7554 (mt) cc_final: 0.7275 (mp) REVERT: A 1183 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7156 (ttm110) REVERT: A 1190 PHE cc_start: 0.7847 (p90) cc_final: 0.7627 (p90) REVERT: A 1214 LYS cc_start: 0.8728 (mmpt) cc_final: 0.8304 (tmtt) REVERT: A 1230 TYR cc_start: 0.7094 (m-10) cc_final: 0.6755 (m-10) REVERT: B 167 THR cc_start: 0.8338 (m) cc_final: 0.7367 (p) REVERT: B 173 VAL cc_start: 0.8695 (t) cc_final: 0.8313 (m) REVERT: B 174 THR cc_start: 0.8362 (m) cc_final: 0.7417 (p) REVERT: B 185 PHE cc_start: 0.7470 (t80) cc_final: 0.6902 (t80) REVERT: B 188 ASP cc_start: 0.7206 (m-30) cc_final: 0.6476 (t70) REVERT: B 204 MET cc_start: 0.6670 (mtp) cc_final: 0.6414 (mtp) REVERT: B 214 MET cc_start: 0.6513 (tpp) cc_final: 0.5977 (tpt) REVERT: B 227 TYR cc_start: 0.7275 (p90) cc_final: 0.7021 (p90) REVERT: B 242 PHE cc_start: 0.7882 (p90) cc_final: 0.7589 (p90) REVERT: B 263 SER cc_start: 0.7889 (t) cc_final: 0.7558 (p) REVERT: B 269 VAL cc_start: 0.8313 (t) cc_final: 0.8098 (p) REVERT: B 272 LYS cc_start: 0.8096 (mttt) cc_final: 0.7824 (mtmm) REVERT: B 276 ASN cc_start: 0.7725 (t0) cc_final: 0.6651 (p0) REVERT: B 280 LEU cc_start: 0.7808 (tp) cc_final: 0.7551 (tp) REVERT: B 328 VAL cc_start: 0.8702 (m) cc_final: 0.8159 (t) REVERT: B 334 SER cc_start: 0.8358 (p) cc_final: 0.8050 (m) REVERT: B 353 SER cc_start: 0.8689 (m) cc_final: 0.8448 (p) REVERT: B 387 PHE cc_start: 0.7685 (t80) cc_final: 0.7452 (t80) REVERT: B 439 TRP cc_start: 0.8137 (p-90) cc_final: 0.7908 (p-90) REVERT: B 444 THR cc_start: 0.8150 (p) cc_final: 0.7582 (t) REVERT: B 485 TYR cc_start: 0.8277 (m-80) cc_final: 0.7998 (m-80) REVERT: B 488 SER cc_start: 0.8444 (m) cc_final: 0.8136 (t) REVERT: B 533 ASP cc_start: 0.7691 (t70) cc_final: 0.7203 (m-30) REVERT: B 552 SER cc_start: 0.8416 (m) cc_final: 0.7623 (t) REVERT: B 553 LEU cc_start: 0.7440 (tp) cc_final: 0.7192 (pt) REVERT: B 593 SER cc_start: 0.8664 (m) cc_final: 0.7732 (p) REVERT: B 594 LEU cc_start: 0.8377 (tp) cc_final: 0.8074 (tp) REVERT: B 600 THR cc_start: 0.7614 (m) cc_final: 0.7309 (t) REVERT: B 601 ILE cc_start: 0.8364 (mt) cc_final: 0.8152 (tt) REVERT: B 613 VAL cc_start: 0.8400 (m) cc_final: 0.8140 (p) REVERT: B 614 LYS cc_start: 0.8466 (ttpt) cc_final: 0.7856 (ptmm) REVERT: B 619 TYR cc_start: 0.7695 (m-80) cc_final: 0.7344 (m-10) REVERT: B 621 GLN cc_start: 0.7619 (tt0) cc_final: 0.6940 (tt0) REVERT: B 642 SER cc_start: 0.8598 (m) cc_final: 0.7993 (p) REVERT: B 647 ASP cc_start: 0.7648 (m-30) cc_final: 0.7439 (m-30) REVERT: B 651 LYS cc_start: 0.8426 (tttt) cc_final: 0.8035 (tttm) REVERT: B 670 PHE cc_start: 0.7996 (m-10) cc_final: 0.7754 (m-10) REVERT: B 679 ASP cc_start: 0.7279 (p0) cc_final: 0.6563 (t70) REVERT: B 709 VAL cc_start: 0.8442 (t) cc_final: 0.8052 (m) REVERT: B 746 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6674 (mm-30) REVERT: B 773 LYS cc_start: 0.8569 (tttt) cc_final: 0.8232 (tttm) REVERT: B 779 THR cc_start: 0.8175 (t) cc_final: 0.7863 (p) REVERT: B 788 PHE cc_start: 0.7819 (m-80) cc_final: 0.7501 (m-10) REVERT: B 790 MET cc_start: 0.7277 (mtt) cc_final: 0.6703 (mtt) REVERT: B 795 GLU cc_start: 0.7734 (tt0) cc_final: 0.7311 (tt0) REVERT: B 820 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7687 (mtpt) REVERT: B 831 LYS cc_start: 0.8259 (tmtt) cc_final: 0.7895 (tptp) REVERT: B 839 LEU cc_start: 0.8378 (mt) cc_final: 0.8123 (mp) REVERT: B 853 THR cc_start: 0.8507 (m) cc_final: 0.8147 (p) REVERT: B 924 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6510 (ttm-80) REVERT: B 928 ASP cc_start: 0.7499 (p0) cc_final: 0.7104 (p0) REVERT: B 949 LYS cc_start: 0.8550 (tttt) cc_final: 0.8072 (ttmm) REVERT: B 961 MET cc_start: 0.7358 (mtp) cc_final: 0.7013 (mtp) REVERT: B 963 LEU cc_start: 0.8111 (tp) cc_final: 0.7785 (tt) REVERT: B 999 LEU cc_start: 0.8802 (mt) cc_final: 0.8444 (mt) REVERT: B 1001 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6612 (mm-30) REVERT: B 1002 SER cc_start: 0.8634 (m) cc_final: 0.8174 (p) REVERT: B 1051 GLN cc_start: 0.7226 (tp-100) cc_final: 0.6950 (tp-100) REVERT: B 1069 ASP cc_start: 0.7262 (t0) cc_final: 0.6728 (t0) REVERT: B 1092 SER cc_start: 0.8189 (m) cc_final: 0.7973 (p) REVERT: B 1099 SER cc_start: 0.8511 (m) cc_final: 0.7712 (p) REVERT: B 1100 GLN cc_start: 0.7438 (mt0) cc_final: 0.7142 (tt0) REVERT: B 1103 THR cc_start: 0.8132 (m) cc_final: 0.7756 (p) REVERT: B 1104 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7811 (tppp) REVERT: B 1118 LYS cc_start: 0.7903 (mttm) cc_final: 0.7415 (mttm) REVERT: B 1132 PHE cc_start: 0.8271 (t80) cc_final: 0.7951 (t80) REVERT: B 1166 VAL cc_start: 0.8417 (m) cc_final: 0.8096 (p) REVERT: B 1213 ARG cc_start: 0.7483 (ptt-90) cc_final: 0.6678 (ptt90) REVERT: B 1218 SER cc_start: 0.8607 (m) cc_final: 0.8163 (p) REVERT: B 1222 GLN cc_start: 0.7920 (tt0) cc_final: 0.7701 (tp40) REVERT: C 48 VAL cc_start: 0.8435 (p) cc_final: 0.8147 (t) REVERT: C 171 ASP cc_start: 0.7849 (t0) cc_final: 0.7558 (t0) REVERT: C 175 VAL cc_start: 0.8512 (t) cc_final: 0.8148 (p) REVERT: C 185 PHE cc_start: 0.7445 (t80) cc_final: 0.6684 (t80) REVERT: C 258 ASN cc_start: 0.7639 (m-40) cc_final: 0.7185 (m-40) REVERT: C 272 LYS cc_start: 0.8241 (mttt) cc_final: 0.7595 (mtmm) REVERT: C 276 ASN cc_start: 0.8287 (t0) cc_final: 0.8028 (m-40) REVERT: C 308 ASN cc_start: 0.6788 (m-40) cc_final: 0.6351 (t0) REVERT: C 332 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6572 (mt-10) REVERT: C 334 SER cc_start: 0.8452 (p) cc_final: 0.8093 (m) REVERT: C 337 LEU cc_start: 0.8192 (mt) cc_final: 0.7951 (mp) REVERT: C 354 ASP cc_start: 0.8224 (t0) cc_final: 0.7828 (t0) REVERT: C 378 ASP cc_start: 0.7984 (m-30) cc_final: 0.7759 (m-30) REVERT: C 403 TYR cc_start: 0.7483 (m-80) cc_final: 0.7219 (m-10) REVERT: C 405 ASP cc_start: 0.7471 (m-30) cc_final: 0.7252 (m-30) REVERT: C 420 ASP cc_start: 0.7111 (m-30) cc_final: 0.6681 (m-30) REVERT: C 426 PHE cc_start: 0.8319 (m-10) cc_final: 0.7711 (m-10) REVERT: C 434 ASP cc_start: 0.6481 (t0) cc_final: 0.5745 (p0) REVERT: C 448 ASP cc_start: 0.7742 (m-30) cc_final: 0.7013 (p0) REVERT: C 452 GLU cc_start: 0.7612 (tt0) cc_final: 0.7220 (tm-30) REVERT: C 485 TYR cc_start: 0.8073 (m-80) cc_final: 0.7586 (m-80) REVERT: C 540 SER cc_start: 0.8186 (p) cc_final: 0.7823 (m) REVERT: C 552 SER cc_start: 0.8058 (m) cc_final: 0.7527 (p) REVERT: C 554 PHE cc_start: 0.7313 (m-80) cc_final: 0.7061 (m-10) REVERT: C 584 SER cc_start: 0.7544 (m) cc_final: 0.7306 (p) REVERT: C 613 VAL cc_start: 0.8347 (p) cc_final: 0.8090 (t) REVERT: C 614 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8255 (ttpp) REVERT: C 616 THR cc_start: 0.7941 (t) cc_final: 0.7577 (m) REVERT: C 619 TYR cc_start: 0.7761 (m-80) cc_final: 0.7332 (m-80) REVERT: C 640 ASP cc_start: 0.7383 (t0) cc_final: 0.7073 (t70) REVERT: C 664 THR cc_start: 0.7768 (m) cc_final: 0.7391 (t) REVERT: C 679 ASP cc_start: 0.7166 (p0) cc_final: 0.6838 (p0) REVERT: C 687 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8340 (ttmm) REVERT: C 698 THR cc_start: 0.8708 (p) cc_final: 0.8473 (p) REVERT: C 704 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6870 (mp0) REVERT: C 724 THR cc_start: 0.8191 (p) cc_final: 0.7672 (t) REVERT: C 730 GLU cc_start: 0.7653 (tt0) cc_final: 0.7432 (tt0) REVERT: C 740 ASP cc_start: 0.7316 (t0) cc_final: 0.6991 (t70) REVERT: C 753 ASN cc_start: 0.8087 (p0) cc_final: 0.7725 (p0) REVERT: C 797 LEU cc_start: 0.7478 (mt) cc_final: 0.6732 (mt) REVERT: C 814 ASN cc_start: 0.8452 (m-40) cc_final: 0.8105 (m-40) REVERT: C 831 LYS cc_start: 0.8134 (tmtt) cc_final: 0.7719 (tmmt) REVERT: C 854 ILE cc_start: 0.7973 (mt) cc_final: 0.7632 (mp) REVERT: C 893 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7816 (mmmm) REVERT: C 894 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8073 (mtm180) REVERT: C 898 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6412 (mt-10) REVERT: C 899 ASP cc_start: 0.7377 (m-30) cc_final: 0.6868 (m-30) REVERT: C 916 ASP cc_start: 0.7077 (t0) cc_final: 0.6801 (t0) REVERT: C 918 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7906 (mtmm) REVERT: C 952 MET cc_start: 0.6855 (mtm) cc_final: 0.6630 (mtm) REVERT: C 974 PHE cc_start: 0.8471 (t80) cc_final: 0.7990 (t80) REVERT: C 999 LEU cc_start: 0.8271 (mt) cc_final: 0.7841 (mp) REVERT: C 1002 SER cc_start: 0.8747 (m) cc_final: 0.8391 (p) REVERT: C 1004 ASN cc_start: 0.7510 (m-40) cc_final: 0.7036 (m110) REVERT: C 1063 ILE cc_start: 0.8774 (pt) cc_final: 0.8190 (mm) REVERT: C 1064 SER cc_start: 0.8461 (p) cc_final: 0.8146 (m) REVERT: C 1066 SER cc_start: 0.8046 (t) cc_final: 0.7734 (p) REVERT: C 1069 ASP cc_start: 0.7750 (t0) cc_final: 0.7239 (t70) REVERT: C 1104 LYS cc_start: 0.7735 (mmpt) cc_final: 0.7395 (ttmm) REVERT: C 1124 LYS cc_start: 0.7974 (mttt) cc_final: 0.7771 (mttm) REVERT: C 1127 SER cc_start: 0.7670 (t) cc_final: 0.7461 (t) REVERT: C 1213 ARG cc_start: 0.7955 (ptt180) cc_final: 0.6987 (ptt90) outliers start: 0 outliers final: 0 residues processed: 867 average time/residue: 0.1771 time to fit residues: 242.5990 Evaluate side-chains 657 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 445 ASN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 771 GLN ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN B 768 GLN B 825 GLN B 979 GLN C 814 ASN C1033 HIS C1109 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095204 restraints weight = 44745.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098614 restraints weight = 22022.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100833 restraints weight = 13141.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102159 restraints weight = 9068.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103235 restraints weight = 7038.894| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26466 Z= 0.234 Angle : 0.642 10.009 36121 Z= 0.332 Chirality : 0.046 0.374 4322 Planarity : 0.004 0.042 4521 Dihedral : 7.323 109.499 4651 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.06 % Allowed : 8.56 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3188 helix: 1.21 (0.21), residues: 611 sheet: -0.37 (0.19), residues: 830 loop : -1.26 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1207 TYR 0.023 0.002 TYR B 675 PHE 0.023 0.002 PHE B 183 TRP 0.013 0.002 TRP A 439 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (26364) covalent geometry : angle 0.61977 / 0.33 (35860) SS BOND : bond 0.00591 / 0.36 ( 45) SS BOND : angle 2.38870 / 1.69 ( 90) hydrogen bonds : bond 0.05491 / 3.63 ( 880) hydrogen bonds : angle 6.35414 / 4.36 ( 2589) link_ALPHA1-3 : bond 0.00743 / 0.38 ( 3) link_ALPHA1-3 : angle 2.04122 / 1.35 ( 9) link_ALPHA1-6 : bond 0.00940 / 0.47 ( 3) link_ALPHA1-6 : angle 1.88654 / 1.27 ( 9) link_BETA1-4 : bond 0.00316 / 0.20 ( 12) link_BETA1-4 : angle 1.74899 / 1.33 ( 36) link_NAG-ASN : bond 0.00296 / 0.20 ( 39) link_NAG-ASN : angle 1.84546 / 1.31 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 649 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8165 (t) cc_final: 0.7869 (p) REVERT: A 247 ASN cc_start: 0.7584 (p0) cc_final: 0.7330 (p0) REVERT: A 314 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7429 (ttm170) REVERT: A 395 VAL cc_start: 0.8450 (t) cc_final: 0.8198 (p) REVERT: A 452 GLU cc_start: 0.7970 (tt0) cc_final: 0.7628 (tt0) REVERT: A 481 ASP cc_start: 0.7595 (m-30) cc_final: 0.7355 (m-30) REVERT: A 487 ILE cc_start: 0.8401 (pt) cc_final: 0.7755 (mt) REVERT: A 507 PHE cc_start: 0.7917 (p90) cc_final: 0.7580 (p90) REVERT: A 510 HIS cc_start: 0.8286 (t-90) cc_final: 0.7950 (t70) REVERT: A 534 THR cc_start: 0.8420 (m) cc_final: 0.8100 (p) REVERT: A 539 PHE cc_start: 0.8026 (m-80) cc_final: 0.7579 (m-10) REVERT: A 569 ASP cc_start: 0.7256 (t0) cc_final: 0.6963 (t0) REVERT: A 593 SER cc_start: 0.8068 (m) cc_final: 0.7717 (p) REVERT: A 651 LYS cc_start: 0.8208 (tttt) cc_final: 0.7922 (ttpp) REVERT: A 660 GLU cc_start: 0.6601 (mp0) cc_final: 0.6216 (mp0) REVERT: A 704 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 716 VAL cc_start: 0.8658 (t) cc_final: 0.8252 (m) REVERT: A 730 GLU cc_start: 0.7374 (tt0) cc_final: 0.7135 (tt0) REVERT: A 735 PHE cc_start: 0.8722 (m-80) cc_final: 0.8181 (m-10) REVERT: A 737 HIS cc_start: 0.8170 (m-70) cc_final: 0.7907 (m-70) REVERT: A 738 SER cc_start: 0.8184 (p) cc_final: 0.7557 (m) REVERT: A 758 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8107 (ttmm) REVERT: A 795 GLU cc_start: 0.7480 (tt0) cc_final: 0.7029 (tt0) REVERT: A 801 ASN cc_start: 0.7992 (p0) cc_final: 0.7790 (p0) REVERT: A 802 THR cc_start: 0.8635 (m) cc_final: 0.8241 (p) REVERT: A 820 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7445 (mttp) REVERT: A 831 LYS cc_start: 0.7080 (tttt) cc_final: 0.6706 (ttpp) REVERT: A 844 GLU cc_start: 0.7537 (tp30) cc_final: 0.7153 (tp30) REVERT: A 853 THR cc_start: 0.7883 (p) cc_final: 0.7646 (p) REVERT: A 859 LEU cc_start: 0.8324 (tp) cc_final: 0.7717 (tp) REVERT: A 918 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7552 (mtmm) REVERT: A 949 LYS cc_start: 0.7472 (tttt) cc_final: 0.7242 (ttpt) REVERT: A 954 SER cc_start: 0.7964 (m) cc_final: 0.7415 (p) REVERT: A 978 VAL cc_start: 0.8074 (t) cc_final: 0.7766 (p) REVERT: A 1007 ILE cc_start: 0.8310 (tp) cc_final: 0.8075 (tp) REVERT: A 1011 THR cc_start: 0.8405 (m) cc_final: 0.8192 (p) REVERT: A 1040 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6760 (tm-30) REVERT: A 1069 ASP cc_start: 0.7051 (t0) cc_final: 0.6778 (t0) REVERT: A 1108 VAL cc_start: 0.8187 (t) cc_final: 0.7814 (p) REVERT: A 1120 ASN cc_start: 0.7639 (m-40) cc_final: 0.7373 (m-40) REVERT: A 1167 ILE cc_start: 0.8194 (mm) cc_final: 0.7960 (mm) REVERT: A 1172 LEU cc_start: 0.7880 (mt) cc_final: 0.7452 (mp) REVERT: A 1183 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.6854 (ttm170) REVERT: A 1184 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 1211 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6534 (mt-10) REVERT: A 1214 LYS cc_start: 0.8670 (mmpt) cc_final: 0.8313 (mmmm) REVERT: A 1230 TYR cc_start: 0.7125 (m-10) cc_final: 0.6846 (m-10) REVERT: B 32 PHE cc_start: 0.7628 (m-10) cc_final: 0.6740 (m-10) REVERT: B 166 ILE cc_start: 0.7843 (tt) cc_final: 0.7398 (tt) REVERT: B 167 THR cc_start: 0.8310 (m) cc_final: 0.7438 (p) REVERT: B 173 VAL cc_start: 0.8495 (t) cc_final: 0.7989 (m) REVERT: B 174 THR cc_start: 0.8340 (m) cc_final: 0.7673 (p) REVERT: B 185 PHE cc_start: 0.7552 (t80) cc_final: 0.6954 (t80) REVERT: B 188 ASP cc_start: 0.7196 (m-30) cc_final: 0.6483 (t0) REVERT: B 227 TYR cc_start: 0.7616 (p90) cc_final: 0.7213 (p90) REVERT: B 242 PHE cc_start: 0.7831 (p90) cc_final: 0.7609 (p90) REVERT: B 263 SER cc_start: 0.7931 (t) cc_final: 0.7668 (p) REVERT: B 276 ASN cc_start: 0.7820 (t0) cc_final: 0.7068 (p0) REVERT: B 280 LEU cc_start: 0.8106 (tp) cc_final: 0.7745 (tp) REVERT: B 328 VAL cc_start: 0.8866 (m) cc_final: 0.8419 (t) REVERT: B 334 SER cc_start: 0.8372 (p) cc_final: 0.7982 (m) REVERT: B 353 SER cc_start: 0.8571 (m) cc_final: 0.8278 (p) REVERT: B 444 THR cc_start: 0.7972 (p) cc_final: 0.7452 (t) REVERT: B 488 SER cc_start: 0.8359 (m) cc_final: 0.8127 (t) REVERT: B 552 SER cc_start: 0.8294 (m) cc_final: 0.7509 (t) REVERT: B 553 LEU cc_start: 0.7769 (tp) cc_final: 0.7427 (pt) REVERT: B 593 SER cc_start: 0.8734 (m) cc_final: 0.7944 (p) REVERT: B 594 LEU cc_start: 0.8370 (tp) cc_final: 0.8145 (tp) REVERT: B 600 THR cc_start: 0.7424 (m) cc_final: 0.7212 (t) REVERT: B 601 ILE cc_start: 0.8280 (mt) cc_final: 0.8032 (tt) REVERT: B 613 VAL cc_start: 0.8450 (m) cc_final: 0.8206 (p) REVERT: B 614 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8002 (ptmm) REVERT: B 619 TYR cc_start: 0.7743 (m-80) cc_final: 0.7213 (m-10) REVERT: B 626 GLU cc_start: 0.6175 (mp0) cc_final: 0.5707 (mp0) REVERT: B 642 SER cc_start: 0.8557 (m) cc_final: 0.7847 (p) REVERT: B 651 LYS cc_start: 0.8609 (tttt) cc_final: 0.8161 (tttp) REVERT: B 670 PHE cc_start: 0.8007 (m-10) cc_final: 0.7624 (m-80) REVERT: B 679 ASP cc_start: 0.7238 (p0) cc_final: 0.6909 (t70) REVERT: B 709 VAL cc_start: 0.8470 (t) cc_final: 0.8209 (m) REVERT: B 746 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6643 (mm-30) REVERT: B 773 LYS cc_start: 0.8514 (tttt) cc_final: 0.8152 (tttm) REVERT: B 779 THR cc_start: 0.8162 (t) cc_final: 0.7896 (p) REVERT: B 790 MET cc_start: 0.7114 (mtt) cc_final: 0.6841 (mtt) REVERT: B 795 GLU cc_start: 0.7743 (tt0) cc_final: 0.7403 (tt0) REVERT: B 820 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7664 (mtpt) REVERT: B 839 LEU cc_start: 0.8420 (mt) cc_final: 0.8164 (mp) REVERT: B 853 THR cc_start: 0.8422 (m) cc_final: 0.8131 (p) REVERT: B 949 LYS cc_start: 0.8657 (tttt) cc_final: 0.8262 (tppt) REVERT: B 954 SER cc_start: 0.8201 (m) cc_final: 0.7898 (t) REVERT: B 961 MET cc_start: 0.7368 (mtp) cc_final: 0.7096 (mtp) REVERT: B 963 LEU cc_start: 0.8127 (tp) cc_final: 0.7724 (tt) REVERT: B 999 LEU cc_start: 0.8843 (mt) cc_final: 0.8323 (mp) REVERT: B 1002 SER cc_start: 0.8643 (m) cc_final: 0.8247 (p) REVERT: B 1040 GLU cc_start: 0.7153 (tp30) cc_final: 0.6561 (tp30) REVERT: B 1051 GLN cc_start: 0.7178 (tp-100) cc_final: 0.6889 (tp-100) REVERT: B 1069 ASP cc_start: 0.7320 (t0) cc_final: 0.6867 (t0) REVERT: B 1087 ILE cc_start: 0.8049 (mt) cc_final: 0.7841 (mm) REVERT: B 1092 SER cc_start: 0.8488 (m) cc_final: 0.8117 (p) REVERT: B 1099 SER cc_start: 0.8517 (m) cc_final: 0.7826 (p) REVERT: B 1100 GLN cc_start: 0.7509 (mt0) cc_final: 0.7212 (tt0) REVERT: B 1103 THR cc_start: 0.8044 (m) cc_final: 0.7703 (p) REVERT: B 1104 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7956 (tppp) REVERT: B 1113 LYS cc_start: 0.8310 (ttmm) cc_final: 0.8050 (tppp) REVERT: B 1132 PHE cc_start: 0.8144 (t80) cc_final: 0.7873 (t80) REVERT: B 1158 LEU cc_start: 0.7041 (mt) cc_final: 0.6717 (mt) REVERT: B 1162 ASP cc_start: 0.7429 (m-30) cc_final: 0.7177 (m-30) REVERT: B 1207 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7739 (mtt-85) REVERT: B 1213 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.6850 (ptt90) REVERT: B 1218 SER cc_start: 0.8552 (m) cc_final: 0.8119 (p) REVERT: C 48 VAL cc_start: 0.8268 (p) cc_final: 0.7968 (t) REVERT: C 171 ASP cc_start: 0.7868 (t0) cc_final: 0.7538 (t0) REVERT: C 175 VAL cc_start: 0.8326 (t) cc_final: 0.7897 (p) REVERT: C 185 PHE cc_start: 0.7584 (t80) cc_final: 0.7031 (t80) REVERT: C 247 ASN cc_start: 0.7909 (p0) cc_final: 0.7482 (p0) REVERT: C 258 ASN cc_start: 0.7924 (m-40) cc_final: 0.7556 (m-40) REVERT: C 260 PHE cc_start: 0.7685 (m-10) cc_final: 0.7445 (m-10) REVERT: C 276 ASN cc_start: 0.8291 (t0) cc_final: 0.7950 (m-40) REVERT: C 289 LYS cc_start: 0.7628 (mttt) cc_final: 0.7059 (mtmm) REVERT: C 308 ASN cc_start: 0.6754 (m-40) cc_final: 0.6473 (m-40) REVERT: C 317 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7074 (tt0) REVERT: C 334 SER cc_start: 0.8553 (p) cc_final: 0.8114 (m) REVERT: C 337 LEU cc_start: 0.8174 (mt) cc_final: 0.7952 (mp) REVERT: C 354 ASP cc_start: 0.8142 (t0) cc_final: 0.7803 (t0) REVERT: C 382 SER cc_start: 0.8579 (t) cc_final: 0.8269 (m) REVERT: C 403 TYR cc_start: 0.7324 (m-80) cc_final: 0.7066 (m-10) REVERT: C 405 ASP cc_start: 0.7430 (m-30) cc_final: 0.7216 (m-30) REVERT: C 420 ASP cc_start: 0.7081 (m-30) cc_final: 0.6735 (m-30) REVERT: C 434 ASP cc_start: 0.6569 (t0) cc_final: 0.6009 (p0) REVERT: C 448 ASP cc_start: 0.7748 (m-30) cc_final: 0.7040 (p0) REVERT: C 545 ASP cc_start: 0.7644 (p0) cc_final: 0.7435 (p0) REVERT: C 584 SER cc_start: 0.7599 (m) cc_final: 0.7345 (p) REVERT: C 595 LEU cc_start: 0.8332 (tp) cc_final: 0.7734 (tp) REVERT: C 614 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8354 (ttpp) REVERT: C 619 TYR cc_start: 0.7779 (m-80) cc_final: 0.7351 (m-80) REVERT: C 640 ASP cc_start: 0.7326 (t0) cc_final: 0.7064 (t70) REVERT: C 724 THR cc_start: 0.8232 (p) cc_final: 0.7728 (t) REVERT: C 753 ASN cc_start: 0.7989 (p0) cc_final: 0.7706 (p0) REVERT: C 758 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8446 (tttp) REVERT: C 767 SER cc_start: 0.8270 (m) cc_final: 0.7743 (p) REVERT: C 854 ILE cc_start: 0.7973 (mt) cc_final: 0.7640 (mp) REVERT: C 898 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6556 (mt-10) REVERT: C 899 ASP cc_start: 0.7112 (m-30) cc_final: 0.6671 (m-30) REVERT: C 916 ASP cc_start: 0.7129 (t0) cc_final: 0.6883 (t0) REVERT: C 918 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8054 (mtmm) REVERT: C 974 PHE cc_start: 0.8369 (t80) cc_final: 0.7949 (t80) REVERT: C 999 LEU cc_start: 0.8196 (mt) cc_final: 0.7800 (mp) REVERT: C 1002 SER cc_start: 0.8573 (m) cc_final: 0.8315 (p) REVERT: C 1004 ASN cc_start: 0.7471 (m-40) cc_final: 0.6965 (m110) REVERT: C 1063 ILE cc_start: 0.8762 (pt) cc_final: 0.8184 (mm) REVERT: C 1064 SER cc_start: 0.8482 (p) cc_final: 0.8129 (m) REVERT: C 1069 ASP cc_start: 0.7674 (t0) cc_final: 0.7228 (t70) REVERT: C 1087 ILE cc_start: 0.8207 (mt) cc_final: 0.7959 (mm) REVERT: C 1108 VAL cc_start: 0.8638 (t) cc_final: 0.8211 (m) REVERT: C 1113 LYS cc_start: 0.8262 (mttp) cc_final: 0.7629 (mtpp) REVERT: C 1127 SER cc_start: 0.7561 (t) cc_final: 0.7058 (p) REVERT: C 1211 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6354 (tp30) REVERT: C 1213 ARG cc_start: 0.7935 (ptt180) cc_final: 0.7199 (ptt90) outliers start: 58 outliers final: 42 residues processed: 679 average time/residue: 0.1674 time to fit residues: 182.4879 Evaluate side-chains 650 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 607 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 636 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1209 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 262 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 323 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 312 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS A 282 ASN A 445 ASN ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN B 621 GLN B 682 GLN B 816 ASN B1222 GLN C 814 ASN C1109 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.095194 restraints weight = 44610.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098609 restraints weight = 21981.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100882 restraints weight = 13055.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102265 restraints weight = 8940.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103296 restraints weight = 6906.891| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26466 Z= 0.176 Angle : 0.613 19.695 36121 Z= 0.316 Chirality : 0.045 0.446 4322 Planarity : 0.004 0.050 4521 Dihedral : 7.037 101.803 4651 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.59 % Allowed : 11.12 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.15), residues: 3188 helix: 1.47 (0.21), residues: 611 sheet: -0.34 (0.19), residues: 836 loop : -1.28 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 924 TYR 0.023 0.001 TYR A 403 PHE 0.023 0.001 PHE B 347 TRP 0.011 0.001 TRP B 168 HIS 0.005 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (26364) covalent geometry : angle 0.58909 / 0.31 (35860) SS BOND : bond 0.00547 / 0.38 ( 45) SS BOND : angle 2.67427 / 1.62 ( 90) hydrogen bonds : bond 0.04631 / 3.11 ( 880) hydrogen bonds : angle 5.80913 / 3.98 ( 2589) link_ALPHA1-3 : bond 0.00722 / 0.37 ( 3) link_ALPHA1-3 : angle 1.95632 / 1.22 ( 9) link_ALPHA1-6 : bond 0.00851 / 0.41 ( 3) link_ALPHA1-6 : angle 2.05404 / 1.31 ( 9) link_BETA1-4 : bond 0.00318 / 0.23 ( 12) link_BETA1-4 : angle 1.64472 / 1.25 ( 36) link_NAG-ASN : bond 0.00218 / 0.16 ( 39) link_NAG-ASN : angle 1.66958 / 1.19 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 619 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8154 (t) cc_final: 0.7868 (p) REVERT: A 212 TYR cc_start: 0.7695 (m-80) cc_final: 0.7406 (m-80) REVERT: A 247 ASN cc_start: 0.7541 (p0) cc_final: 0.7294 (p0) REVERT: A 314 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7440 (ttm170) REVERT: A 317 GLU cc_start: 0.7097 (pt0) cc_final: 0.6740 (pm20) REVERT: A 395 VAL cc_start: 0.8390 (t) cc_final: 0.8163 (p) REVERT: A 481 ASP cc_start: 0.7590 (m-30) cc_final: 0.7348 (m-30) REVERT: A 487 ILE cc_start: 0.8407 (pt) cc_final: 0.7915 (mt) REVERT: A 507 PHE cc_start: 0.7885 (p90) cc_final: 0.7543 (p90) REVERT: A 508 ASN cc_start: 0.7954 (t0) cc_final: 0.7687 (t0) REVERT: A 510 HIS cc_start: 0.8267 (t-90) cc_final: 0.7963 (t-170) REVERT: A 534 THR cc_start: 0.8356 (m) cc_final: 0.8030 (p) REVERT: A 539 PHE cc_start: 0.7998 (m-80) cc_final: 0.7538 (m-10) REVERT: A 569 ASP cc_start: 0.7156 (t0) cc_final: 0.6934 (t0) REVERT: A 593 SER cc_start: 0.8115 (m) cc_final: 0.7722 (p) REVERT: A 635 LEU cc_start: 0.8844 (mp) cc_final: 0.8595 (mt) REVERT: A 651 LYS cc_start: 0.8210 (tttt) cc_final: 0.7895 (ttpp) REVERT: A 660 GLU cc_start: 0.6570 (mp0) cc_final: 0.6165 (mp0) REVERT: A 704 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: A 716 VAL cc_start: 0.8643 (t) cc_final: 0.8239 (m) REVERT: A 730 GLU cc_start: 0.7329 (tt0) cc_final: 0.7115 (tt0) REVERT: A 735 PHE cc_start: 0.8570 (m-80) cc_final: 0.7811 (m-10) REVERT: A 738 SER cc_start: 0.8108 (p) cc_final: 0.7738 (t) REVERT: A 758 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8100 (ttmm) REVERT: A 773 LYS cc_start: 0.8106 (tttm) cc_final: 0.7570 (ttpp) REVERT: A 795 GLU cc_start: 0.7448 (tt0) cc_final: 0.7028 (tt0) REVERT: A 801 ASN cc_start: 0.8032 (p0) cc_final: 0.7821 (p0) REVERT: A 820 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7448 (mttp) REVERT: A 831 LYS cc_start: 0.6976 (tttt) cc_final: 0.6636 (ttpp) REVERT: A 844 GLU cc_start: 0.7589 (tp30) cc_final: 0.7060 (tp30) REVERT: A 853 THR cc_start: 0.7893 (p) cc_final: 0.7640 (p) REVERT: A 918 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7575 (mtmm) REVERT: A 949 LYS cc_start: 0.7392 (tttt) cc_final: 0.7115 (ttpt) REVERT: A 954 SER cc_start: 0.8039 (m) cc_final: 0.7477 (p) REVERT: A 978 VAL cc_start: 0.8070 (t) cc_final: 0.7734 (p) REVERT: A 1007 ILE cc_start: 0.8297 (tp) cc_final: 0.8083 (tp) REVERT: A 1011 THR cc_start: 0.8428 (m) cc_final: 0.8193 (p) REVERT: A 1040 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 1069 ASP cc_start: 0.7098 (t0) cc_final: 0.6830 (t0) REVERT: A 1108 VAL cc_start: 0.8197 (t) cc_final: 0.7857 (p) REVERT: A 1120 ASN cc_start: 0.7672 (m-40) cc_final: 0.7396 (m-40) REVERT: A 1167 ILE cc_start: 0.8195 (mm) cc_final: 0.7981 (mm) REVERT: A 1172 LEU cc_start: 0.7941 (mt) cc_final: 0.7458 (mp) REVERT: A 1183 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7332 (ttm-80) REVERT: A 1184 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7116 (mm-30) REVERT: A 1211 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6520 (mt-10) REVERT: A 1214 LYS cc_start: 0.8706 (mmpt) cc_final: 0.8325 (mmmm) REVERT: A 1230 TYR cc_start: 0.7038 (m-10) cc_final: 0.6755 (m-10) REVERT: B 32 PHE cc_start: 0.7368 (m-10) cc_final: 0.6675 (m-10) REVERT: B 35 PHE cc_start: 0.7925 (t80) cc_final: 0.7532 (t80) REVERT: B 167 THR cc_start: 0.8348 (m) cc_final: 0.7309 (p) REVERT: B 174 THR cc_start: 0.8362 (m) cc_final: 0.7751 (p) REVERT: B 185 PHE cc_start: 0.7582 (t80) cc_final: 0.6749 (t80) REVERT: B 188 ASP cc_start: 0.7133 (m-30) cc_final: 0.6605 (t70) REVERT: B 209 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7143 (mm-30) REVERT: B 227 TYR cc_start: 0.7601 (p90) cc_final: 0.7188 (p90) REVERT: B 242 PHE cc_start: 0.7862 (p90) cc_final: 0.7536 (p90) REVERT: B 263 SER cc_start: 0.7895 (t) cc_final: 0.7676 (p) REVERT: B 276 ASN cc_start: 0.7845 (t0) cc_final: 0.7194 (p0) REVERT: B 280 LEU cc_start: 0.8052 (tp) cc_final: 0.7742 (tp) REVERT: B 328 VAL cc_start: 0.8846 (m) cc_final: 0.8388 (t) REVERT: B 334 SER cc_start: 0.8287 (p) cc_final: 0.7938 (m) REVERT: B 353 SER cc_start: 0.8567 (m) cc_final: 0.8251 (p) REVERT: B 372 TYR cc_start: 0.8153 (m-80) cc_final: 0.7952 (m-10) REVERT: B 376 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7519 (ttmt) REVERT: B 426 PHE cc_start: 0.7568 (m-10) cc_final: 0.7230 (m-10) REVERT: B 444 THR cc_start: 0.7988 (p) cc_final: 0.7468 (t) REVERT: B 488 SER cc_start: 0.8363 (m) cc_final: 0.8026 (p) REVERT: B 552 SER cc_start: 0.8210 (m) cc_final: 0.7487 (t) REVERT: B 553 LEU cc_start: 0.7761 (tp) cc_final: 0.7469 (pt) REVERT: B 593 SER cc_start: 0.8717 (m) cc_final: 0.7891 (p) REVERT: B 594 LEU cc_start: 0.8432 (tp) cc_final: 0.8040 (tp) REVERT: B 601 ILE cc_start: 0.8291 (mt) cc_final: 0.8006 (tt) REVERT: B 613 VAL cc_start: 0.8407 (m) cc_final: 0.8163 (p) REVERT: B 614 LYS cc_start: 0.8554 (ttpt) cc_final: 0.7998 (ptmm) REVERT: B 619 TYR cc_start: 0.7737 (m-80) cc_final: 0.7511 (m-80) REVERT: B 626 GLU cc_start: 0.6179 (mp0) cc_final: 0.5716 (mp0) REVERT: B 640 ASP cc_start: 0.7363 (t0) cc_final: 0.7052 (t70) REVERT: B 642 SER cc_start: 0.8509 (m) cc_final: 0.7936 (p) REVERT: B 651 LYS cc_start: 0.8608 (tttt) cc_final: 0.8170 (tttp) REVERT: B 670 PHE cc_start: 0.8020 (m-10) cc_final: 0.7625 (m-80) REVERT: B 679 ASP cc_start: 0.7452 (p0) cc_final: 0.6866 (t70) REVERT: B 709 VAL cc_start: 0.8485 (t) cc_final: 0.8239 (m) REVERT: B 746 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6601 (mm-30) REVERT: B 773 LYS cc_start: 0.8511 (tttt) cc_final: 0.8155 (tttm) REVERT: B 788 PHE cc_start: 0.7554 (m-80) cc_final: 0.7311 (m-10) REVERT: B 790 MET cc_start: 0.7089 (mtt) cc_final: 0.6778 (mtt) REVERT: B 795 GLU cc_start: 0.7598 (tt0) cc_final: 0.7325 (tt0) REVERT: B 820 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7558 (mtpt) REVERT: B 839 LEU cc_start: 0.8396 (mt) cc_final: 0.8169 (mp) REVERT: B 847 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7046 (mm-30) REVERT: B 853 THR cc_start: 0.8454 (m) cc_final: 0.8178 (p) REVERT: B 924 ARG cc_start: 0.7460 (ttm110) cc_final: 0.6744 (mtm110) REVERT: B 949 LYS cc_start: 0.8486 (tttt) cc_final: 0.8112 (tppt) REVERT: B 954 SER cc_start: 0.8228 (m) cc_final: 0.7885 (t) REVERT: B 961 MET cc_start: 0.7351 (mtp) cc_final: 0.7098 (mtp) REVERT: B 963 LEU cc_start: 0.8085 (tp) cc_final: 0.7732 (tt) REVERT: B 999 LEU cc_start: 0.8906 (mt) cc_final: 0.8413 (mp) REVERT: B 1002 SER cc_start: 0.8634 (m) cc_final: 0.8250 (p) REVERT: B 1040 GLU cc_start: 0.7178 (tp30) cc_final: 0.6520 (tp30) REVERT: B 1051 GLN cc_start: 0.7162 (tp-100) cc_final: 0.6840 (tp-100) REVERT: B 1069 ASP cc_start: 0.7339 (t0) cc_final: 0.6825 (t0) REVERT: B 1092 SER cc_start: 0.8464 (m) cc_final: 0.8107 (p) REVERT: B 1099 SER cc_start: 0.8539 (m) cc_final: 0.7757 (p) REVERT: B 1100 GLN cc_start: 0.7492 (mt0) cc_final: 0.7136 (tt0) REVERT: B 1103 THR cc_start: 0.8005 (m) cc_final: 0.7619 (p) REVERT: B 1104 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7912 (tppp) REVERT: B 1108 VAL cc_start: 0.8221 (t) cc_final: 0.7906 (p) REVERT: B 1132 PHE cc_start: 0.8205 (t80) cc_final: 0.7903 (t80) REVERT: B 1136 ASP cc_start: 0.7150 (m-30) cc_final: 0.6910 (m-30) REVERT: B 1162 ASP cc_start: 0.7363 (m-30) cc_final: 0.7138 (m-30) REVERT: B 1207 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7322 (mtm-85) REVERT: B 1213 ARG cc_start: 0.7616 (ptt-90) cc_final: 0.6855 (ptt90) REVERT: C 48 VAL cc_start: 0.8254 (p) cc_final: 0.7989 (t) REVERT: C 171 ASP cc_start: 0.7881 (t0) cc_final: 0.7447 (t0) REVERT: C 175 VAL cc_start: 0.8290 (t) cc_final: 0.7836 (p) REVERT: C 176 PHE cc_start: 0.8002 (m-80) cc_final: 0.7557 (m-80) REVERT: C 247 ASN cc_start: 0.7976 (p0) cc_final: 0.7555 (p0) REVERT: C 252 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 258 ASN cc_start: 0.7877 (m-40) cc_final: 0.7610 (m-40) REVERT: C 260 PHE cc_start: 0.7798 (m-10) cc_final: 0.7570 (m-10) REVERT: C 289 LYS cc_start: 0.7676 (mttt) cc_final: 0.7072 (mtmm) REVERT: C 308 ASN cc_start: 0.6815 (m-40) cc_final: 0.6437 (m-40) REVERT: C 334 SER cc_start: 0.8515 (p) cc_final: 0.8093 (m) REVERT: C 337 LEU cc_start: 0.8150 (mt) cc_final: 0.7933 (mp) REVERT: C 354 ASP cc_start: 0.8128 (t0) cc_final: 0.7755 (t0) REVERT: C 405 ASP cc_start: 0.7448 (m-30) cc_final: 0.7217 (m-30) REVERT: C 420 ASP cc_start: 0.7089 (m-30) cc_final: 0.6767 (m-30) REVERT: C 434 ASP cc_start: 0.6544 (t0) cc_final: 0.6011 (p0) REVERT: C 448 ASP cc_start: 0.7718 (m-30) cc_final: 0.7088 (p0) REVERT: C 534 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8344 (p) REVERT: C 584 SER cc_start: 0.7675 (m) cc_final: 0.7369 (p) REVERT: C 614 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8393 (ttpp) REVERT: C 619 TYR cc_start: 0.7783 (m-80) cc_final: 0.7340 (m-80) REVERT: C 640 ASP cc_start: 0.7328 (t0) cc_final: 0.7059 (t70) REVERT: C 704 GLU cc_start: 0.7208 (mp0) cc_final: 0.6606 (mp0) REVERT: C 724 THR cc_start: 0.8257 (p) cc_final: 0.7753 (t) REVERT: C 753 ASN cc_start: 0.7971 (p0) cc_final: 0.7663 (p0) REVERT: C 758 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8460 (tttp) REVERT: C 795 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 816 ASN cc_start: 0.7900 (t0) cc_final: 0.7331 (t0) REVERT: C 854 ILE cc_start: 0.7945 (mt) cc_final: 0.7652 (mp) REVERT: C 898 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6585 (mt-10) REVERT: C 916 ASP cc_start: 0.7181 (t0) cc_final: 0.6981 (t0) REVERT: C 918 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8059 (mtmm) REVERT: C 974 PHE cc_start: 0.8345 (t80) cc_final: 0.7931 (t80) REVERT: C 999 LEU cc_start: 0.8141 (mt) cc_final: 0.7738 (mp) REVERT: C 1002 SER cc_start: 0.8528 (m) cc_final: 0.7959 (p) REVERT: C 1004 ASN cc_start: 0.7417 (m-40) cc_final: 0.6897 (m110) REVERT: C 1005 SER cc_start: 0.8264 (t) cc_final: 0.7902 (p) REVERT: C 1063 ILE cc_start: 0.8758 (pt) cc_final: 0.8192 (mm) REVERT: C 1064 SER cc_start: 0.8469 (p) cc_final: 0.8144 (m) REVERT: C 1069 ASP cc_start: 0.7682 (t0) cc_final: 0.7212 (t70) REVERT: C 1087 ILE cc_start: 0.8264 (mt) cc_final: 0.7946 (mm) REVERT: C 1108 VAL cc_start: 0.8683 (t) cc_final: 0.8301 (p) REVERT: C 1109 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: C 1113 LYS cc_start: 0.8288 (mttp) cc_final: 0.7725 (mtpp) REVERT: C 1127 SER cc_start: 0.7471 (t) cc_final: 0.7015 (p) REVERT: C 1190 PHE cc_start: 0.8057 (p90) cc_final: 0.7661 (p90) REVERT: C 1209 MET cc_start: 0.6454 (mtp) cc_final: 0.6230 (mtp) REVERT: C 1213 ARG cc_start: 0.7923 (ptt180) cc_final: 0.7329 (ptt90) outliers start: 73 outliers final: 53 residues processed: 650 average time/residue: 0.1690 time to fit residues: 176.6566 Evaluate side-chains 654 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 598 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1109 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 294 optimal weight: 0.1980 chunk 270 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 996 GLN C 566 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096404 restraints weight = 43878.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099597 restraints weight = 22397.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101745 restraints weight = 13635.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103019 restraints weight = 9483.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104004 restraints weight = 7414.444| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26466 Z= 0.202 Angle : 0.625 13.815 36121 Z= 0.320 Chirality : 0.045 0.343 4322 Planarity : 0.004 0.057 4521 Dihedral : 7.044 96.267 4651 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.09 % Allowed : 11.76 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3188 helix: 1.47 (0.21), residues: 617 sheet: -0.34 (0.19), residues: 826 loop : -1.32 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1235 TYR 0.021 0.001 TYR A 403 PHE 0.021 0.002 PHE B 347 TRP 0.011 0.001 TRP B 168 HIS 0.015 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (26364) covalent geometry : angle 0.59961 / 0.31 (35860) SS BOND : bond 0.00581 / 0.38 ( 45) SS BOND : angle 2.69970 / 1.69 ( 90) hydrogen bonds : bond 0.04604 / 3.09 ( 880) hydrogen bonds : angle 5.69891 / 3.91 ( 2589) link_ALPHA1-3 : bond 0.00756 / 0.39 ( 3) link_ALPHA1-3 : angle 2.01053 / 1.26 ( 9) link_ALPHA1-6 : bond 0.00932 / 0.46 ( 3) link_ALPHA1-6 : angle 2.20895 / 1.44 ( 9) link_BETA1-4 : bond 0.00301 / 0.20 ( 12) link_BETA1-4 : angle 1.70909 / 1.30 ( 36) link_NAG-ASN : bond 0.00249 / 0.18 ( 39) link_NAG-ASN : angle 1.74952 / 1.24 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 621 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8184 (t) cc_final: 0.7911 (p) REVERT: A 48 VAL cc_start: 0.7944 (t) cc_final: 0.7732 (t) REVERT: A 238 SER cc_start: 0.8490 (p) cc_final: 0.7824 (t) REVERT: A 247 ASN cc_start: 0.7572 (p0) cc_final: 0.7334 (p0) REVERT: A 269 VAL cc_start: 0.8497 (t) cc_final: 0.8199 (m) REVERT: A 284 LEU cc_start: 0.8518 (tp) cc_final: 0.8166 (tt) REVERT: A 314 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7465 (ttm170) REVERT: A 397 GLU cc_start: 0.7332 (tt0) cc_final: 0.7129 (tt0) REVERT: A 445 ASN cc_start: 0.7376 (m-40) cc_final: 0.7006 (m-40) REVERT: A 454 GLN cc_start: 0.7843 (tp40) cc_final: 0.6829 (tp-100) REVERT: A 481 ASP cc_start: 0.7573 (m-30) cc_final: 0.7335 (m-30) REVERT: A 487 ILE cc_start: 0.8394 (pt) cc_final: 0.8039 (mt) REVERT: A 507 PHE cc_start: 0.7814 (p90) cc_final: 0.7570 (p90) REVERT: A 508 ASN cc_start: 0.7951 (t0) cc_final: 0.7704 (t0) REVERT: A 534 THR cc_start: 0.8360 (m) cc_final: 0.8022 (p) REVERT: A 539 PHE cc_start: 0.8104 (m-80) cc_final: 0.7706 (m-10) REVERT: A 593 SER cc_start: 0.8104 (m) cc_final: 0.7738 (p) REVERT: A 651 LYS cc_start: 0.8251 (tttt) cc_final: 0.7938 (ttpp) REVERT: A 660 GLU cc_start: 0.6532 (mp0) cc_final: 0.6145 (mp0) REVERT: A 716 VAL cc_start: 0.8635 (t) cc_final: 0.8372 (m) REVERT: A 730 GLU cc_start: 0.7298 (tt0) cc_final: 0.7077 (tt0) REVERT: A 735 PHE cc_start: 0.8573 (m-80) cc_final: 0.7757 (m-10) REVERT: A 738 SER cc_start: 0.8205 (p) cc_final: 0.7520 (m) REVERT: A 758 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8087 (ttmm) REVERT: A 773 LYS cc_start: 0.8086 (tttm) cc_final: 0.7542 (ttpp) REVERT: A 777 MET cc_start: 0.7621 (mmm) cc_final: 0.7363 (mmm) REVERT: A 795 GLU cc_start: 0.7434 (tt0) cc_final: 0.7048 (tt0) REVERT: A 801 ASN cc_start: 0.8057 (p0) cc_final: 0.7846 (p0) REVERT: A 820 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7493 (mttp) REVERT: A 831 LYS cc_start: 0.7136 (tttt) cc_final: 0.6863 (ttpp) REVERT: A 844 GLU cc_start: 0.7532 (tp30) cc_final: 0.7082 (tp30) REVERT: A 853 THR cc_start: 0.7929 (p) cc_final: 0.7668 (p) REVERT: A 949 LYS cc_start: 0.7391 (tttt) cc_final: 0.7100 (ttpt) REVERT: A 954 SER cc_start: 0.8040 (m) cc_final: 0.7487 (p) REVERT: A 978 VAL cc_start: 0.8100 (t) cc_final: 0.7719 (p) REVERT: A 1007 ILE cc_start: 0.8335 (tp) cc_final: 0.8121 (tp) REVERT: A 1040 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6708 (tm-30) REVERT: A 1069 ASP cc_start: 0.7119 (t0) cc_final: 0.6815 (t0) REVERT: A 1108 VAL cc_start: 0.8258 (t) cc_final: 0.7937 (p) REVERT: A 1120 ASN cc_start: 0.7665 (m-40) cc_final: 0.7372 (m-40) REVERT: A 1172 LEU cc_start: 0.8021 (mt) cc_final: 0.7439 (mp) REVERT: A 1184 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 1211 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6558 (mt-10) REVERT: A 1214 LYS cc_start: 0.8648 (mmpt) cc_final: 0.8276 (mmmm) REVERT: B 32 PHE cc_start: 0.7349 (m-10) cc_final: 0.6689 (m-10) REVERT: B 174 THR cc_start: 0.8342 (m) cc_final: 0.7957 (p) REVERT: B 185 PHE cc_start: 0.7534 (t80) cc_final: 0.6695 (t80) REVERT: B 188 ASP cc_start: 0.7124 (m-30) cc_final: 0.6545 (t70) REVERT: B 209 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7140 (mm-30) REVERT: B 227 TYR cc_start: 0.7594 (p90) cc_final: 0.7179 (p90) REVERT: B 242 PHE cc_start: 0.7779 (p90) cc_final: 0.7532 (p90) REVERT: B 263 SER cc_start: 0.7932 (t) cc_final: 0.7713 (p) REVERT: B 276 ASN cc_start: 0.7872 (t0) cc_final: 0.7186 (p0) REVERT: B 280 LEU cc_start: 0.8184 (tp) cc_final: 0.7680 (tp) REVERT: B 328 VAL cc_start: 0.8792 (m) cc_final: 0.8310 (t) REVERT: B 334 SER cc_start: 0.8292 (p) cc_final: 0.7943 (m) REVERT: B 353 SER cc_start: 0.8600 (m) cc_final: 0.8257 (p) REVERT: B 354 ASP cc_start: 0.7495 (t0) cc_final: 0.7185 (p0) REVERT: B 426 PHE cc_start: 0.7635 (m-10) cc_final: 0.7311 (m-10) REVERT: B 444 THR cc_start: 0.8028 (p) cc_final: 0.7499 (t) REVERT: B 488 SER cc_start: 0.8343 (m) cc_final: 0.8062 (p) REVERT: B 552 SER cc_start: 0.8202 (m) cc_final: 0.7646 (t) REVERT: B 553 LEU cc_start: 0.7757 (tp) cc_final: 0.7475 (tp) REVERT: B 593 SER cc_start: 0.8759 (m) cc_final: 0.7989 (p) REVERT: B 601 ILE cc_start: 0.8313 (mt) cc_final: 0.8021 (tt) REVERT: B 613 VAL cc_start: 0.8408 (m) cc_final: 0.8189 (p) REVERT: B 614 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8036 (ptmm) REVERT: B 619 TYR cc_start: 0.7740 (m-80) cc_final: 0.7247 (m-10) REVERT: B 626 GLU cc_start: 0.6186 (mp0) cc_final: 0.5709 (mp0) REVERT: B 640 ASP cc_start: 0.7379 (t0) cc_final: 0.7103 (t70) REVERT: B 642 SER cc_start: 0.8513 (m) cc_final: 0.7899 (p) REVERT: B 651 LYS cc_start: 0.8619 (tttt) cc_final: 0.8210 (tttp) REVERT: B 670 PHE cc_start: 0.8044 (m-10) cc_final: 0.7735 (m-80) REVERT: B 679 ASP cc_start: 0.7422 (p0) cc_final: 0.6873 (t70) REVERT: B 709 VAL cc_start: 0.8492 (t) cc_final: 0.8238 (m) REVERT: B 746 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6565 (mm-30) REVERT: B 773 LYS cc_start: 0.8529 (tttt) cc_final: 0.8115 (tttm) REVERT: B 790 MET cc_start: 0.7073 (mtt) cc_final: 0.6719 (mtt) REVERT: B 820 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7591 (mtpt) REVERT: B 839 LEU cc_start: 0.8364 (mt) cc_final: 0.8155 (mm) REVERT: B 847 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 853 THR cc_start: 0.8435 (m) cc_final: 0.8194 (p) REVERT: B 924 ARG cc_start: 0.7475 (ttm110) cc_final: 0.7021 (ttm110) REVERT: B 949 LYS cc_start: 0.8497 (tttt) cc_final: 0.8122 (tppt) REVERT: B 954 SER cc_start: 0.8253 (m) cc_final: 0.7900 (t) REVERT: B 961 MET cc_start: 0.7333 (mtp) cc_final: 0.7095 (mtp) REVERT: B 963 LEU cc_start: 0.8113 (tp) cc_final: 0.7739 (tt) REVERT: B 999 LEU cc_start: 0.8913 (mt) cc_final: 0.8451 (mp) REVERT: B 1002 SER cc_start: 0.8606 (m) cc_final: 0.8235 (p) REVERT: B 1040 GLU cc_start: 0.7126 (tp30) cc_final: 0.6467 (tp30) REVERT: B 1069 ASP cc_start: 0.7344 (t0) cc_final: 0.6833 (t0) REVERT: B 1092 SER cc_start: 0.8464 (m) cc_final: 0.8148 (p) REVERT: B 1099 SER cc_start: 0.8555 (m) cc_final: 0.7788 (p) REVERT: B 1100 GLN cc_start: 0.7435 (mt0) cc_final: 0.7079 (tt0) REVERT: B 1103 THR cc_start: 0.7886 (m) cc_final: 0.7531 (p) REVERT: B 1104 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7908 (tppp) REVERT: B 1132 PHE cc_start: 0.8210 (t80) cc_final: 0.7933 (t80) REVERT: B 1136 ASP cc_start: 0.7129 (m-30) cc_final: 0.6875 (m-30) REVERT: B 1162 ASP cc_start: 0.7373 (m-30) cc_final: 0.7150 (m-30) REVERT: B 1207 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7603 (mtm-85) REVERT: B 1213 ARG cc_start: 0.7634 (ptt-90) cc_final: 0.6902 (ptt90) REVERT: C 48 VAL cc_start: 0.8327 (p) cc_final: 0.8077 (t) REVERT: C 171 ASP cc_start: 0.7813 (t0) cc_final: 0.7361 (t0) REVERT: C 185 PHE cc_start: 0.7820 (t80) cc_final: 0.7224 (t80) REVERT: C 252 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 289 LYS cc_start: 0.7734 (mttt) cc_final: 0.7053 (mtpp) REVERT: C 308 ASN cc_start: 0.6850 (m-40) cc_final: 0.6440 (m-40) REVERT: C 334 SER cc_start: 0.8463 (p) cc_final: 0.8073 (m) REVERT: C 337 LEU cc_start: 0.8154 (mt) cc_final: 0.7951 (mp) REVERT: C 354 ASP cc_start: 0.8073 (t0) cc_final: 0.7739 (t0) REVERT: C 420 ASP cc_start: 0.7084 (m-30) cc_final: 0.6789 (m-30) REVERT: C 434 ASP cc_start: 0.6520 (t0) cc_final: 0.6000 (p0) REVERT: C 448 ASP cc_start: 0.7680 (m-30) cc_final: 0.7086 (p0) REVERT: C 584 SER cc_start: 0.7646 (m) cc_final: 0.7373 (p) REVERT: C 619 TYR cc_start: 0.7759 (m-80) cc_final: 0.7375 (m-80) REVERT: C 640 ASP cc_start: 0.7293 (t0) cc_final: 0.7067 (t70) REVERT: C 704 GLU cc_start: 0.7254 (mp0) cc_final: 0.6584 (mp0) REVERT: C 724 THR cc_start: 0.8250 (p) cc_final: 0.7759 (t) REVERT: C 758 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8468 (tttp) REVERT: C 795 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 816 ASN cc_start: 0.7910 (t0) cc_final: 0.7294 (t0) REVERT: C 854 ILE cc_start: 0.7945 (mt) cc_final: 0.7645 (mp) REVERT: C 898 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6497 (mt-10) REVERT: C 899 ASP cc_start: 0.7015 (m-30) cc_final: 0.6641 (m-30) REVERT: C 916 ASP cc_start: 0.7167 (t0) cc_final: 0.6938 (t0) REVERT: C 918 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8090 (mtmm) REVERT: C 974 PHE cc_start: 0.8381 (t80) cc_final: 0.7961 (t80) REVERT: C 999 LEU cc_start: 0.8151 (mt) cc_final: 0.7760 (mp) REVERT: C 1002 SER cc_start: 0.8574 (m) cc_final: 0.8027 (p) REVERT: C 1004 ASN cc_start: 0.7400 (m-40) cc_final: 0.6931 (m110) REVERT: C 1005 SER cc_start: 0.8230 (t) cc_final: 0.7866 (p) REVERT: C 1063 ILE cc_start: 0.8733 (pt) cc_final: 0.8194 (mm) REVERT: C 1064 SER cc_start: 0.8539 (p) cc_final: 0.8196 (m) REVERT: C 1069 ASP cc_start: 0.7677 (t0) cc_final: 0.7179 (t70) REVERT: C 1104 LYS cc_start: 0.7905 (mmmm) cc_final: 0.7001 (tppt) REVERT: C 1108 VAL cc_start: 0.8706 (t) cc_final: 0.8466 (p) REVERT: C 1113 LYS cc_start: 0.8273 (mttp) cc_final: 0.7653 (mtpp) REVERT: C 1127 SER cc_start: 0.7422 (t) cc_final: 0.6967 (p) REVERT: C 1190 PHE cc_start: 0.8051 (p90) cc_final: 0.7655 (p90) REVERT: C 1209 MET cc_start: 0.6551 (mtp) cc_final: 0.6239 (mtp) REVERT: C 1213 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7332 (ptt90) outliers start: 87 outliers final: 66 residues processed: 669 average time/residue: 0.1708 time to fit residues: 183.7669 Evaluate side-chains 668 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 602 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 922 ASN Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1218 SER Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 35 optimal weight: 0.5980 chunk 282 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 264 optimal weight: 0.0980 chunk 142 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 445 ASN A 454 GLN A1045 GLN A1145 GLN ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096331 restraints weight = 42804.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099677 restraints weight = 21948.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101833 restraints weight = 13432.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103279 restraints weight = 9440.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104269 restraints weight = 7317.351| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 26466 Z= 0.131 Angle : 0.611 25.281 36121 Z= 0.309 Chirality : 0.045 0.334 4322 Planarity : 0.004 0.055 4521 Dihedral : 6.844 94.461 4651 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.02 % Allowed : 12.86 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3188 helix: 1.67 (0.21), residues: 617 sheet: -0.28 (0.19), residues: 816 loop : -1.26 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1235 TYR 0.026 0.001 TYR A 403 PHE 0.028 0.001 PHE B 347 TRP 0.011 0.001 TRP B 168 HIS 0.010 0.001 HIS A 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (26364) covalent geometry : angle 0.58686 / 0.30 (35860) SS BOND : bond 0.00638 / 0.44 ( 45) SS BOND : angle 2.73680 / 1.70 ( 90) hydrogen bonds : bond 0.04068 / 2.75 ( 880) hydrogen bonds : angle 5.40152 / 3.73 ( 2589) link_ALPHA1-3 : bond 0.00785 / 0.40 ( 3) link_ALPHA1-3 : angle 1.77385 / 1.14 ( 9) link_ALPHA1-6 : bond 0.01131 / 0.56 ( 3) link_ALPHA1-6 : angle 2.16306 / 1.40 ( 9) link_BETA1-4 : bond 0.00344 / 0.24 ( 12) link_BETA1-4 : angle 1.63429 / 1.24 ( 36) link_NAG-ASN : bond 0.00206 / 0.15 ( 39) link_NAG-ASN : angle 1.58201 / 1.13 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 611 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8159 (t) cc_final: 0.7892 (p) REVERT: A 228 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: A 238 SER cc_start: 0.8414 (p) cc_final: 0.7822 (t) REVERT: A 247 ASN cc_start: 0.7567 (p0) cc_final: 0.7329 (p0) REVERT: A 317 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: A 379 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7089 (p) REVERT: A 397 GLU cc_start: 0.7336 (tt0) cc_final: 0.7099 (tt0) REVERT: A 439 TRP cc_start: 0.6320 (m100) cc_final: 0.6092 (m100) REVERT: A 481 ASP cc_start: 0.7484 (m-30) cc_final: 0.7252 (m-30) REVERT: A 487 ILE cc_start: 0.8450 (pt) cc_final: 0.8075 (mt) REVERT: A 507 PHE cc_start: 0.7869 (p90) cc_final: 0.7594 (p90) REVERT: A 539 PHE cc_start: 0.8004 (m-80) cc_final: 0.7637 (m-10) REVERT: A 593 SER cc_start: 0.7970 (m) cc_final: 0.7618 (p) REVERT: A 651 LYS cc_start: 0.8275 (tttt) cc_final: 0.7968 (ttpp) REVERT: A 660 GLU cc_start: 0.6519 (mp0) cc_final: 0.6172 (mp0) REVERT: A 682 GLN cc_start: 0.5905 (mp10) cc_final: 0.5686 (mp10) REVERT: A 716 VAL cc_start: 0.8646 (t) cc_final: 0.8373 (m) REVERT: A 735 PHE cc_start: 0.8532 (m-80) cc_final: 0.7753 (m-10) REVERT: A 738 SER cc_start: 0.8018 (p) cc_final: 0.7721 (t) REVERT: A 758 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8121 (ttmm) REVERT: A 773 LYS cc_start: 0.8168 (tttm) cc_final: 0.7681 (ttpp) REVERT: A 795 GLU cc_start: 0.7383 (tt0) cc_final: 0.7023 (tt0) REVERT: A 801 ASN cc_start: 0.8059 (p0) cc_final: 0.7858 (p0) REVERT: A 820 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7471 (mttp) REVERT: A 831 LYS cc_start: 0.6966 (tttt) cc_final: 0.6662 (ttpp) REVERT: A 844 GLU cc_start: 0.7550 (tp30) cc_final: 0.6993 (tp30) REVERT: A 853 THR cc_start: 0.7901 (p) cc_final: 0.7645 (p) REVERT: A 949 LYS cc_start: 0.7328 (tttt) cc_final: 0.7016 (ttpt) REVERT: A 954 SER cc_start: 0.7932 (m) cc_final: 0.7388 (p) REVERT: A 1040 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6779 (tp30) REVERT: A 1069 ASP cc_start: 0.6968 (t0) cc_final: 0.6672 (t0) REVERT: A 1108 VAL cc_start: 0.8214 (t) cc_final: 0.7879 (p) REVERT: A 1120 ASN cc_start: 0.7624 (m-40) cc_final: 0.7373 (m-40) REVERT: A 1121 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 1214 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8272 (mmmm) REVERT: B 32 PHE cc_start: 0.7295 (m-10) cc_final: 0.6633 (m-10) REVERT: B 174 THR cc_start: 0.8335 (m) cc_final: 0.7990 (p) REVERT: B 185 PHE cc_start: 0.7437 (t80) cc_final: 0.6564 (t80) REVERT: B 188 ASP cc_start: 0.7062 (m-30) cc_final: 0.6522 (t70) REVERT: B 209 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 227 TYR cc_start: 0.7506 (p90) cc_final: 0.7187 (p90) REVERT: B 242 PHE cc_start: 0.7713 (p90) cc_final: 0.7507 (p90) REVERT: B 263 SER cc_start: 0.7867 (t) cc_final: 0.7632 (p) REVERT: B 276 ASN cc_start: 0.7885 (t0) cc_final: 0.7194 (p0) REVERT: B 280 LEU cc_start: 0.8209 (tp) cc_final: 0.7969 (tp) REVERT: B 328 VAL cc_start: 0.8813 (m) cc_final: 0.8337 (t) REVERT: B 334 SER cc_start: 0.8253 (p) cc_final: 0.7920 (m) REVERT: B 353 SER cc_start: 0.8592 (m) cc_final: 0.8257 (p) REVERT: B 354 ASP cc_start: 0.7416 (t0) cc_final: 0.7164 (p0) REVERT: B 372 TYR cc_start: 0.8059 (m-80) cc_final: 0.7702 (m-10) REVERT: B 426 PHE cc_start: 0.7660 (m-10) cc_final: 0.7400 (m-10) REVERT: B 488 SER cc_start: 0.8267 (m) cc_final: 0.8008 (p) REVERT: B 552 SER cc_start: 0.8197 (m) cc_final: 0.7541 (t) REVERT: B 553 LEU cc_start: 0.7804 (tp) cc_final: 0.7517 (pt) REVERT: B 593 SER cc_start: 0.8813 (m) cc_final: 0.8074 (p) REVERT: B 601 ILE cc_start: 0.8351 (mt) cc_final: 0.8086 (tt) REVERT: B 614 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8047 (ptmm) REVERT: B 619 TYR cc_start: 0.7720 (m-80) cc_final: 0.7291 (m-10) REVERT: B 626 GLU cc_start: 0.6178 (mp0) cc_final: 0.5707 (mp0) REVERT: B 640 ASP cc_start: 0.7368 (t0) cc_final: 0.7096 (t70) REVERT: B 642 SER cc_start: 0.8462 (m) cc_final: 0.7886 (p) REVERT: B 651 LYS cc_start: 0.8614 (tttt) cc_final: 0.8255 (tttp) REVERT: B 670 PHE cc_start: 0.8067 (m-10) cc_final: 0.7658 (m-80) REVERT: B 679 ASP cc_start: 0.7335 (p0) cc_final: 0.6915 (t70) REVERT: B 709 VAL cc_start: 0.8491 (t) cc_final: 0.8245 (m) REVERT: B 746 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6551 (mm-30) REVERT: B 773 LYS cc_start: 0.8496 (tttt) cc_final: 0.8069 (tttm) REVERT: B 790 MET cc_start: 0.7037 (mtt) cc_final: 0.6693 (mtt) REVERT: B 820 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7555 (mtpt) REVERT: B 839 LEU cc_start: 0.8405 (mt) cc_final: 0.8200 (mm) REVERT: B 847 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 853 THR cc_start: 0.8452 (m) cc_final: 0.8169 (p) REVERT: B 924 ARG cc_start: 0.7524 (ttm110) cc_final: 0.7131 (ttm110) REVERT: B 949 LYS cc_start: 0.8445 (tttt) cc_final: 0.8081 (tppt) REVERT: B 954 SER cc_start: 0.8277 (m) cc_final: 0.7859 (t) REVERT: B 961 MET cc_start: 0.7214 (mtp) cc_final: 0.6968 (mtp) REVERT: B 963 LEU cc_start: 0.8086 (tp) cc_final: 0.7797 (tp) REVERT: B 999 LEU cc_start: 0.8900 (mt) cc_final: 0.8411 (mp) REVERT: B 1002 SER cc_start: 0.8455 (m) cc_final: 0.8144 (p) REVERT: B 1040 GLU cc_start: 0.7048 (tp30) cc_final: 0.6437 (tp30) REVERT: B 1069 ASP cc_start: 0.7261 (t0) cc_final: 0.6745 (t0) REVERT: B 1092 SER cc_start: 0.8437 (m) cc_final: 0.8122 (p) REVERT: B 1099 SER cc_start: 0.8574 (m) cc_final: 0.7818 (p) REVERT: B 1100 GLN cc_start: 0.7444 (mt0) cc_final: 0.7098 (tt0) REVERT: B 1103 THR cc_start: 0.8029 (m) cc_final: 0.7688 (p) REVERT: B 1104 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7839 (tppp) REVERT: B 1132 PHE cc_start: 0.8168 (t80) cc_final: 0.7923 (t80) REVERT: B 1136 ASP cc_start: 0.7087 (m-30) cc_final: 0.6866 (m-30) REVERT: B 1213 ARG cc_start: 0.7500 (ptt-90) cc_final: 0.6858 (ptt90) REVERT: C 48 VAL cc_start: 0.8330 (p) cc_final: 0.8093 (t) REVERT: C 171 ASP cc_start: 0.7837 (t0) cc_final: 0.7436 (t0) REVERT: C 176 PHE cc_start: 0.7988 (m-80) cc_final: 0.7580 (m-80) REVERT: C 185 PHE cc_start: 0.7724 (t80) cc_final: 0.7280 (t80) REVERT: C 247 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7693 (p0) REVERT: C 252 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 289 LYS cc_start: 0.7666 (mttt) cc_final: 0.6943 (ttmm) REVERT: C 308 ASN cc_start: 0.6823 (m-40) cc_final: 0.6563 (m-40) REVERT: C 334 SER cc_start: 0.8361 (p) cc_final: 0.8017 (m) REVERT: C 354 ASP cc_start: 0.7987 (t0) cc_final: 0.7696 (t0) REVERT: C 371 TYR cc_start: 0.7583 (m-10) cc_final: 0.7173 (m-80) REVERT: C 403 TYR cc_start: 0.7374 (m-10) cc_final: 0.7053 (m-80) REVERT: C 420 ASP cc_start: 0.7076 (m-30) cc_final: 0.6773 (m-30) REVERT: C 434 ASP cc_start: 0.6454 (t0) cc_final: 0.6014 (p0) REVERT: C 448 ASP cc_start: 0.7633 (m-30) cc_final: 0.7127 (p0) REVERT: C 584 SER cc_start: 0.7672 (m) cc_final: 0.7404 (p) REVERT: C 619 TYR cc_start: 0.7688 (m-80) cc_final: 0.7424 (m-80) REVERT: C 704 GLU cc_start: 0.7271 (mp0) cc_final: 0.6616 (mp0) REVERT: C 724 THR cc_start: 0.8229 (p) cc_final: 0.7720 (t) REVERT: C 758 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8426 (tttp) REVERT: C 795 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7628 (tm-30) REVERT: C 816 ASN cc_start: 0.7837 (t0) cc_final: 0.7526 (t0) REVERT: C 918 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8153 (mtmm) REVERT: C 974 PHE cc_start: 0.8359 (t80) cc_final: 0.7995 (t80) REVERT: C 999 LEU cc_start: 0.8126 (mt) cc_final: 0.7711 (mp) REVERT: C 1002 SER cc_start: 0.8499 (m) cc_final: 0.8014 (p) REVERT: C 1003 PHE cc_start: 0.8468 (t80) cc_final: 0.8132 (t80) REVERT: C 1004 ASN cc_start: 0.7468 (m-40) cc_final: 0.6905 (m110) REVERT: C 1005 SER cc_start: 0.8139 (t) cc_final: 0.7843 (p) REVERT: C 1063 ILE cc_start: 0.8717 (pt) cc_final: 0.8171 (mm) REVERT: C 1064 SER cc_start: 0.8503 (p) cc_final: 0.8142 (m) REVERT: C 1069 ASP cc_start: 0.7595 (t0) cc_final: 0.7193 (t70) REVERT: C 1104 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7532 (tppt) REVERT: C 1127 SER cc_start: 0.7375 (t) cc_final: 0.6952 (p) REVERT: C 1190 PHE cc_start: 0.8016 (p90) cc_final: 0.7609 (p90) REVERT: C 1209 MET cc_start: 0.6440 (mtp) cc_final: 0.6106 (mtp) REVERT: C 1213 ARG cc_start: 0.7833 (ptt180) cc_final: 0.7388 (ptt90) outliers start: 85 outliers final: 62 residues processed: 652 average time/residue: 0.1697 time to fit residues: 178.4429 Evaluate side-chains 652 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 586 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1218 SER Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 156 optimal weight: 0.0000 chunk 304 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN B1109 GLN C 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094728 restraints weight = 43069.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098039 restraints weight = 22198.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100229 restraints weight = 13596.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101643 restraints weight = 9519.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102637 restraints weight = 7390.926| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26466 Z= 0.225 Angle : 0.666 20.965 36121 Z= 0.339 Chirality : 0.047 0.423 4322 Planarity : 0.004 0.058 4521 Dihedral : 6.949 92.921 4651 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.45 % Allowed : 14.21 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3188 helix: 1.54 (0.21), residues: 619 sheet: -0.36 (0.19), residues: 825 loop : -1.36 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1207 TYR 0.031 0.002 TYR A 403 PHE 0.016 0.002 PHE C 478 TRP 0.012 0.002 TRP B 168 HIS 0.009 0.001 HIS A 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (26364) covalent geometry : angle 0.63829 / 0.33 (35860) SS BOND : bond 0.00642 / 0.44 ( 45) SS BOND : angle 2.98661 / 1.80 ( 90) hydrogen bonds : bond 0.04564 / 3.07 ( 880) hydrogen bonds : angle 5.47502 / 3.77 ( 2589) link_ALPHA1-3 : bond 0.00827 / 0.42 ( 3) link_ALPHA1-3 : angle 2.10791 / 1.30 ( 9) link_ALPHA1-6 : bond 0.00974 / 0.48 ( 3) link_ALPHA1-6 : angle 2.36605 / 1.52 ( 9) link_BETA1-4 : bond 0.00362 / 0.24 ( 12) link_BETA1-4 : angle 1.75468 / 1.36 ( 36) link_NAG-ASN : bond 0.00284 / 0.20 ( 39) link_NAG-ASN : angle 1.81248 / 1.28 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 600 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8323 (t) cc_final: 0.8060 (p) REVERT: A 228 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: A 238 SER cc_start: 0.8499 (p) cc_final: 0.7999 (t) REVERT: A 247 ASN cc_start: 0.7605 (p0) cc_final: 0.7383 (p0) REVERT: A 317 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: A 379 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7104 (p) REVERT: A 452 GLU cc_start: 0.7788 (tt0) cc_final: 0.7510 (tt0) REVERT: A 481 ASP cc_start: 0.7483 (m-30) cc_final: 0.7275 (m-30) REVERT: A 487 ILE cc_start: 0.8445 (pt) cc_final: 0.7804 (mt) REVERT: A 534 THR cc_start: 0.8358 (m) cc_final: 0.7975 (p) REVERT: A 539 PHE cc_start: 0.8044 (m-80) cc_final: 0.7650 (m-10) REVERT: A 593 SER cc_start: 0.8110 (m) cc_final: 0.7860 (p) REVERT: A 651 LYS cc_start: 0.8298 (tttt) cc_final: 0.8009 (ttpp) REVERT: A 660 GLU cc_start: 0.6511 (mp0) cc_final: 0.6171 (mp0) REVERT: A 682 GLN cc_start: 0.5946 (mp10) cc_final: 0.5723 (mp10) REVERT: A 716 VAL cc_start: 0.8648 (t) cc_final: 0.8364 (m) REVERT: A 738 SER cc_start: 0.8246 (p) cc_final: 0.7538 (m) REVERT: A 758 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8127 (ttmm) REVERT: A 773 LYS cc_start: 0.8184 (tttm) cc_final: 0.7726 (ttpp) REVERT: A 795 GLU cc_start: 0.7395 (tt0) cc_final: 0.7061 (tt0) REVERT: A 801 ASN cc_start: 0.8075 (p0) cc_final: 0.7873 (p0) REVERT: A 820 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7512 (mttp) REVERT: A 831 LYS cc_start: 0.7228 (tttt) cc_final: 0.6874 (ttpp) REVERT: A 844 GLU cc_start: 0.7553 (tp30) cc_final: 0.7023 (tp30) REVERT: A 853 THR cc_start: 0.7950 (p) cc_final: 0.7689 (p) REVERT: A 931 CYS cc_start: 0.5622 (m) cc_final: 0.5381 (m) REVERT: A 949 LYS cc_start: 0.7379 (tttt) cc_final: 0.7061 (ttpt) REVERT: A 954 SER cc_start: 0.7946 (m) cc_final: 0.7426 (p) REVERT: A 1040 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6751 (tm-30) REVERT: A 1069 ASP cc_start: 0.7046 (t0) cc_final: 0.6771 (t0) REVERT: A 1108 VAL cc_start: 0.8322 (t) cc_final: 0.8039 (p) REVERT: A 1120 ASN cc_start: 0.7617 (m-40) cc_final: 0.7362 (m-40) REVERT: A 1211 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6581 (mt-10) REVERT: A 1214 LYS cc_start: 0.8676 (mmpt) cc_final: 0.8284 (mmmm) REVERT: A 1230 TYR cc_start: 0.7207 (m-10) cc_final: 0.6866 (m-10) REVERT: B 32 PHE cc_start: 0.7123 (m-10) cc_final: 0.6078 (m-10) REVERT: B 167 THR cc_start: 0.8289 (m) cc_final: 0.7254 (p) REVERT: B 174 THR cc_start: 0.8344 (m) cc_final: 0.7804 (p) REVERT: B 185 PHE cc_start: 0.7503 (t80) cc_final: 0.6657 (t80) REVERT: B 188 ASP cc_start: 0.7107 (m-30) cc_final: 0.6560 (t70) REVERT: B 209 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7055 (mm-30) REVERT: B 227 TYR cc_start: 0.7517 (p90) cc_final: 0.7196 (p90) REVERT: B 242 PHE cc_start: 0.7732 (p90) cc_final: 0.7519 (p90) REVERT: B 276 ASN cc_start: 0.7901 (t0) cc_final: 0.7181 (p0) REVERT: B 328 VAL cc_start: 0.8786 (m) cc_final: 0.8315 (t) REVERT: B 334 SER cc_start: 0.8302 (p) cc_final: 0.7994 (m) REVERT: B 354 ASP cc_start: 0.7443 (t0) cc_final: 0.7158 (p0) REVERT: B 372 TYR cc_start: 0.8168 (m-80) cc_final: 0.7753 (m-10) REVERT: B 388 LEU cc_start: 0.8324 (mt) cc_final: 0.7927 (mp) REVERT: B 426 PHE cc_start: 0.7704 (m-10) cc_final: 0.7367 (m-10) REVERT: B 488 SER cc_start: 0.8295 (m) cc_final: 0.8070 (p) REVERT: B 552 SER cc_start: 0.8216 (m) cc_final: 0.7704 (t) REVERT: B 553 LEU cc_start: 0.7827 (tp) cc_final: 0.7400 (tp) REVERT: B 593 SER cc_start: 0.8781 (m) cc_final: 0.8029 (p) REVERT: B 601 ILE cc_start: 0.8393 (mt) cc_final: 0.8086 (tt) REVERT: B 614 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8139 (ptmm) REVERT: B 619 TYR cc_start: 0.7747 (m-80) cc_final: 0.7330 (m-10) REVERT: B 626 GLU cc_start: 0.6171 (mp0) cc_final: 0.5588 (mp0) REVERT: B 640 ASP cc_start: 0.7414 (t0) cc_final: 0.7110 (t70) REVERT: B 642 SER cc_start: 0.8471 (m) cc_final: 0.7873 (p) REVERT: B 651 LYS cc_start: 0.8680 (tttt) cc_final: 0.8284 (tttp) REVERT: B 670 PHE cc_start: 0.8074 (m-10) cc_final: 0.7683 (m-80) REVERT: B 679 ASP cc_start: 0.7353 (p0) cc_final: 0.6964 (t70) REVERT: B 709 VAL cc_start: 0.8537 (t) cc_final: 0.8289 (m) REVERT: B 746 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6498 (mm-30) REVERT: B 773 LYS cc_start: 0.8489 (tttt) cc_final: 0.8081 (tttm) REVERT: B 790 MET cc_start: 0.7045 (mtt) cc_final: 0.6724 (mtt) REVERT: B 820 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7554 (mtpt) REVERT: B 839 LEU cc_start: 0.8423 (mt) cc_final: 0.8197 (mm) REVERT: B 847 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7081 (mm-30) REVERT: B 853 THR cc_start: 0.8520 (m) cc_final: 0.8234 (p) REVERT: B 949 LYS cc_start: 0.8627 (tttt) cc_final: 0.8130 (ttmt) REVERT: B 954 SER cc_start: 0.8293 (m) cc_final: 0.7907 (t) REVERT: B 961 MET cc_start: 0.7258 (mtp) cc_final: 0.7015 (mtp) REVERT: B 963 LEU cc_start: 0.8108 (tp) cc_final: 0.7844 (tp) REVERT: B 999 LEU cc_start: 0.8938 (mt) cc_final: 0.8436 (mp) REVERT: B 1002 SER cc_start: 0.8540 (m) cc_final: 0.8181 (p) REVERT: B 1040 GLU cc_start: 0.7076 (tp30) cc_final: 0.6444 (tp30) REVERT: B 1069 ASP cc_start: 0.7296 (t0) cc_final: 0.6820 (t0) REVERT: B 1092 SER cc_start: 0.8483 (m) cc_final: 0.8155 (p) REVERT: B 1099 SER cc_start: 0.8566 (m) cc_final: 0.8136 (p) REVERT: B 1104 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7994 (tppp) REVERT: B 1132 PHE cc_start: 0.8188 (t80) cc_final: 0.7860 (t80) REVERT: B 1213 ARG cc_start: 0.7575 (ptt-90) cc_final: 0.7086 (ptt-90) REVERT: C 48 VAL cc_start: 0.8374 (p) cc_final: 0.8093 (t) REVERT: C 171 ASP cc_start: 0.7850 (t0) cc_final: 0.7530 (t0) REVERT: C 176 PHE cc_start: 0.8032 (m-80) cc_final: 0.7610 (m-80) REVERT: C 184 TYR cc_start: 0.7589 (t80) cc_final: 0.7336 (t80) REVERT: C 252 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 289 LYS cc_start: 0.7782 (mttt) cc_final: 0.7064 (mtmm) REVERT: C 308 ASN cc_start: 0.6835 (m-40) cc_final: 0.6562 (m-40) REVERT: C 334 SER cc_start: 0.8390 (p) cc_final: 0.8030 (m) REVERT: C 354 ASP cc_start: 0.7975 (t0) cc_final: 0.7668 (t0) REVERT: C 403 TYR cc_start: 0.7413 (m-10) cc_final: 0.7112 (m-80) REVERT: C 420 ASP cc_start: 0.7070 (m-30) cc_final: 0.6771 (m-30) REVERT: C 448 ASP cc_start: 0.7665 (m-30) cc_final: 0.7167 (p0) REVERT: C 452 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 584 SER cc_start: 0.7647 (m) cc_final: 0.7394 (p) REVERT: C 619 TYR cc_start: 0.7743 (m-80) cc_final: 0.7490 (m-80) REVERT: C 674 VAL cc_start: 0.8879 (m) cc_final: 0.8614 (t) REVERT: C 704 GLU cc_start: 0.7260 (mp0) cc_final: 0.6751 (mp0) REVERT: C 724 THR cc_start: 0.8247 (p) cc_final: 0.7742 (t) REVERT: C 753 ASN cc_start: 0.7812 (p0) cc_final: 0.7609 (p0) REVERT: C 758 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8456 (tttp) REVERT: C 795 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 802 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8629 (p) REVERT: C 816 ASN cc_start: 0.7923 (t0) cc_final: 0.7418 (t0) REVERT: C 974 PHE cc_start: 0.8384 (t80) cc_final: 0.8029 (t80) REVERT: C 999 LEU cc_start: 0.8142 (mt) cc_final: 0.7709 (mp) REVERT: C 1002 SER cc_start: 0.8536 (m) cc_final: 0.8065 (p) REVERT: C 1004 ASN cc_start: 0.7441 (m-40) cc_final: 0.6918 (m110) REVERT: C 1005 SER cc_start: 0.8191 (t) cc_final: 0.7876 (p) REVERT: C 1063 ILE cc_start: 0.8713 (pt) cc_final: 0.8179 (mm) REVERT: C 1064 SER cc_start: 0.8495 (p) cc_final: 0.8148 (m) REVERT: C 1069 ASP cc_start: 0.7603 (t0) cc_final: 0.7206 (t70) REVERT: C 1127 SER cc_start: 0.7399 (t) cc_final: 0.6777 (p) REVERT: C 1132 PHE cc_start: 0.8234 (t80) cc_final: 0.7915 (t80) REVERT: C 1190 PHE cc_start: 0.8024 (p90) cc_final: 0.7625 (p90) REVERT: C 1209 MET cc_start: 0.6594 (mtp) cc_final: 0.6236 (mtp) REVERT: C 1213 ARG cc_start: 0.7828 (ptt180) cc_final: 0.7292 (ptt90) outliers start: 97 outliers final: 79 residues processed: 651 average time/residue: 0.1695 time to fit residues: 177.4063 Evaluate side-chains 656 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 573 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1216 THR Chi-restraints excluded: chain B residue 1218 SER Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 290 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 293 optimal weight: 0.3980 chunk 251 optimal weight: 0.0470 chunk 145 optimal weight: 0.0470 chunk 185 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 GLN A1045 GLN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098358 restraints weight = 42679.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101780 restraints weight = 21682.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104069 restraints weight = 13179.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105541 restraints weight = 9147.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106587 restraints weight = 7061.354| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26466 Z= 0.112 Angle : 0.627 23.771 36121 Z= 0.311 Chirality : 0.046 0.439 4322 Planarity : 0.004 0.050 4521 Dihedral : 6.678 83.456 4651 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.77 % Allowed : 15.74 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3188 helix: 1.78 (0.21), residues: 613 sheet: -0.33 (0.19), residues: 820 loop : -1.22 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1235 TYR 0.027 0.001 TYR C 237 PHE 0.020 0.001 PHE B 347 TRP 0.011 0.001 TRP B 168 HIS 0.008 0.001 HIS A 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (26364) covalent geometry : angle 0.58514 / 0.30 (35860) SS BOND : bond 0.00605 / 0.41 ( 45) SS BOND : angle 2.68791 / 1.57 ( 90) hydrogen bonds : bond 0.03815 / 2.60 ( 880) hydrogen bonds : angle 5.21195 / 3.60 ( 2589) link_ALPHA1-3 : bond 0.00931 / 0.47 ( 3) link_ALPHA1-3 : angle 1.62855 / 1.06 ( 9) link_ALPHA1-6 : bond 0.01167 / 0.58 ( 3) link_ALPHA1-6 : angle 2.36766 / 1.50 ( 9) link_BETA1-4 : bond 0.00529 / 0.33 ( 12) link_BETA1-4 : angle 1.73639 / 1.19 ( 36) link_NAG-ASN : bond 0.00411 / 0.30 ( 39) link_NAG-ASN : angle 3.06654 / 1.77 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 598 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8149 (t) cc_final: 0.7882 (p) REVERT: A 228 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: A 238 SER cc_start: 0.8501 (p) cc_final: 0.7984 (t) REVERT: A 247 ASN cc_start: 0.7539 (p0) cc_final: 0.7303 (p0) REVERT: A 317 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: A 348 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 379 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7051 (p) REVERT: A 396 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7646 (mtp85) REVERT: A 452 GLU cc_start: 0.7810 (tt0) cc_final: 0.7496 (tt0) REVERT: A 481 ASP cc_start: 0.7584 (m-30) cc_final: 0.7331 (m-30) REVERT: A 487 ILE cc_start: 0.8111 (pt) cc_final: 0.7526 (mt) REVERT: A 510 HIS cc_start: 0.8222 (t-90) cc_final: 0.8006 (t-170) REVERT: A 534 THR cc_start: 0.8322 (m) cc_final: 0.7985 (p) REVERT: A 539 PHE cc_start: 0.8064 (m-80) cc_final: 0.7745 (m-10) REVERT: A 593 SER cc_start: 0.8091 (m) cc_final: 0.7745 (p) REVERT: A 651 LYS cc_start: 0.8234 (tttt) cc_final: 0.7928 (ttpp) REVERT: A 660 GLU cc_start: 0.6627 (mp0) cc_final: 0.6299 (mp0) REVERT: A 682 GLN cc_start: 0.5936 (mp10) cc_final: 0.5646 (mp10) REVERT: A 704 GLU cc_start: 0.7410 (mp0) cc_final: 0.7012 (mp0) REVERT: A 716 VAL cc_start: 0.8567 (t) cc_final: 0.8225 (m) REVERT: A 735 PHE cc_start: 0.8603 (m-80) cc_final: 0.8248 (m-10) REVERT: A 738 SER cc_start: 0.7915 (p) cc_final: 0.7369 (m) REVERT: A 758 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8160 (ttmm) REVERT: A 773 LYS cc_start: 0.8220 (tttm) cc_final: 0.7710 (ttpp) REVERT: A 790 MET cc_start: 0.8353 (mtt) cc_final: 0.7892 (mmm) REVERT: A 795 GLU cc_start: 0.7425 (tt0) cc_final: 0.7027 (tt0) REVERT: A 801 ASN cc_start: 0.8120 (p0) cc_final: 0.7913 (p0) REVERT: A 820 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7510 (mttp) REVERT: A 831 LYS cc_start: 0.6798 (tttt) cc_final: 0.6591 (ttpp) REVERT: A 844 GLU cc_start: 0.7622 (tp30) cc_final: 0.7043 (tp30) REVERT: A 853 THR cc_start: 0.7896 (p) cc_final: 0.7645 (p) REVERT: A 949 LYS cc_start: 0.7341 (tttt) cc_final: 0.7012 (ttpt) REVERT: A 954 SER cc_start: 0.7941 (m) cc_final: 0.7407 (p) REVERT: A 1040 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6801 (tm-30) REVERT: A 1050 SER cc_start: 0.8044 (m) cc_final: 0.7663 (p) REVERT: A 1069 ASP cc_start: 0.7026 (t0) cc_final: 0.6714 (t0) REVERT: A 1108 VAL cc_start: 0.8199 (t) cc_final: 0.7843 (p) REVERT: A 1120 ASN cc_start: 0.7691 (m-40) cc_final: 0.7395 (m-40) REVERT: A 1211 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6791 (mt-10) REVERT: A 1214 LYS cc_start: 0.8674 (mmpt) cc_final: 0.8198 (mmmm) REVERT: A 1230 TYR cc_start: 0.7123 (m-10) cc_final: 0.6854 (m-10) REVERT: B 32 PHE cc_start: 0.7060 (m-10) cc_final: 0.6037 (m-10) REVERT: B 167 THR cc_start: 0.8388 (m) cc_final: 0.7186 (p) REVERT: B 174 THR cc_start: 0.8342 (m) cc_final: 0.7730 (p) REVERT: B 185 PHE cc_start: 0.7419 (t80) cc_final: 0.6431 (t80) REVERT: B 188 ASP cc_start: 0.7137 (m-30) cc_final: 0.6515 (t70) REVERT: B 209 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7117 (mm-30) REVERT: B 212 TYR cc_start: 0.7794 (m-80) cc_final: 0.7586 (m-10) REVERT: B 227 TYR cc_start: 0.7514 (p90) cc_final: 0.7192 (p90) REVERT: B 242 PHE cc_start: 0.7652 (p90) cc_final: 0.7436 (p90) REVERT: B 276 ASN cc_start: 0.7809 (t0) cc_final: 0.7159 (p0) REVERT: B 301 GLN cc_start: 0.8495 (mt0) cc_final: 0.8167 (mt0) REVERT: B 328 VAL cc_start: 0.8755 (m) cc_final: 0.8258 (t) REVERT: B 334 SER cc_start: 0.8385 (p) cc_final: 0.7927 (m) REVERT: B 354 ASP cc_start: 0.7594 (t0) cc_final: 0.7175 (p0) REVERT: B 372 TYR cc_start: 0.7915 (m-80) cc_final: 0.7486 (m-10) REVERT: B 388 LEU cc_start: 0.8278 (mt) cc_final: 0.7859 (mp) REVERT: B 426 PHE cc_start: 0.7574 (m-10) cc_final: 0.7229 (m-10) REVERT: B 488 SER cc_start: 0.8319 (m) cc_final: 0.8051 (p) REVERT: B 552 SER cc_start: 0.8133 (m) cc_final: 0.7485 (t) REVERT: B 553 LEU cc_start: 0.7813 (tp) cc_final: 0.7501 (pt) REVERT: B 593 SER cc_start: 0.8722 (m) cc_final: 0.7988 (p) REVERT: B 601 ILE cc_start: 0.8292 (mt) cc_final: 0.7995 (tt) REVERT: B 614 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8104 (ptmm) REVERT: B 626 GLU cc_start: 0.6203 (mp0) cc_final: 0.5681 (mp0) REVERT: B 640 ASP cc_start: 0.7480 (t0) cc_final: 0.7211 (t70) REVERT: B 642 SER cc_start: 0.8470 (m) cc_final: 0.7877 (p) REVERT: B 651 LYS cc_start: 0.8555 (tttt) cc_final: 0.8174 (tttp) REVERT: B 670 PHE cc_start: 0.8054 (m-10) cc_final: 0.7637 (m-80) REVERT: B 679 ASP cc_start: 0.7425 (p0) cc_final: 0.7001 (t70) REVERT: B 709 VAL cc_start: 0.8482 (t) cc_final: 0.8248 (m) REVERT: B 721 SER cc_start: 0.8524 (p) cc_final: 0.7954 (t) REVERT: B 746 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6605 (mm-30) REVERT: B 773 LYS cc_start: 0.8553 (tttt) cc_final: 0.8260 (tttm) REVERT: B 790 MET cc_start: 0.7014 (mtt) cc_final: 0.6763 (mtt) REVERT: B 820 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7477 (mtpt) REVERT: B 839 LEU cc_start: 0.8348 (mt) cc_final: 0.8097 (mp) REVERT: B 847 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 853 THR cc_start: 0.8500 (m) cc_final: 0.8226 (p) REVERT: B 949 LYS cc_start: 0.8450 (tttt) cc_final: 0.8030 (ttmt) REVERT: B 954 SER cc_start: 0.8222 (m) cc_final: 0.7941 (t) REVERT: B 961 MET cc_start: 0.7343 (mtp) cc_final: 0.7113 (mtp) REVERT: B 963 LEU cc_start: 0.8110 (tp) cc_final: 0.7620 (tt) REVERT: B 999 LEU cc_start: 0.8935 (mt) cc_final: 0.8484 (mp) REVERT: B 1002 SER cc_start: 0.8479 (m) cc_final: 0.8141 (p) REVERT: B 1040 GLU cc_start: 0.7083 (tp30) cc_final: 0.6455 (tp30) REVERT: B 1069 ASP cc_start: 0.7337 (t0) cc_final: 0.6795 (t0) REVERT: B 1092 SER cc_start: 0.8379 (m) cc_final: 0.8055 (p) REVERT: B 1099 SER cc_start: 0.8560 (m) cc_final: 0.7936 (p) REVERT: B 1104 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7865 (tppp) REVERT: B 1132 PHE cc_start: 0.8108 (t80) cc_final: 0.7901 (t80) REVERT: B 1211 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6551 (mm-30) REVERT: B 1213 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.6882 (ptt90) REVERT: C 48 VAL cc_start: 0.8322 (p) cc_final: 0.8044 (t) REVERT: C 171 ASP cc_start: 0.7768 (t0) cc_final: 0.7308 (t0) REVERT: C 176 PHE cc_start: 0.7979 (m-80) cc_final: 0.7616 (m-80) REVERT: C 184 TYR cc_start: 0.7460 (t80) cc_final: 0.7259 (t80) REVERT: C 247 ASN cc_start: 0.8149 (p0) cc_final: 0.7737 (p0) REVERT: C 252 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7186 (mm-30) REVERT: C 289 LYS cc_start: 0.7700 (mttt) cc_final: 0.6896 (ttmm) REVERT: C 308 ASN cc_start: 0.6868 (m-40) cc_final: 0.6556 (m-40) REVERT: C 334 SER cc_start: 0.8384 (p) cc_final: 0.7969 (m) REVERT: C 354 ASP cc_start: 0.8067 (t0) cc_final: 0.7678 (t0) REVERT: C 403 TYR cc_start: 0.7409 (m-10) cc_final: 0.7088 (m-80) REVERT: C 420 ASP cc_start: 0.7088 (m-30) cc_final: 0.6731 (m-30) REVERT: C 434 ASP cc_start: 0.6500 (t0) cc_final: 0.5978 (p0) REVERT: C 448 ASP cc_start: 0.7680 (m-30) cc_final: 0.6949 (p0) REVERT: C 543 CYS cc_start: 0.4451 (OUTLIER) cc_final: 0.4168 (p) REVERT: C 584 SER cc_start: 0.7724 (m) cc_final: 0.7389 (p) REVERT: C 619 TYR cc_start: 0.7736 (m-80) cc_final: 0.7318 (m-80) REVERT: C 704 GLU cc_start: 0.7331 (mp0) cc_final: 0.6621 (mp0) REVERT: C 724 THR cc_start: 0.8276 (p) cc_final: 0.7764 (t) REVERT: C 758 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8327 (tttp) REVERT: C 795 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 802 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 900 LEU cc_start: 0.8345 (tp) cc_final: 0.7911 (tt) REVERT: C 948 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7089 (mm-30) REVERT: C 974 PHE cc_start: 0.8310 (t80) cc_final: 0.7906 (t80) REVERT: C 999 LEU cc_start: 0.8152 (mt) cc_final: 0.7754 (mp) REVERT: C 1002 SER cc_start: 0.8556 (m) cc_final: 0.8028 (p) REVERT: C 1003 PHE cc_start: 0.8491 (t80) cc_final: 0.8138 (t80) REVERT: C 1004 ASN cc_start: 0.7505 (m-40) cc_final: 0.6914 (m110) REVERT: C 1005 SER cc_start: 0.8164 (t) cc_final: 0.7840 (p) REVERT: C 1063 ILE cc_start: 0.8702 (pt) cc_final: 0.8181 (mm) REVERT: C 1064 SER cc_start: 0.8466 (p) cc_final: 0.8195 (m) REVERT: C 1066 SER cc_start: 0.7979 (t) cc_final: 0.7667 (p) REVERT: C 1069 ASP cc_start: 0.7643 (t0) cc_final: 0.7071 (t70) REVERT: C 1127 SER cc_start: 0.7366 (t) cc_final: 0.6929 (p) REVERT: C 1209 MET cc_start: 0.6452 (mtp) cc_final: 0.6203 (mtp) REVERT: C 1213 ARG cc_start: 0.7769 (ptt180) cc_final: 0.7226 (ptt90) REVERT: C 1237 GLN cc_start: 0.8554 (mp10) cc_final: 0.8176 (mp10) outliers start: 78 outliers final: 58 residues processed: 638 average time/residue: 0.1690 time to fit residues: 173.3151 Evaluate side-chains 652 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 588 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 816 ASN Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1218 SER Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 543 CYS Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1109 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 106 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 212 optimal weight: 2.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS A 282 ASN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097469 restraints weight = 42836.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.100675 restraints weight = 22412.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102810 restraints weight = 13936.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104215 restraints weight = 9817.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105191 restraints weight = 7638.271| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26466 Z= 0.224 Angle : 0.680 23.489 36121 Z= 0.340 Chirality : 0.047 0.553 4322 Planarity : 0.004 0.056 4521 Dihedral : 6.801 82.035 4651 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.02 % Allowed : 15.67 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 3188 helix: 1.69 (0.21), residues: 613 sheet: -0.29 (0.19), residues: 803 loop : -1.31 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1235 TYR 0.028 0.002 TYR A 403 PHE 0.021 0.002 PHE A 622 TRP 0.012 0.002 TRP B 439 HIS 0.006 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (26364) covalent geometry : angle 0.63648 / 0.33 (35860) SS BOND : bond 0.00661 / 0.46 ( 45) SS BOND : angle 2.57030 / 1.62 ( 90) hydrogen bonds : bond 0.04423 / 2.98 ( 880) hydrogen bonds : angle 5.32877 / 3.67 ( 2589) link_ALPHA1-3 : bond 0.00762 / 0.39 ( 3) link_ALPHA1-3 : angle 2.03240 / 1.24 ( 9) link_ALPHA1-6 : bond 0.01057 / 0.52 ( 3) link_ALPHA1-6 : angle 2.57783 / 1.61 ( 9) link_BETA1-4 : bond 0.00491 / 0.32 ( 12) link_BETA1-4 : angle 1.90328 / 1.39 ( 36) link_NAG-ASN : bond 0.00451 / 0.33 ( 39) link_NAG-ASN : angle 3.42522 / 2.07 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 592 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8212 (t) cc_final: 0.7959 (p) REVERT: A 238 SER cc_start: 0.8511 (p) cc_final: 0.8187 (t) REVERT: A 247 ASN cc_start: 0.7610 (p0) cc_final: 0.7375 (p0) REVERT: A 317 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: A 348 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7690 (p) REVERT: A 379 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7163 (p) REVERT: A 452 GLU cc_start: 0.7711 (tt0) cc_final: 0.7441 (tt0) REVERT: A 481 ASP cc_start: 0.7463 (m-30) cc_final: 0.7247 (m-30) REVERT: A 487 ILE cc_start: 0.8235 (pt) cc_final: 0.7695 (mt) REVERT: A 534 THR cc_start: 0.8368 (m) cc_final: 0.7944 (p) REVERT: A 539 PHE cc_start: 0.8074 (m-80) cc_final: 0.7714 (m-10) REVERT: A 593 SER cc_start: 0.8157 (m) cc_final: 0.7923 (p) REVERT: A 651 LYS cc_start: 0.8286 (tttt) cc_final: 0.8030 (ttpp) REVERT: A 660 GLU cc_start: 0.6620 (mp0) cc_final: 0.6332 (mp0) REVERT: A 682 GLN cc_start: 0.5990 (mp10) cc_final: 0.5696 (mp10) REVERT: A 704 GLU cc_start: 0.7483 (mp0) cc_final: 0.7174 (mp0) REVERT: A 716 VAL cc_start: 0.8618 (t) cc_final: 0.8353 (m) REVERT: A 738 SER cc_start: 0.8210 (p) cc_final: 0.7574 (m) REVERT: A 749 LEU cc_start: 0.8093 (mt) cc_final: 0.7889 (mp) REVERT: A 758 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8104 (ttmm) REVERT: A 773 LYS cc_start: 0.8147 (tttm) cc_final: 0.7481 (ttpp) REVERT: A 795 GLU cc_start: 0.7389 (tt0) cc_final: 0.7080 (tt0) REVERT: A 820 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7545 (mttp) REVERT: A 831 LYS cc_start: 0.7176 (tttt) cc_final: 0.6871 (ttpp) REVERT: A 844 GLU cc_start: 0.7532 (tp30) cc_final: 0.7000 (tp30) REVERT: A 853 THR cc_start: 0.7949 (p) cc_final: 0.7687 (p) REVERT: A 915 GLU cc_start: 0.6373 (tp30) cc_final: 0.6146 (tp30) REVERT: A 931 CYS cc_start: 0.5632 (m) cc_final: 0.5350 (m) REVERT: A 949 LYS cc_start: 0.7390 (tttt) cc_final: 0.7070 (ttpt) REVERT: A 954 SER cc_start: 0.7942 (m) cc_final: 0.7448 (p) REVERT: A 1040 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6808 (tm-30) REVERT: A 1050 SER cc_start: 0.8267 (m) cc_final: 0.7844 (p) REVERT: A 1069 ASP cc_start: 0.7008 (t0) cc_final: 0.6739 (t0) REVERT: A 1108 VAL cc_start: 0.8301 (t) cc_final: 0.8023 (p) REVERT: A 1120 ASN cc_start: 0.7627 (m-40) cc_final: 0.7405 (m110) REVERT: A 1130 TYR cc_start: 0.7941 (t80) cc_final: 0.7741 (t80) REVERT: A 1138 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 1172 LEU cc_start: 0.8233 (mp) cc_final: 0.7644 (mt) REVERT: A 1214 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8233 (mmmm) REVERT: B 32 PHE cc_start: 0.7159 (m-10) cc_final: 0.6161 (m-10) REVERT: B 35 PHE cc_start: 0.7934 (t80) cc_final: 0.7646 (t80) REVERT: B 167 THR cc_start: 0.8367 (m) cc_final: 0.7209 (p) REVERT: B 174 THR cc_start: 0.8306 (m) cc_final: 0.7734 (p) REVERT: B 185 PHE cc_start: 0.7384 (t80) cc_final: 0.6514 (t80) REVERT: B 188 ASP cc_start: 0.7115 (m-30) cc_final: 0.6555 (t70) REVERT: B 209 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 212 TYR cc_start: 0.7795 (m-80) cc_final: 0.7558 (m-10) REVERT: B 227 TYR cc_start: 0.7574 (p90) cc_final: 0.7356 (p90) REVERT: B 276 ASN cc_start: 0.7916 (t0) cc_final: 0.6941 (p0) REVERT: B 328 VAL cc_start: 0.8780 (m) cc_final: 0.8297 (t) REVERT: B 334 SER cc_start: 0.8365 (p) cc_final: 0.7994 (m) REVERT: B 354 ASP cc_start: 0.7487 (t0) cc_final: 0.7197 (p0) REVERT: B 372 TYR cc_start: 0.8045 (m-80) cc_final: 0.7593 (m-10) REVERT: B 388 LEU cc_start: 0.8210 (mt) cc_final: 0.7793 (mp) REVERT: B 426 PHE cc_start: 0.7720 (m-10) cc_final: 0.7437 (m-10) REVERT: B 488 SER cc_start: 0.8313 (m) cc_final: 0.8085 (p) REVERT: B 552 SER cc_start: 0.8210 (m) cc_final: 0.7727 (t) REVERT: B 553 LEU cc_start: 0.7827 (tp) cc_final: 0.7396 (tp) REVERT: B 593 SER cc_start: 0.8774 (m) cc_final: 0.8073 (p) REVERT: B 614 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8171 (ptmm) REVERT: B 626 GLU cc_start: 0.6173 (mp0) cc_final: 0.5562 (mp0) REVERT: B 640 ASP cc_start: 0.7433 (t0) cc_final: 0.7127 (t70) REVERT: B 642 SER cc_start: 0.8472 (m) cc_final: 0.7868 (p) REVERT: B 651 LYS cc_start: 0.8667 (tttt) cc_final: 0.8279 (tttp) REVERT: B 670 PHE cc_start: 0.8083 (m-10) cc_final: 0.7689 (m-80) REVERT: B 679 ASP cc_start: 0.7323 (p0) cc_final: 0.6980 (t70) REVERT: B 709 VAL cc_start: 0.8549 (t) cc_final: 0.8322 (m) REVERT: B 746 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6472 (mm-30) REVERT: B 773 LYS cc_start: 0.8529 (tttt) cc_final: 0.8075 (tttp) REVERT: B 820 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7550 (mtpt) REVERT: B 839 LEU cc_start: 0.8434 (mt) cc_final: 0.8216 (mm) REVERT: B 853 THR cc_start: 0.8498 (m) cc_final: 0.8250 (p) REVERT: B 949 LYS cc_start: 0.8570 (tttt) cc_final: 0.8155 (ttmt) REVERT: B 954 SER cc_start: 0.8318 (m) cc_final: 0.7934 (t) REVERT: B 961 MET cc_start: 0.7211 (mtp) cc_final: 0.6970 (mtp) REVERT: B 963 LEU cc_start: 0.8090 (tp) cc_final: 0.7844 (tp) REVERT: B 999 LEU cc_start: 0.8948 (mt) cc_final: 0.8435 (mp) REVERT: B 1002 SER cc_start: 0.8465 (m) cc_final: 0.8148 (p) REVERT: B 1040 GLU cc_start: 0.7045 (tp30) cc_final: 0.6442 (tp30) REVERT: B 1069 ASP cc_start: 0.7288 (t0) cc_final: 0.6796 (t0) REVERT: B 1092 SER cc_start: 0.8479 (m) cc_final: 0.8158 (p) REVERT: B 1099 SER cc_start: 0.8685 (m) cc_final: 0.8085 (p) REVERT: B 1132 PHE cc_start: 0.8131 (t80) cc_final: 0.7894 (t80) REVERT: B 1213 ARG cc_start: 0.7577 (ptt-90) cc_final: 0.7108 (ptt-90) REVERT: C 48 VAL cc_start: 0.8404 (p) cc_final: 0.8127 (t) REVERT: C 171 ASP cc_start: 0.7873 (t0) cc_final: 0.7201 (t0) REVERT: C 247 ASN cc_start: 0.8069 (p0) cc_final: 0.7637 (p0) REVERT: C 252 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 289 LYS cc_start: 0.7731 (mttt) cc_final: 0.7033 (ttmm) REVERT: C 308 ASN cc_start: 0.6850 (m-40) cc_final: 0.6516 (m-40) REVERT: C 334 SER cc_start: 0.8365 (p) cc_final: 0.8021 (m) REVERT: C 354 ASP cc_start: 0.7939 (t0) cc_final: 0.7671 (t0) REVERT: C 403 TYR cc_start: 0.7285 (m-10) cc_final: 0.6986 (m-80) REVERT: C 420 ASP cc_start: 0.7047 (m-30) cc_final: 0.6755 (m-30) REVERT: C 448 ASP cc_start: 0.7642 (m-30) cc_final: 0.7082 (p0) REVERT: C 452 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7222 (tm-30) REVERT: C 584 SER cc_start: 0.7617 (m) cc_final: 0.7342 (p) REVERT: C 619 TYR cc_start: 0.7756 (m-80) cc_final: 0.7532 (m-80) REVERT: C 674 VAL cc_start: 0.8877 (m) cc_final: 0.8618 (t) REVERT: C 704 GLU cc_start: 0.7290 (mp0) cc_final: 0.6838 (mp0) REVERT: C 724 THR cc_start: 0.8238 (p) cc_final: 0.7738 (t) REVERT: C 753 ASN cc_start: 0.7777 (p0) cc_final: 0.7569 (p0) REVERT: C 758 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8414 (tttp) REVERT: C 795 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7523 (tm-30) REVERT: C 802 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 900 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8057 (tt) REVERT: C 948 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7057 (mm-30) REVERT: C 974 PHE cc_start: 0.8408 (t80) cc_final: 0.7969 (t80) REVERT: C 999 LEU cc_start: 0.8124 (mt) cc_final: 0.7740 (mp) REVERT: C 1002 SER cc_start: 0.8492 (m) cc_final: 0.8042 (p) REVERT: C 1004 ASN cc_start: 0.7511 (m-40) cc_final: 0.6968 (m110) REVERT: C 1005 SER cc_start: 0.8167 (t) cc_final: 0.7862 (p) REVERT: C 1063 ILE cc_start: 0.8675 (pt) cc_final: 0.8206 (mm) REVERT: C 1064 SER cc_start: 0.8474 (p) cc_final: 0.8139 (m) REVERT: C 1069 ASP cc_start: 0.7576 (t0) cc_final: 0.7185 (t70) REVERT: C 1127 SER cc_start: 0.7266 (t) cc_final: 0.6764 (p) REVERT: C 1190 PHE cc_start: 0.7972 (p90) cc_final: 0.7677 (p90) REVERT: C 1213 ARG cc_start: 0.7828 (ptt180) cc_final: 0.7371 (ptt90) outliers start: 85 outliers final: 71 residues processed: 634 average time/residue: 0.1662 time to fit residues: 169.9186 Evaluate side-chains 659 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 583 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1218 SER Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 231 optimal weight: 0.0070 chunk 252 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 271 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098191 restraints weight = 42819.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101430 restraints weight = 22350.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103564 restraints weight = 13859.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105021 restraints weight = 9778.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106028 restraints weight = 7582.842| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26466 Z= 0.159 Angle : 0.670 22.076 36121 Z= 0.332 Chirality : 0.046 0.512 4322 Planarity : 0.004 0.051 4521 Dihedral : 6.602 75.808 4651 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.06 % Allowed : 16.24 % Favored : 80.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3188 helix: 1.74 (0.21), residues: 606 sheet: -0.37 (0.19), residues: 815 loop : -1.25 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1235 TYR 0.034 0.001 TYR C 407 PHE 0.018 0.001 PHE C 788 TRP 0.010 0.001 TRP B 439 HIS 0.005 0.001 HIS A 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (26364) covalent geometry : angle 0.62260 / 0.32 (35860) SS BOND : bond 0.00637 / 0.43 ( 45) SS BOND : angle 2.54775 / 1.57 ( 90) hydrogen bonds : bond 0.04147 / 2.81 ( 880) hydrogen bonds : angle 5.25869 / 3.63 ( 2589) link_ALPHA1-3 : bond 0.00846 / 0.43 ( 3) link_ALPHA1-3 : angle 1.87725 / 1.17 ( 9) link_ALPHA1-6 : bond 0.01181 / 0.58 ( 3) link_ALPHA1-6 : angle 2.48380 / 1.56 ( 9) link_BETA1-4 : bond 0.00442 / 0.28 ( 12) link_BETA1-4 : angle 1.82117 / 1.30 ( 36) link_NAG-ASN : bond 0.00397 / 0.29 ( 39) link_NAG-ASN : angle 3.61201 / 2.44 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 587 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8203 (t) cc_final: 0.7948 (p) REVERT: A 238 SER cc_start: 0.8500 (p) cc_final: 0.8140 (t) REVERT: A 247 ASN cc_start: 0.7590 (p0) cc_final: 0.7367 (p0) REVERT: A 317 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: A 348 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7685 (p) REVERT: A 379 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 452 GLU cc_start: 0.7755 (tt0) cc_final: 0.7493 (tt0) REVERT: A 481 ASP cc_start: 0.7456 (m-30) cc_final: 0.7239 (m-30) REVERT: A 487 ILE cc_start: 0.8226 (pt) cc_final: 0.7698 (mt) REVERT: A 534 THR cc_start: 0.8348 (m) cc_final: 0.7926 (p) REVERT: A 539 PHE cc_start: 0.8044 (m-80) cc_final: 0.7751 (m-10) REVERT: A 593 SER cc_start: 0.8120 (m) cc_final: 0.7914 (p) REVERT: A 615 PHE cc_start: 0.8331 (m-80) cc_final: 0.8092 (m-80) REVERT: A 651 LYS cc_start: 0.8276 (tttt) cc_final: 0.8022 (ttpp) REVERT: A 660 GLU cc_start: 0.6618 (mp0) cc_final: 0.6340 (mp0) REVERT: A 682 GLN cc_start: 0.5997 (mp10) cc_final: 0.5703 (mp10) REVERT: A 704 GLU cc_start: 0.7520 (mp0) cc_final: 0.7184 (mp0) REVERT: A 716 VAL cc_start: 0.8624 (t) cc_final: 0.8333 (m) REVERT: A 735 PHE cc_start: 0.8609 (m-80) cc_final: 0.8306 (m-10) REVERT: A 738 SER cc_start: 0.8031 (p) cc_final: 0.7494 (m) REVERT: A 758 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8104 (ttmm) REVERT: A 773 LYS cc_start: 0.8179 (tttm) cc_final: 0.7428 (ttpp) REVERT: A 795 GLU cc_start: 0.7368 (tt0) cc_final: 0.7064 (tt0) REVERT: A 820 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7537 (mttp) REVERT: A 831 LYS cc_start: 0.7079 (tttt) cc_final: 0.6774 (ttpp) REVERT: A 844 GLU cc_start: 0.7505 (tp30) cc_final: 0.6992 (tp30) REVERT: A 853 THR cc_start: 0.7935 (p) cc_final: 0.7681 (p) REVERT: A 949 LYS cc_start: 0.7366 (tttt) cc_final: 0.7053 (ttpt) REVERT: A 954 SER cc_start: 0.7952 (m) cc_final: 0.7456 (p) REVERT: A 1010 MET cc_start: 0.7220 (ttp) cc_final: 0.6857 (tmm) REVERT: A 1040 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6791 (tm-30) REVERT: A 1050 SER cc_start: 0.8228 (m) cc_final: 0.7807 (p) REVERT: A 1069 ASP cc_start: 0.6960 (t0) cc_final: 0.6676 (t0) REVERT: A 1108 VAL cc_start: 0.8273 (t) cc_final: 0.7986 (p) REVERT: A 1120 ASN cc_start: 0.7624 (m-40) cc_final: 0.7398 (m-40) REVERT: A 1130 TYR cc_start: 0.7922 (t80) cc_final: 0.7690 (t80) REVERT: A 1138 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 1214 LYS cc_start: 0.8611 (mmpt) cc_final: 0.8234 (mmmm) REVERT: B 32 PHE cc_start: 0.7139 (m-10) cc_final: 0.6141 (m-10) REVERT: B 35 PHE cc_start: 0.7906 (t80) cc_final: 0.7632 (t80) REVERT: B 167 THR cc_start: 0.8372 (m) cc_final: 0.7209 (p) REVERT: B 174 THR cc_start: 0.8299 (m) cc_final: 0.7729 (p) REVERT: B 185 PHE cc_start: 0.7337 (t80) cc_final: 0.6449 (t80) REVERT: B 188 ASP cc_start: 0.7119 (m-30) cc_final: 0.6535 (t70) REVERT: B 209 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 212 TYR cc_start: 0.7756 (m-80) cc_final: 0.7509 (m-10) REVERT: B 227 TYR cc_start: 0.7556 (p90) cc_final: 0.7335 (p90) REVERT: B 276 ASN cc_start: 0.7897 (t0) cc_final: 0.6934 (p0) REVERT: B 328 VAL cc_start: 0.8760 (m) cc_final: 0.8276 (t) REVERT: B 334 SER cc_start: 0.8286 (p) cc_final: 0.7949 (m) REVERT: B 372 TYR cc_start: 0.8017 (m-80) cc_final: 0.7537 (m-10) REVERT: B 388 LEU cc_start: 0.8213 (mt) cc_final: 0.7800 (mp) REVERT: B 426 PHE cc_start: 0.7697 (m-10) cc_final: 0.7375 (m-10) REVERT: B 488 SER cc_start: 0.8314 (m) cc_final: 0.8095 (p) REVERT: B 552 SER cc_start: 0.8200 (m) cc_final: 0.7599 (t) REVERT: B 553 LEU cc_start: 0.7882 (tp) cc_final: 0.7465 (tp) REVERT: B 593 SER cc_start: 0.8797 (m) cc_final: 0.8048 (p) REVERT: B 601 ILE cc_start: 0.8417 (mt) cc_final: 0.8085 (tt) REVERT: B 614 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8173 (ptmm) REVERT: B 626 GLU cc_start: 0.6174 (mp0) cc_final: 0.5677 (mp0) REVERT: B 640 ASP cc_start: 0.7431 (t0) cc_final: 0.7126 (t70) REVERT: B 642 SER cc_start: 0.8447 (m) cc_final: 0.7870 (p) REVERT: B 651 LYS cc_start: 0.8697 (tttt) cc_final: 0.8315 (tttp) REVERT: B 670 PHE cc_start: 0.8043 (m-10) cc_final: 0.7672 (m-80) REVERT: B 679 ASP cc_start: 0.7320 (p0) cc_final: 0.7007 (t70) REVERT: B 709 VAL cc_start: 0.8555 (t) cc_final: 0.8310 (m) REVERT: B 746 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6497 (mm-30) REVERT: B 773 LYS cc_start: 0.8566 (tttt) cc_final: 0.8115 (tttp) REVERT: B 790 MET cc_start: 0.7047 (mtt) cc_final: 0.6485 (mtt) REVERT: B 820 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7521 (mtpt) REVERT: B 839 LEU cc_start: 0.8423 (mt) cc_final: 0.8195 (mm) REVERT: B 853 THR cc_start: 0.8457 (m) cc_final: 0.8179 (p) REVERT: B 902 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6816 (t80) REVERT: B 949 LYS cc_start: 0.8564 (tttt) cc_final: 0.8171 (ttmt) REVERT: B 954 SER cc_start: 0.8299 (m) cc_final: 0.7910 (t) REVERT: B 961 MET cc_start: 0.7211 (mtp) cc_final: 0.6943 (mtp) REVERT: B 963 LEU cc_start: 0.8108 (tp) cc_final: 0.7711 (tt) REVERT: B 999 LEU cc_start: 0.8919 (mt) cc_final: 0.8423 (mp) REVERT: B 1002 SER cc_start: 0.8444 (m) cc_final: 0.8088 (p) REVERT: B 1040 GLU cc_start: 0.7021 (tp30) cc_final: 0.6448 (tp30) REVERT: B 1069 ASP cc_start: 0.7265 (t0) cc_final: 0.6770 (t0) REVERT: B 1092 SER cc_start: 0.8448 (m) cc_final: 0.8124 (p) REVERT: B 1099 SER cc_start: 0.8689 (m) cc_final: 0.8131 (p) REVERT: B 1132 PHE cc_start: 0.8106 (t80) cc_final: 0.7876 (t80) REVERT: B 1213 ARG cc_start: 0.7587 (ptt-90) cc_final: 0.7110 (ptt-90) REVERT: C 48 VAL cc_start: 0.8365 (p) cc_final: 0.8036 (t) REVERT: C 171 ASP cc_start: 0.7869 (t0) cc_final: 0.7179 (t0) REVERT: C 176 PHE cc_start: 0.7960 (m-80) cc_final: 0.7569 (m-80) REVERT: C 247 ASN cc_start: 0.8088 (p0) cc_final: 0.7652 (p0) REVERT: C 252 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7132 (mm-30) REVERT: C 289 LYS cc_start: 0.7700 (mttt) cc_final: 0.7015 (ttmm) REVERT: C 308 ASN cc_start: 0.6841 (m-40) cc_final: 0.6495 (m-40) REVERT: C 334 SER cc_start: 0.8342 (p) cc_final: 0.8009 (m) REVERT: C 354 ASP cc_start: 0.7941 (t0) cc_final: 0.7664 (t0) REVERT: C 420 ASP cc_start: 0.7025 (m-30) cc_final: 0.6731 (m-30) REVERT: C 448 ASP cc_start: 0.7610 (m-30) cc_final: 0.7063 (p0) REVERT: C 584 SER cc_start: 0.7638 (m) cc_final: 0.7363 (p) REVERT: C 619 TYR cc_start: 0.7740 (m-80) cc_final: 0.7473 (m-80) REVERT: C 704 GLU cc_start: 0.7302 (mp0) cc_final: 0.6841 (mp0) REVERT: C 724 THR cc_start: 0.8234 (p) cc_final: 0.7737 (t) REVERT: C 758 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8342 (tttp) REVERT: C 795 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 802 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8583 (p) REVERT: C 900 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8051 (tt) REVERT: C 948 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7043 (mm-30) REVERT: C 974 PHE cc_start: 0.8390 (t80) cc_final: 0.7960 (t80) REVERT: C 999 LEU cc_start: 0.8157 (mt) cc_final: 0.7727 (mp) REVERT: C 1002 SER cc_start: 0.8465 (m) cc_final: 0.8029 (p) REVERT: C 1004 ASN cc_start: 0.7476 (m-40) cc_final: 0.6974 (m110) REVERT: C 1005 SER cc_start: 0.8133 (t) cc_final: 0.7854 (p) REVERT: C 1063 ILE cc_start: 0.8682 (pt) cc_final: 0.8209 (mm) REVERT: C 1064 SER cc_start: 0.8480 (p) cc_final: 0.8131 (m) REVERT: C 1066 SER cc_start: 0.8038 (t) cc_final: 0.7810 (p) REVERT: C 1069 ASP cc_start: 0.7559 (t0) cc_final: 0.7026 (t70) REVERT: C 1123 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7774 (t) REVERT: C 1127 SER cc_start: 0.7266 (t) cc_final: 0.6766 (p) REVERT: C 1213 ARG cc_start: 0.7791 (ptt180) cc_final: 0.7347 (ptt90) outliers start: 86 outliers final: 70 residues processed: 630 average time/residue: 0.1655 time to fit residues: 169.0912 Evaluate side-chains 660 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 583 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 1026 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1109 GLN Chi-restraints excluded: chain C residue 1123 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 263 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B1109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094386 restraints weight = 42795.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097596 restraints weight = 22405.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099722 restraints weight = 13858.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101126 restraints weight = 9778.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102042 restraints weight = 7617.926| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26466 Z= 0.241 Angle : 0.724 21.743 36121 Z= 0.361 Chirality : 0.048 0.545 4322 Planarity : 0.004 0.055 4521 Dihedral : 6.726 63.156 4651 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.84 % Allowed : 16.84 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 3188 helix: 1.61 (0.21), residues: 607 sheet: -0.40 (0.19), residues: 806 loop : -1.37 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1235 TYR 0.031 0.002 TYR C 407 PHE 0.029 0.002 PHE B 347 TRP 0.016 0.002 TRP A 439 HIS 0.007 0.001 HIS C 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (26364) covalent geometry : angle 0.67891 / 0.35 (35860) SS BOND : bond 0.00738 / 0.50 ( 45) SS BOND : angle 2.67933 / 1.69 ( 90) hydrogen bonds : bond 0.04633 / 3.11 ( 880) hydrogen bonds : angle 5.37833 / 3.70 ( 2589) link_ALPHA1-3 : bond 0.00720 / 0.37 ( 3) link_ALPHA1-3 : angle 2.22220 / 1.37 ( 9) link_ALPHA1-6 : bond 0.01256 / 0.62 ( 3) link_ALPHA1-6 : angle 2.41338 / 1.54 ( 9) link_BETA1-4 : bond 0.00489 / 0.33 ( 12) link_BETA1-4 : angle 1.96567 / 1.42 ( 36) link_NAG-ASN : bond 0.00446 / 0.32 ( 39) link_NAG-ASN : angle 3.58224 / 2.40 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6376 Ramachandran restraints generated. 3188 Oldfield, 0 Emsley, 3188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 597 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8342 (t) cc_final: 0.8089 (p) REVERT: A 238 SER cc_start: 0.8507 (p) cc_final: 0.8169 (t) REVERT: A 247 ASN cc_start: 0.7557 (p0) cc_final: 0.7328 (p0) REVERT: A 317 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6557 (pm20) REVERT: A 379 THR cc_start: 0.7487 (OUTLIER) cc_final: 0.7174 (p) REVERT: A 445 ASN cc_start: 0.7290 (m110) cc_final: 0.6738 (m-40) REVERT: A 452 GLU cc_start: 0.7794 (tt0) cc_final: 0.7513 (tt0) REVERT: A 481 ASP cc_start: 0.7473 (m-30) cc_final: 0.7254 (m-30) REVERT: A 487 ILE cc_start: 0.8200 (pt) cc_final: 0.7684 (mt) REVERT: A 508 ASN cc_start: 0.7811 (t0) cc_final: 0.7485 (p0) REVERT: A 539 PHE cc_start: 0.8148 (m-80) cc_final: 0.7798 (m-10) REVERT: A 651 LYS cc_start: 0.8265 (tttt) cc_final: 0.8027 (ttpp) REVERT: A 660 GLU cc_start: 0.6585 (mp0) cc_final: 0.6301 (mp0) REVERT: A 682 GLN cc_start: 0.6037 (mp10) cc_final: 0.5738 (mp10) REVERT: A 704 GLU cc_start: 0.7507 (mp0) cc_final: 0.7165 (mp0) REVERT: A 716 VAL cc_start: 0.8621 (t) cc_final: 0.8338 (m) REVERT: A 735 PHE cc_start: 0.8595 (m-80) cc_final: 0.8311 (m-10) REVERT: A 738 SER cc_start: 0.8221 (p) cc_final: 0.7538 (m) REVERT: A 758 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8107 (ttmm) REVERT: A 773 LYS cc_start: 0.8169 (tttm) cc_final: 0.7504 (ttpp) REVERT: A 795 GLU cc_start: 0.7418 (tt0) cc_final: 0.7085 (tt0) REVERT: A 820 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7549 (mttp) REVERT: A 831 LYS cc_start: 0.7273 (tttt) cc_final: 0.7020 (ttpp) REVERT: A 844 GLU cc_start: 0.7542 (tp30) cc_final: 0.7028 (tp30) REVERT: A 853 THR cc_start: 0.7871 (p) cc_final: 0.7628 (p) REVERT: A 949 LYS cc_start: 0.7353 (tttt) cc_final: 0.7102 (ttpt) REVERT: A 954 SER cc_start: 0.7994 (m) cc_final: 0.7522 (p) REVERT: A 1040 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6819 (tm-30) REVERT: A 1050 SER cc_start: 0.8226 (m) cc_final: 0.7839 (p) REVERT: A 1069 ASP cc_start: 0.7045 (t0) cc_final: 0.6783 (t0) REVERT: A 1108 VAL cc_start: 0.8317 (t) cc_final: 0.8045 (p) REVERT: A 1120 ASN cc_start: 0.7637 (m-40) cc_final: 0.7390 (m110) REVERT: A 1130 TYR cc_start: 0.7944 (t80) cc_final: 0.7687 (t80) REVERT: A 1214 LYS cc_start: 0.8603 (mmpt) cc_final: 0.8226 (mmmm) REVERT: B 32 PHE cc_start: 0.7157 (m-10) cc_final: 0.6145 (m-10) REVERT: B 35 PHE cc_start: 0.8010 (t80) cc_final: 0.7683 (t80) REVERT: B 167 THR cc_start: 0.8390 (m) cc_final: 0.7282 (p) REVERT: B 174 THR cc_start: 0.8286 (m) cc_final: 0.7740 (p) REVERT: B 185 PHE cc_start: 0.7413 (t80) cc_final: 0.6555 (t80) REVERT: B 188 ASP cc_start: 0.7188 (m-30) cc_final: 0.6566 (t70) REVERT: B 209 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 212 TYR cc_start: 0.7807 (m-80) cc_final: 0.7587 (m-10) REVERT: B 213 TYR cc_start: 0.7944 (m-80) cc_final: 0.7704 (m-80) REVERT: B 227 TYR cc_start: 0.7520 (p90) cc_final: 0.7305 (p90) REVERT: B 276 ASN cc_start: 0.7888 (t0) cc_final: 0.6931 (p0) REVERT: B 328 VAL cc_start: 0.8791 (m) cc_final: 0.8319 (t) REVERT: B 334 SER cc_start: 0.8292 (p) cc_final: 0.7955 (m) REVERT: B 372 TYR cc_start: 0.8048 (m-80) cc_final: 0.7612 (m-10) REVERT: B 388 LEU cc_start: 0.8224 (mt) cc_final: 0.7770 (mp) REVERT: B 488 SER cc_start: 0.8324 (m) cc_final: 0.8097 (p) REVERT: B 552 SER cc_start: 0.8216 (m) cc_final: 0.7710 (t) REVERT: B 553 LEU cc_start: 0.7837 (tp) cc_final: 0.7395 (tp) REVERT: B 593 SER cc_start: 0.8755 (m) cc_final: 0.7976 (p) REVERT: B 601 ILE cc_start: 0.8417 (mt) cc_final: 0.8114 (tt) REVERT: B 614 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8178 (ptmm) REVERT: B 619 TYR cc_start: 0.7780 (m-80) cc_final: 0.7398 (m-10) REVERT: B 626 GLU cc_start: 0.6175 (mp0) cc_final: 0.5557 (mp0) REVERT: B 640 ASP cc_start: 0.7404 (t0) cc_final: 0.7117 (t70) REVERT: B 642 SER cc_start: 0.8486 (m) cc_final: 0.7890 (p) REVERT: B 651 LYS cc_start: 0.8723 (tttt) cc_final: 0.8315 (tttp) REVERT: B 670 PHE cc_start: 0.8052 (m-10) cc_final: 0.7650 (m-80) REVERT: B 709 VAL cc_start: 0.8553 (t) cc_final: 0.8328 (m) REVERT: B 746 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6483 (mm-30) REVERT: B 773 LYS cc_start: 0.8584 (tttt) cc_final: 0.8132 (tttp) REVERT: B 790 MET cc_start: 0.7097 (mtt) cc_final: 0.6483 (mtt) REVERT: B 820 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7565 (mtpp) REVERT: B 839 LEU cc_start: 0.8424 (mt) cc_final: 0.8205 (mm) REVERT: B 853 THR cc_start: 0.8503 (m) cc_final: 0.8285 (p) REVERT: B 949 LYS cc_start: 0.8681 (tttt) cc_final: 0.8341 (ttmt) REVERT: B 954 SER cc_start: 0.8310 (m) cc_final: 0.7938 (t) REVERT: B 961 MET cc_start: 0.7276 (mtp) cc_final: 0.7043 (mtp) REVERT: B 963 LEU cc_start: 0.8105 (tp) cc_final: 0.7857 (tp) REVERT: B 999 LEU cc_start: 0.8946 (mt) cc_final: 0.8577 (mt) REVERT: B 1002 SER cc_start: 0.8499 (m) cc_final: 0.8130 (p) REVERT: B 1040 GLU cc_start: 0.7067 (tp30) cc_final: 0.6449 (tp30) REVERT: B 1069 ASP cc_start: 0.7299 (t0) cc_final: 0.6790 (t0) REVERT: B 1092 SER cc_start: 0.8558 (m) cc_final: 0.8219 (p) REVERT: B 1099 SER cc_start: 0.8694 (m) cc_final: 0.8079 (p) REVERT: B 1213 ARG cc_start: 0.7629 (ptt-90) cc_final: 0.7179 (ptt-90) REVERT: C 171 ASP cc_start: 0.7887 (t0) cc_final: 0.7326 (t0) REVERT: C 247 ASN cc_start: 0.8084 (p0) cc_final: 0.7648 (p0) REVERT: C 252 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 289 LYS cc_start: 0.7788 (mttt) cc_final: 0.7035 (ttmm) REVERT: C 308 ASN cc_start: 0.6942 (m-40) cc_final: 0.6582 (m-40) REVERT: C 334 SER cc_start: 0.8398 (p) cc_final: 0.8019 (m) REVERT: C 354 ASP cc_start: 0.8007 (t0) cc_final: 0.7711 (t0) REVERT: C 420 ASP cc_start: 0.7042 (m-30) cc_final: 0.6749 (m-30) REVERT: C 433 ASP cc_start: 0.7377 (t0) cc_final: 0.7110 (t0) REVERT: C 434 ASP cc_start: 0.6383 (t0) cc_final: 0.6095 (t0) REVERT: C 448 ASP cc_start: 0.7584 (m-30) cc_final: 0.6968 (p0) REVERT: C 584 SER cc_start: 0.7633 (m) cc_final: 0.7367 (p) REVERT: C 602 ASP cc_start: 0.7219 (m-30) cc_final: 0.6855 (m-30) REVERT: C 619 TYR cc_start: 0.7809 (m-80) cc_final: 0.7504 (m-80) REVERT: C 674 VAL cc_start: 0.8877 (m) cc_final: 0.8658 (t) REVERT: C 704 GLU cc_start: 0.7306 (mp0) cc_final: 0.6804 (mp0) REVERT: C 724 THR cc_start: 0.8242 (p) cc_final: 0.7750 (t) REVERT: C 753 ASN cc_start: 0.7773 (p0) cc_final: 0.7552 (p0) REVERT: C 795 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 802 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8569 (p) REVERT: C 816 ASN cc_start: 0.7935 (t0) cc_final: 0.7598 (t0) REVERT: C 900 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8007 (tt) REVERT: C 948 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 974 PHE cc_start: 0.8420 (t80) cc_final: 0.8045 (t80) REVERT: C 989 THR cc_start: 0.7514 (p) cc_final: 0.6622 (t) REVERT: C 999 LEU cc_start: 0.8170 (mt) cc_final: 0.7777 (mp) REVERT: C 1002 SER cc_start: 0.8491 (m) cc_final: 0.8040 (p) REVERT: C 1004 ASN cc_start: 0.7470 (m-40) cc_final: 0.6950 (m110) REVERT: C 1005 SER cc_start: 0.8198 (t) cc_final: 0.7885 (p) REVERT: C 1063 ILE cc_start: 0.8665 (pt) cc_final: 0.8195 (mm) REVERT: C 1064 SER cc_start: 0.8488 (p) cc_final: 0.8161 (m) REVERT: C 1066 SER cc_start: 0.8041 (t) cc_final: 0.7825 (p) REVERT: C 1069 ASP cc_start: 0.7600 (t0) cc_final: 0.7084 (t70) REVERT: C 1127 SER cc_start: 0.7264 (t) cc_final: 0.6767 (p) REVERT: C 1190 PHE cc_start: 0.7991 (p90) cc_final: 0.7661 (p90) REVERT: C 1211 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6399 (tp30) REVERT: C 1213 ARG cc_start: 0.7878 (ptt180) cc_final: 0.7414 (ptt90) outliers start: 80 outliers final: 72 residues processed: 638 average time/residue: 0.1727 time to fit residues: 177.2150 Evaluate side-chains 666 residues out of total 2814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 590 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 830 CYS Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 660 GLU Chi-restraints excluded: chain B residue 701 SER Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 857 GLU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1174 VAL Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 966 PHE Chi-restraints excluded: chain C residue 1001 GLU Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 59 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 289 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.119820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098042 restraints weight = 42564.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101258 restraints weight = 22233.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103391 restraints weight = 13742.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104832 restraints weight = 9704.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105598 restraints weight = 7540.823| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26466 Z= 0.156 Angle : 0.681 20.975 36121 Z= 0.338 Chirality : 0.047 0.513 4322 Planarity : 0.004 0.064 4521 Dihedral : 6.437 55.281 4651 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.70 % Allowed : 17.38 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.15), residues: 3188 helix: 1.67 (0.21), residues: 607 sheet: -0.39 (0.19), residues: 805 loop : -1.31 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1235 TYR 0.028 0.001 TYR C 184 PHE 0.024 0.001 PHE B 539 TRP 0.010 0.001 TRP B 168 HIS 0.008 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (26364) covalent geometry : angle 0.63840 / 0.33 (35860) SS BOND : bond 0.00668 / 0.45 ( 45) SS BOND : angle 2.58410 / 1.65 ( 90) hydrogen bonds : bond 0.04174 / 2.83 ( 880) hydrogen bonds : angle 5.23623 / 3.61 ( 2589) link_ALPHA1-3 : bond 0.00825 / 0.42 ( 3) link_ALPHA1-3 : angle 1.84021 / 1.17 ( 9) link_ALPHA1-6 : bond 0.01173 / 0.58 ( 3) link_ALPHA1-6 : angle 2.12551 / 1.38 ( 9) link_BETA1-4 : bond 0.00504 / 0.34 ( 12) link_BETA1-4 : angle 1.81444 / 1.29 ( 36) link_NAG-ASN : bond 0.00397 / 0.29 ( 39) link_NAG-ASN : angle 3.37210 / 2.25 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4969.05 seconds wall clock time: 86 minutes 33.41 seconds (5193.41 seconds total)