Starting phenix.real_space_refine on Sun Jul 5 12:49:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.map" model { file = "/net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7to4_26029/07_2026/7to4_26029.cif" } resolution = 3.4 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= 0.003 sd= 0.040 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 120 5.16 5 C 17613 2.51 5 N 4473 2.21 5 O 5466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 195 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27672 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8737 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 4 Chain: "B" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 Chain: "C" Number of atoms: 8789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 8789 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 3 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 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 chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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 chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" 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 chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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 chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" 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 chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 chiralities: 8 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.26, per 1000 atoms: 0.23 Number of scatterers: 27672 At special positions: 0 Unit cell: (148.57, 138.61, 220.78, 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 120 16.00 O 5466 8.00 N 4473 7.00 C 17613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.06 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG O 2 " - " MAN O 3 " " NAG Q 2 " - " MAN Q 3 " " NAG R 2 " - " MAN R 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG W 2 " - " MAN W 3 " " NAG Y 2 " - " MAN Y 3 " " NAG Z 2 " - " MAN Z 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1158 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1158 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 883.4 milliseconds 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6298 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 51 sheets defined 27.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.557A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.597A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.133A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.557A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.483A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.213A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.697A pdb=" N ALA A 845 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.751A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.519A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.604A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.678A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.652A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.805A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.071A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.161A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.600A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.049A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.105A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 4.207A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.704A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.708A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.554A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.178A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.867A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1161 removed outlier: 3.923A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.865A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.754A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.090A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.393A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.955A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 756 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.102A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.266A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.601A pdb=" N ALA C 846 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.584A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.566A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.039A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.539A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.116A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.599A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.509A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 removed outlier: 4.139A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.981A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.735A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.571A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.735A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.663A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 144 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.992A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.047A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.289A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.696A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.887A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.596A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.572A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.669A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.961A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 158 through 160 removed outlier: 8.048A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 12.662A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.840A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE B 144 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.405A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.108A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.934A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.415A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.934A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.890A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.418A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.752A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.809A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.199A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.853A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE C 144 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.891A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.197A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.974A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.603A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.330A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.330A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.204A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.787A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 2982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4409 1.29 - 1.43: 7540 1.43 - 1.56: 16190 1.56 - 1.70: 2 1.70 - 1.83: 150 Bond restraints: 28291 Sorted by residual: bond pdb=" CA LEU C 118 " pdb=" C LEU C 118 " ideal model delta sigma weight residual 1.522 1.620 -0.097 1.18e-02 7.18e+03 6.81e+01 bond pdb=" C ARG A 983 " pdb=" O ARG A 983 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.11e-02 8.12e+03 5.10e+01 bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.22e-02 6.72e+03 2.57e+01 bond pdb=" C ARG A1019 " pdb=" O ARG A1019 " ideal model delta sigma weight residual 1.237 1.178 0.059 1.16e-02 7.43e+03 2.57e+01 bond pdb=" C ARG C1019 " pdb=" O ARG C1019 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.22e-02 6.72e+03 2.42e+01 ... (remaining 28286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 31152 2.43 - 4.86: 6716 4.86 - 7.29: 555 7.29 - 9.72: 34 9.72 - 12.15: 9 Bond angle restraints: 38466 Sorted by residual: angle pdb=" N ASN C 164 " pdb=" CA ASN C 164 " pdb=" C ASN C 164 " ideal model delta sigma weight residual 110.97 123.12 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N ARG A1091 " pdb=" CA ARG A1091 " pdb=" C ARG A1091 " ideal model delta sigma weight residual 111.03 102.31 8.72 1.11e+00 8.12e-01 6.18e+01 angle pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" C TYR A 421 " ideal model delta sigma weight residual 113.50 122.46 -8.96 1.23e+00 6.61e-01 5.31e+01 angle pdb=" CA ASP B 389 " pdb=" CB ASP B 389 " pdb=" CG ASP B 389 " ideal model delta sigma weight residual 112.60 119.79 -7.19 1.00e+00 1.00e+00 5.16e+01 angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 109.30 118.64 -9.34 1.31e+00 5.83e-01 5.08e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.70: 14858 18.70 - 37.40: 990 37.40 - 56.11: 191 56.11 - 74.81: 47 74.81 - 93.51: 31 Dihedral angle restraints: 16117 sinusoidal: 6335 harmonic: 9782 Sorted by residual: dihedral pdb=" C ASN C 122 " pdb=" N ASN C 122 " pdb=" CA ASN C 122 " pdb=" CB ASN C 122 " ideal model delta harmonic sigma weight residual -122.60 -138.91 16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" C CYS C1126 " pdb=" N CYS C1126 " pdb=" CA CYS C1126 " pdb=" CB CYS C1126 " ideal model delta harmonic sigma weight residual -122.60 -137.29 14.69 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -36.03 -49.97 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 16114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.320: 4583 0.320 - 0.639: 37 0.639 - 0.959: 7 0.959 - 1.279: 3 1.279 - 1.598: 5 Chirality restraints: 4635 Sorted by residual: chirality pdb=" C1 MAN Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 MAN Z 3 " pdb=" O5 MAN Z 3 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 MAN f 3 " pdb=" O4 NAG f 2 " pdb=" C2 MAN f 3 " pdb=" O5 MAN f 3 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.19 2.00e-02 2.50e+03 9.34e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 4632 not shown) Planarity restraints: 4881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.103 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C 234 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.256 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 104 " -0.144 2.00e-02 2.50e+03 7.54e-02 1.42e+02 pdb=" CG TRP A 104 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 104 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 104 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP A 104 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 104 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 104 " -0.091 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 104 " 0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 104 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.100 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A1074 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.160 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.125 2.00e-02 2.50e+03 ... (remaining 4878 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 81 2.59 - 3.17: 22407 3.17 - 3.74: 41775 3.74 - 4.32: 58970 4.32 - 4.90: 94396 Nonbonded interactions: 217629 Sorted by model distance: nonbonded pdb=" O ASN B 17 " pdb=" OD1 ASN B 17 " model vdw 2.009 3.040 nonbonded pdb=" O ASN C 17 " pdb=" OD1 ASN C 17 " model vdw 2.138 3.040 nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 2 " model vdw 2.210 3.040 nonbonded pdb=" N GLN C 836 " pdb=" OE1 GLN C 836 " model vdw 2.211 3.120 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.251 3.120 ... (remaining 217624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1307) selection = (chain 'B' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1307)) selection = (chain 'C' and (resid 14 through 626 or resid 633 through 679 or resid 687 throu \ gh 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'V' selection = chain 'X' selection = chain 'a' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.320 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: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.570 Find NCS groups from input model: 0.940 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.015 0.097 28437 Z= 0.834 Angle : 2.080 50.622 38859 Z= 1.269 Chirality : 0.129 1.598 4635 Planarity : 0.013 0.093 4827 Dihedral : 13.988 93.509 9684 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.19 % Favored : 92.03 % Rotamer: Outliers : 2.60 % Allowed : 5.77 % Favored : 91.63 % Cbeta Deviations : 0.64 % 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: -2.22 (0.13), residues: 3324 helix: -1.76 (0.15), residues: 775 sheet: 0.03 (0.21), residues: 533 loop : -1.85 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 493 TYR 0.120 0.021 TYR B 660 PHE 0.097 0.016 PHE B 898 TRP 0.144 0.026 TRP A 104 HIS 0.022 0.007 HIS A1159 Details of bonding type rmsd/Z covalent geometry : bond 0.01472 / 0.83 (28291) covalent geometry : angle 1.89904 / 1.24 (38466) SS BOND : bond 0.01337 / 0.83 ( 45) SS BOND : angle 2.61879 / 1.70 ( 90) hydrogen bonds : bond 0.17076 / 11.15 ( 1074) hydrogen bonds : angle 8.55754 / 5.84 ( 2982) link_ALPHA1-4 : bond 0.02641 / 1.54 ( 15) link_ALPHA1-4 : angle 4.64069 / 3.21 ( 45) link_BETA1-4 : bond 0.01968 / 1.23 ( 29) link_BETA1-4 : angle 3.61699 / 2.36 ( 87) link_BETA1-6 : bond 0.01663 / 0.87 ( 3) link_BETA1-6 : angle 2.43629 / 1.41 ( 9) link_NAG-ASN : bond 0.01661 / 1.01 ( 54) link_NAG-ASN : angle 12.81470 / 8.46 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 747 time to evaluate : 0.879 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 26 PRO cc_start: 0.7665 (Cg_endo) cc_final: 0.7386 (Cg_exo) REVERT: A 52 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 62 VAL cc_start: 0.8763 (m) cc_final: 0.8539 (p) REVERT: A 116 SER cc_start: 0.8853 (m) cc_final: 0.8576 (m) REVERT: A 120 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 190 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7728 (mmm-85) REVERT: A 197 ILE cc_start: 0.8709 (mm) cc_final: 0.8508 (mm) REVERT: A 224 GLU cc_start: 0.8442 (mp0) cc_final: 0.8188 (mp0) REVERT: A 228 ASP cc_start: 0.7630 (p0) cc_final: 0.7416 (p0) REVERT: A 309 GLU cc_start: 0.8510 (mp0) cc_final: 0.8237 (mp0) REVERT: A 319 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (tpt170) REVERT: A 338 PHE cc_start: 0.7831 (m-80) cc_final: 0.7601 (p90) REVERT: A 424 LYS cc_start: 0.5081 (tptt) cc_final: 0.4568 (tttm) REVERT: A 541 PHE cc_start: 0.6328 (p90) cc_final: 0.5759 (p90) REVERT: A 565 PHE cc_start: 0.7774 (p90) cc_final: 0.7545 (p90) REVERT: A 588 THR cc_start: 0.9018 (m) cc_final: 0.8792 (t) REVERT: A 740 MET cc_start: 0.9044 (tpt) cc_final: 0.8739 (tpp) REVERT: A 773 GLU cc_start: 0.8340 (tt0) cc_final: 0.8023 (tt0) REVERT: A 780 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 811 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7237 (tmtt) REVERT: A 814 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7699 (mmmt) REVERT: A 819 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 820 ASP cc_start: 0.8739 (t70) cc_final: 0.8478 (m-30) REVERT: A 848 ASP cc_start: 0.8429 (t0) cc_final: 0.7573 (p0) REVERT: A 849 LEU cc_start: 0.8750 (mt) cc_final: 0.8329 (mm) REVERT: A 854 LYS cc_start: 0.9288 (tttt) cc_final: 0.9033 (tttt) REVERT: A 856 LYS cc_start: 0.9159 (mptt) cc_final: 0.8888 (mptt) REVERT: A 921 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8484 (mtpp) REVERT: A 925 ASN cc_start: 0.8795 (m110) cc_final: 0.8579 (m-40) REVERT: A 935 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: A 936 ASP cc_start: 0.8845 (m-30) cc_final: 0.8512 (m-30) REVERT: A 950 ASP cc_start: 0.8464 (p0) cc_final: 0.8112 (p0) REVERT: A 964 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8582 (mtpp) REVERT: A 975 SER cc_start: 0.8758 (p) cc_final: 0.8505 (p) REVERT: A 981 PHE cc_start: 0.7738 (m-80) cc_final: 0.6627 (m-80) REVERT: A 1005 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8101 (mm-40) REVERT: A 1019 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8064 (ttp-110) REVERT: A 1072 GLU cc_start: 0.8837 (pm20) cc_final: 0.8355 (pm20) REVERT: A 1073 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8461 (mtpp) REVERT: A 1107 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7339 (mtt-85) REVERT: B 41 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8410 (mmmm) REVERT: B 92 PHE cc_start: 0.8691 (t80) cc_final: 0.8304 (t80) REVERT: B 133 PHE cc_start: 0.7069 (m-80) cc_final: 0.6564 (m-10) REVERT: B 196 ASN cc_start: 0.7978 (t0) cc_final: 0.7685 (t0) REVERT: B 197 ILE cc_start: 0.9020 (tp) cc_final: 0.8708 (pt) REVERT: B 200 TYR cc_start: 0.7650 (m-80) cc_final: 0.7008 (m-80) REVERT: B 202 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8289 (mmmt) REVERT: B 203 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8588 (tt) REVERT: B 204 TYR cc_start: 0.8984 (m-80) cc_final: 0.8604 (m-80) REVERT: B 210 ILE cc_start: 0.8702 (tp) cc_final: 0.8471 (tt) REVERT: B 275 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 323 THR cc_start: 0.8705 (t) cc_final: 0.8251 (p) REVERT: B 388 ASN cc_start: 0.8346 (t0) cc_final: 0.8135 (t0) REVERT: B 422 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.6997 (p0) REVERT: B 607 GLN cc_start: 0.8696 (tt0) cc_final: 0.8489 (tp40) REVERT: B 643 PHE cc_start: 0.8555 (t80) cc_final: 0.8262 (t80) REVERT: B 646 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7597 (ttt90) REVERT: B 654 GLU cc_start: 0.8529 (tp30) cc_final: 0.8325 (tp30) REVERT: B 675 GLN cc_start: 0.7695 (pp30) cc_final: 0.7429 (pp30) REVERT: B 751 ASN cc_start: 0.8769 (m110) cc_final: 0.8483 (m110) REVERT: B 755 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: B 765 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8015 (ttm-80) REVERT: B 780 GLU cc_start: 0.8653 (tp30) cc_final: 0.8253 (tp30) REVERT: B 814 LYS cc_start: 0.8550 (mptt) cc_final: 0.8201 (mmmt) REVERT: B 900 MET cc_start: 0.8739 (tpp) cc_final: 0.8381 (mtp) REVERT: B 964 LYS cc_start: 0.9297 (tppt) cc_final: 0.9016 (mmmm) REVERT: B 994 ASP cc_start: 0.8474 (t0) cc_final: 0.8196 (t0) REVERT: B 1005 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8517 (tp40) REVERT: B 1041 ASP cc_start: 0.8538 (t0) cc_final: 0.8074 (t0) REVERT: C 34 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (mtp85) REVERT: C 79 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5890 (m-80) REVERT: C 102 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6762 (mtp180) REVERT: C 154 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: C 218 GLN cc_start: 0.8246 (tt0) cc_final: 0.7989 (tt0) REVERT: C 224 GLU cc_start: 0.8478 (mp0) cc_final: 0.8123 (mp0) REVERT: C 320 VAL cc_start: 0.8948 (t) cc_final: 0.8451 (m) REVERT: C 332 ILE cc_start: 0.8499 (tp) cc_final: 0.8273 (tp) REVERT: C 360 ASN cc_start: 0.8931 (t0) cc_final: 0.8643 (t0) REVERT: C 365 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 377 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 456 PHE cc_start: 0.7416 (m-80) cc_final: 0.7193 (m-10) REVERT: C 547 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8594 (mmmm) REVERT: C 559 PHE cc_start: 0.8330 (m-10) cc_final: 0.7982 (m-10) REVERT: C 564 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8209 (tp40) REVERT: C 565 PHE cc_start: 0.8909 (m-80) cc_final: 0.8677 (m-10) REVERT: C 568 ASP cc_start: 0.7860 (t0) cc_final: 0.7405 (t0) REVERT: C 571 ASP cc_start: 0.7858 (t0) cc_final: 0.7427 (t0) REVERT: C 577 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8517 (ttm170) REVERT: C 584 ILE cc_start: 0.8900 (mm) cc_final: 0.8414 (mm) REVERT: C 610 VAL cc_start: 0.9252 (t) cc_final: 0.8937 (m) REVERT: C 613 GLN cc_start: 0.7975 (mt0) cc_final: 0.7617 (mt0) REVERT: C 661 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 765 ARG cc_start: 0.8454 (ptp-110) cc_final: 0.8207 (mtm110) REVERT: C 780 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 849 LEU cc_start: 0.8779 (mt) cc_final: 0.8553 (tp) REVERT: C 854 LYS cc_start: 0.9183 (tptp) cc_final: 0.8969 (tptp) REVERT: C 855 PHE cc_start: 0.8500 (m-10) cc_final: 0.8056 (m-80) REVERT: C 935 GLN cc_start: 0.8996 (tt0) cc_final: 0.8637 (tt0) REVERT: C 950 ASP cc_start: 0.8373 (p0) cc_final: 0.7826 (p0) REVERT: C 954 HIS cc_start: 0.8222 (m-70) cc_final: 0.8002 (m170) REVERT: C 957 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 991 VAL cc_start: 0.9436 (t) cc_final: 0.9209 (t) REVERT: C 1019 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (ttt-90) outliers start: 76 outliers final: 12 residues processed: 793 average time/residue: 0.1883 time to fit residues: 227.2568 Evaluate side-chains 623 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 596 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 164 ASN A 314 GLN A 417 ASN A 481 ASN A 536 ASN A 901 GLN A 925 ASN B 207 HIS B 239 GLN B 519 HIS B 751 ASN B 935 GLN B 965 GLN B1023 ASN B1119 ASN C 146 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 544 ASN C 564 GLN C 675 GLN C 762 GLN C 913 GLN C 953 ASN C1002 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077526 restraints weight = 76606.261| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.09 r_work: 0.3097 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28437 Z= 0.169 Angle : 0.864 17.698 38859 Z= 0.421 Chirality : 0.052 0.572 4635 Planarity : 0.005 0.051 4827 Dihedral : 7.445 84.428 3665 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 2.77 % Allowed : 11.24 % Favored : 85.99 % 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 (0.14), residues: 3324 helix: 0.55 (0.18), residues: 780 sheet: -0.05 (0.19), residues: 600 loop : -1.42 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 190 TYR 0.034 0.002 TYR C 636 PHE 0.045 0.002 PHE A 133 TRP 0.017 0.002 TRP A 436 HIS 0.010 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (28291) covalent geometry : angle 0.80215 / 0.41 (38466) SS BOND : bond 0.00476 / 0.32 ( 45) SS BOND : angle 1.76098 / 1.17 ( 90) hydrogen bonds : bond 0.04781 / 3.19 ( 1074) hydrogen bonds : angle 6.16876 / 4.20 ( 2982) link_ALPHA1-4 : bond 0.00779 / 0.46 ( 15) link_ALPHA1-4 : angle 2.58179 / 1.75 ( 45) link_BETA1-4 : bond 0.00379 / 0.26 ( 29) link_BETA1-4 : angle 1.85947 / 1.20 ( 87) link_BETA1-6 : bond 0.00623 / 0.31 ( 3) link_BETA1-6 : angle 1.58054 / 0.91 ( 9) link_NAG-ASN : bond 0.00577 / 0.35 ( 54) link_NAG-ASN : angle 4.54139 / 3.03 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 624 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PRO cc_start: 0.7435 (Cg_endo) cc_final: 0.7098 (Cg_exo) REVERT: A 41 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8455 (mmmm) REVERT: A 52 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8293 (tm-30) REVERT: A 62 VAL cc_start: 0.8763 (m) cc_final: 0.8514 (p) REVERT: A 111 ASP cc_start: 0.8203 (p0) cc_final: 0.7473 (t70) REVERT: A 129 LYS cc_start: 0.8850 (tttt) cc_final: 0.8377 (ttmm) REVERT: A 190 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8097 (mmm-85) REVERT: A 195 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8246 (ttpt) REVERT: A 224 GLU cc_start: 0.8454 (mp0) cc_final: 0.8194 (mp0) REVERT: A 228 ASP cc_start: 0.8012 (p0) cc_final: 0.7742 (p0) REVERT: A 287 ASP cc_start: 0.8620 (t0) cc_final: 0.8292 (t0) REVERT: A 306 PHE cc_start: 0.8330 (m-10) cc_final: 0.7826 (m-10) REVERT: A 406 GLU cc_start: 0.0948 (OUTLIER) cc_final: 0.0688 (mp0) REVERT: A 456 PHE cc_start: 0.8285 (m-10) cc_final: 0.8083 (m-10) REVERT: A 565 PHE cc_start: 0.7796 (p90) cc_final: 0.7547 (p90) REVERT: A 588 THR cc_start: 0.8978 (m) cc_final: 0.8728 (t) REVERT: A 607 GLN cc_start: 0.8302 (mp10) cc_final: 0.8094 (mp10) REVERT: A 658 ASN cc_start: 0.8239 (t0) cc_final: 0.7978 (t0) REVERT: A 660 TYR cc_start: 0.8690 (m-80) cc_final: 0.8279 (m-80) REVERT: A 740 MET cc_start: 0.9168 (tpt) cc_final: 0.8829 (tpp) REVERT: A 752 LEU cc_start: 0.9406 (mm) cc_final: 0.9186 (mp) REVERT: A 773 GLU cc_start: 0.8733 (tt0) cc_final: 0.8341 (tt0) REVERT: A 780 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8471 (mm-30) REVERT: A 819 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 820 ASP cc_start: 0.8585 (t70) cc_final: 0.8382 (m-30) REVERT: A 823 PHE cc_start: 0.8082 (m-80) cc_final: 0.7580 (t80) REVERT: A 848 ASP cc_start: 0.8492 (t0) cc_final: 0.7634 (p0) REVERT: A 849 LEU cc_start: 0.8663 (mt) cc_final: 0.8325 (mm) REVERT: A 851 CYS cc_start: 0.8353 (t) cc_final: 0.8063 (t) REVERT: A 854 LYS cc_start: 0.9455 (tttt) cc_final: 0.9212 (tttt) REVERT: A 856 LYS cc_start: 0.9299 (mptt) cc_final: 0.9000 (mptt) REVERT: A 867 ASP cc_start: 0.8592 (m-30) cc_final: 0.8385 (m-30) REVERT: A 921 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8657 (mtmm) REVERT: A 935 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8643 (tm-30) REVERT: A 950 ASP cc_start: 0.8389 (p0) cc_final: 0.8030 (p0) REVERT: A 969 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8803 (mtpp) REVERT: A 1019 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8244 (ttp-110) REVERT: A 1071 GLN cc_start: 0.8400 (mt0) cc_final: 0.8164 (mt0) REVERT: A 1072 GLU cc_start: 0.8840 (pm20) cc_final: 0.8490 (pm20) REVERT: A 1148 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6097 (t80) REVERT: B 41 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8459 (mmmm) REVERT: B 52 GLN cc_start: 0.8808 (tp40) cc_final: 0.8323 (tp40) REVERT: B 65 PHE cc_start: 0.8515 (m-10) cc_final: 0.8242 (m-10) REVERT: B 92 PHE cc_start: 0.8654 (t80) cc_final: 0.8311 (t80) REVERT: B 194 PHE cc_start: 0.8763 (m-80) cc_final: 0.8420 (m-10) REVERT: B 200 TYR cc_start: 0.8134 (m-80) cc_final: 0.7858 (m-80) REVERT: B 202 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8715 (mmtm) REVERT: B 237 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8136 (ptt90) REVERT: B 293 LEU cc_start: 0.9114 (tp) cc_final: 0.8812 (tt) REVERT: B 297 SER cc_start: 0.9254 (m) cc_final: 0.8821 (p) REVERT: B 305 SER cc_start: 0.9159 (t) cc_final: 0.8942 (t) REVERT: B 388 ASN cc_start: 0.8445 (t0) cc_final: 0.8124 (t0) REVERT: B 518 LEU cc_start: 0.9286 (mm) cc_final: 0.8994 (tp) REVERT: B 571 ASP cc_start: 0.8854 (t0) cc_final: 0.8240 (t0) REVERT: B 646 ARG cc_start: 0.8394 (ttt90) cc_final: 0.8191 (ttt90) REVERT: B 654 GLU cc_start: 0.8716 (tp30) cc_final: 0.8472 (tp30) REVERT: B 661 GLU cc_start: 0.8473 (pm20) cc_final: 0.8125 (pm20) REVERT: B 675 GLN cc_start: 0.7587 (pp30) cc_final: 0.7378 (pp30) REVERT: B 752 LEU cc_start: 0.9374 (mt) cc_final: 0.8634 (mp) REVERT: B 765 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8435 (mtm110) REVERT: B 780 GLU cc_start: 0.8974 (tp30) cc_final: 0.8745 (tp30) REVERT: B 868 GLU cc_start: 0.8601 (mp0) cc_final: 0.8331 (mp0) REVERT: B 900 MET cc_start: 0.8834 (tpp) cc_final: 0.8616 (mtp) REVERT: B 912 THR cc_start: 0.9265 (m) cc_final: 0.9064 (p) REVERT: B 936 ASP cc_start: 0.8429 (m-30) cc_final: 0.8223 (m-30) REVERT: B 983 ARG cc_start: 0.8518 (mpp80) cc_final: 0.8131 (mpp80) REVERT: B 1005 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8631 (tp40) REVERT: B 1010 GLN cc_start: 0.8837 (mt0) cc_final: 0.8496 (mm-40) REVERT: C 81 ASN cc_start: 0.8871 (m-40) cc_final: 0.8447 (m-40) REVERT: C 114 THR cc_start: 0.8323 (t) cc_final: 0.7987 (m) REVERT: C 154 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: C 224 GLU cc_start: 0.8545 (mp0) cc_final: 0.8024 (mp0) REVERT: C 242 LEU cc_start: 0.8570 (mm) cc_final: 0.8011 (mm) REVERT: C 360 ASN cc_start: 0.9071 (t0) cc_final: 0.8550 (t0) REVERT: C 377 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7119 (t80) REVERT: C 547 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8687 (mtpp) REVERT: C 564 GLN cc_start: 0.8914 (tp40) cc_final: 0.8626 (tp40) REVERT: C 568 ASP cc_start: 0.7867 (t0) cc_final: 0.7655 (t0) REVERT: C 571 ASP cc_start: 0.8229 (t0) cc_final: 0.7958 (t0) REVERT: C 610 VAL cc_start: 0.9269 (t) cc_final: 0.8989 (m) REVERT: C 613 GLN cc_start: 0.7914 (mt0) cc_final: 0.7655 (mt0) REVERT: C 646 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8629 (ttp80) REVERT: C 661 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7725 (tm-30) REVERT: C 675 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7723 (pp30) REVERT: C 752 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8816 (mm) REVERT: C 755 GLN cc_start: 0.8860 (mp10) cc_final: 0.8537 (mp10) REVERT: C 759 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7538 (t80) REVERT: C 773 GLU cc_start: 0.8739 (tt0) cc_final: 0.8049 (tm-30) REVERT: C 780 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8400 (mm-30) REVERT: C 855 PHE cc_start: 0.8799 (m-10) cc_final: 0.8539 (m-80) REVERT: C 950 ASP cc_start: 0.8134 (p0) cc_final: 0.7815 (p0) REVERT: C 953 ASN cc_start: 0.8736 (m110) cc_final: 0.8423 (m-40) REVERT: C 957 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 979 ASP cc_start: 0.8869 (t0) cc_final: 0.8610 (t0) REVERT: C 1144 GLU cc_start: 0.8588 (mp0) cc_final: 0.8330 (mp0) outliers start: 81 outliers final: 46 residues processed: 660 average time/residue: 0.1783 time to fit residues: 184.7629 Evaluate side-chains 602 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 548 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 156 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 318 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 784 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.098128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076059 restraints weight = 77427.345| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.10 r_work: 0.3062 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28437 Z= 0.193 Angle : 0.791 17.130 38859 Z= 0.385 Chirality : 0.049 0.495 4635 Planarity : 0.005 0.061 4827 Dihedral : 6.557 83.952 3625 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 3.01 % Allowed : 13.39 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3324 helix: 1.01 (0.19), residues: 785 sheet: -0.16 (0.18), residues: 683 loop : -1.32 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 319 TYR 0.032 0.002 TYR C 636 PHE 0.028 0.002 PHE A 133 TRP 0.030 0.002 TRP A 436 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (28291) covalent geometry : angle 0.73769 / 0.37 (38466) SS BOND : bond 0.00455 / 0.29 ( 45) SS BOND : angle 1.77703 / 1.15 ( 90) hydrogen bonds : bond 0.04523 / 3.02 ( 1074) hydrogen bonds : angle 5.87598 / 4.00 ( 2982) link_ALPHA1-4 : bond 0.00886 / 0.53 ( 15) link_ALPHA1-4 : angle 2.29312 / 1.53 ( 45) link_BETA1-4 : bond 0.00306 / 0.20 ( 29) link_BETA1-4 : angle 1.61296 / 1.05 ( 87) link_BETA1-6 : bond 0.00444 / 0.22 ( 3) link_BETA1-6 : angle 1.46123 / 0.90 ( 9) link_NAG-ASN : bond 0.00478 / 0.29 ( 54) link_NAG-ASN : angle 4.03242 / 2.66 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 579 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8599 (mmmm) REVERT: A 99 ASN cc_start: 0.7990 (t0) cc_final: 0.7771 (t0) REVERT: A 111 ASP cc_start: 0.8155 (p0) cc_final: 0.7511 (t70) REVERT: A 129 LYS cc_start: 0.8976 (tttt) cc_final: 0.8513 (ttmm) REVERT: A 190 ARG cc_start: 0.8551 (mmm160) cc_final: 0.7752 (mmm-85) REVERT: A 224 GLU cc_start: 0.8438 (mp0) cc_final: 0.8152 (mp0) REVERT: A 228 ASP cc_start: 0.8112 (p0) cc_final: 0.7852 (p0) REVERT: A 266 TYR cc_start: 0.8190 (m-80) cc_final: 0.7841 (m-80) REVERT: A 287 ASP cc_start: 0.8679 (t0) cc_final: 0.8277 (t0) REVERT: A 306 PHE cc_start: 0.8389 (m-10) cc_final: 0.7752 (m-10) REVERT: A 456 PHE cc_start: 0.8387 (m-10) cc_final: 0.8180 (m-10) REVERT: A 565 PHE cc_start: 0.7920 (p90) cc_final: 0.7633 (p90) REVERT: A 588 THR cc_start: 0.8961 (m) cc_final: 0.8696 (t) REVERT: A 663 ASP cc_start: 0.8358 (t0) cc_final: 0.7969 (t0) REVERT: A 740 MET cc_start: 0.9207 (tpt) cc_final: 0.8981 (tpp) REVERT: A 752 LEU cc_start: 0.9436 (mm) cc_final: 0.9206 (mp) REVERT: A 780 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 819 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 820 ASP cc_start: 0.8591 (t70) cc_final: 0.8366 (m-30) REVERT: A 823 PHE cc_start: 0.8090 (m-80) cc_final: 0.7486 (t80) REVERT: A 848 ASP cc_start: 0.8445 (t0) cc_final: 0.8009 (t0) REVERT: A 854 LYS cc_start: 0.9445 (tttt) cc_final: 0.9208 (tttt) REVERT: A 856 LYS cc_start: 0.9318 (mptt) cc_final: 0.9047 (mptt) REVERT: A 867 ASP cc_start: 0.8624 (m-30) cc_final: 0.8397 (m-30) REVERT: A 935 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8753 (tm-30) REVERT: A 936 ASP cc_start: 0.8741 (m-30) cc_final: 0.8524 (m-30) REVERT: A 1045 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8464 (tptt) REVERT: A 1072 GLU cc_start: 0.8915 (pm20) cc_final: 0.8605 (pm20) REVERT: B 40 ASP cc_start: 0.9041 (t0) cc_final: 0.8583 (t70) REVERT: B 41 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8482 (mmmm) REVERT: B 52 GLN cc_start: 0.8756 (tp40) cc_final: 0.8245 (tp40) REVERT: B 105 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8272 (tp) REVERT: B 200 TYR cc_start: 0.8064 (m-80) cc_final: 0.7815 (m-80) REVERT: B 202 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8622 (mmtm) REVERT: B 218 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 237 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8139 (ptt90) REVERT: B 297 SER cc_start: 0.9237 (m) cc_final: 0.8808 (p) REVERT: B 354 ASN cc_start: 0.8198 (t0) cc_final: 0.7807 (p0) REVERT: B 388 ASN cc_start: 0.8490 (t0) cc_final: 0.8153 (t0) REVERT: B 518 LEU cc_start: 0.9290 (mm) cc_final: 0.8970 (tp) REVERT: B 571 ASP cc_start: 0.8864 (t0) cc_final: 0.8238 (t0) REVERT: B 654 GLU cc_start: 0.8754 (tp30) cc_final: 0.8519 (tp30) REVERT: B 661 GLU cc_start: 0.8467 (pm20) cc_final: 0.8148 (pm20) REVERT: B 675 GLN cc_start: 0.7578 (pp30) cc_final: 0.7352 (pp30) REVERT: B 755 GLN cc_start: 0.8552 (pt0) cc_final: 0.8189 (mp10) REVERT: B 765 ARG cc_start: 0.8743 (ttm-80) cc_final: 0.8459 (mtm110) REVERT: B 868 GLU cc_start: 0.8628 (mp0) cc_final: 0.8413 (mp0) REVERT: B 912 THR cc_start: 0.9236 (m) cc_final: 0.9011 (p) REVERT: B 983 ARG cc_start: 0.8533 (mpp80) cc_final: 0.8180 (ptp90) REVERT: B 1005 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8638 (tp40) REVERT: B 1010 GLN cc_start: 0.8890 (mt0) cc_final: 0.8608 (mm-40) REVERT: C 63 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8477 (p) REVERT: C 114 THR cc_start: 0.8268 (t) cc_final: 0.8040 (m) REVERT: C 133 PHE cc_start: 0.7702 (m-80) cc_final: 0.7496 (m-80) REVERT: C 191 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7991 (mt-10) REVERT: C 218 GLN cc_start: 0.8383 (tt0) cc_final: 0.8124 (tt0) REVERT: C 224 GLU cc_start: 0.8567 (mp0) cc_final: 0.8150 (mp0) REVERT: C 242 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8324 (mm) REVERT: C 360 ASN cc_start: 0.9055 (t0) cc_final: 0.8599 (t0) REVERT: C 365 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7478 (t80) REVERT: C 377 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7164 (t80) REVERT: C 386 LYS cc_start: 0.8809 (mttp) cc_final: 0.8388 (mttp) REVERT: C 516 GLU cc_start: 0.8060 (tp30) cc_final: 0.7696 (tp30) REVERT: C 547 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8702 (mtpp) REVERT: C 564 GLN cc_start: 0.8917 (tp40) cc_final: 0.8588 (tp40) REVERT: C 568 ASP cc_start: 0.8110 (t0) cc_final: 0.7859 (t0) REVERT: C 571 ASP cc_start: 0.8334 (t0) cc_final: 0.8006 (t0) REVERT: C 610 VAL cc_start: 0.9243 (t) cc_final: 0.8947 (m) REVERT: C 613 GLN cc_start: 0.7907 (mt0) cc_final: 0.7639 (mt0) REVERT: C 646 ARG cc_start: 0.9220 (tpp80) cc_final: 0.8621 (ttp80) REVERT: C 654 GLU cc_start: 0.8679 (tt0) cc_final: 0.8448 (pt0) REVERT: C 661 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 752 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8829 (mm) REVERT: C 755 GLN cc_start: 0.8883 (mp10) cc_final: 0.8577 (mp10) REVERT: C 773 GLU cc_start: 0.8691 (tt0) cc_final: 0.7936 (tm-30) REVERT: C 780 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8437 (mm-30) REVERT: C 918 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8562 (mt-10) REVERT: C 950 ASP cc_start: 0.8160 (p0) cc_final: 0.7837 (p0) REVERT: C 957 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 1091 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8249 (mtp85) outliers start: 88 outliers final: 63 residues processed: 628 average time/residue: 0.1903 time to fit residues: 188.2570 Evaluate side-chains 593 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 523 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 115 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 173 optimal weight: 0.0020 chunk 206 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 125 ASN B 207 HIS B 394 ASN B 935 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075434 restraints weight = 77207.231| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 4.09 r_work: 0.3048 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28437 Z= 0.210 Angle : 0.770 17.197 38859 Z= 0.374 Chirality : 0.048 0.484 4635 Planarity : 0.005 0.075 4827 Dihedral : 6.357 85.182 3622 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 3.93 % Allowed : 14.66 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3324 helix: 1.13 (0.19), residues: 779 sheet: -0.09 (0.18), residues: 678 loop : -1.36 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1019 TYR 0.020 0.002 TYR C 636 PHE 0.027 0.002 PHE C 342 TRP 0.029 0.002 TRP C 436 HIS 0.007 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (28291) covalent geometry : angle 0.72368 / 0.36 (38466) SS BOND : bond 0.00437 / 0.25 ( 45) SS BOND : angle 1.60241 / 1.01 ( 90) hydrogen bonds : bond 0.04332 / 2.89 ( 1074) hydrogen bonds : angle 5.73172 / 3.89 ( 2982) link_ALPHA1-4 : bond 0.00859 / 0.53 ( 15) link_ALPHA1-4 : angle 2.14155 / 1.41 ( 45) link_BETA1-4 : bond 0.00337 / 0.22 ( 29) link_BETA1-4 : angle 1.54790 / 0.99 ( 87) link_BETA1-6 : bond 0.00474 / 0.23 ( 3) link_BETA1-6 : angle 1.59781 / 0.97 ( 9) link_NAG-ASN : bond 0.00480 / 0.29 ( 54) link_NAG-ASN : angle 3.72616 / 2.43 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 563 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8623 (mmmm) REVERT: A 115 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8696 (tp-100) REVERT: A 120 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8609 (m) REVERT: A 129 LYS cc_start: 0.8922 (tttt) cc_final: 0.8455 (ttmm) REVERT: A 190 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8059 (mmm-85) REVERT: A 224 GLU cc_start: 0.8407 (mp0) cc_final: 0.8103 (mp0) REVERT: A 228 ASP cc_start: 0.8120 (p0) cc_final: 0.7833 (p0) REVERT: A 266 TYR cc_start: 0.8229 (m-80) cc_final: 0.7778 (m-80) REVERT: A 287 ASP cc_start: 0.8707 (t0) cc_final: 0.8308 (t0) REVERT: A 319 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7712 (tpt170) REVERT: A 421 TYR cc_start: 0.6506 (m-10) cc_final: 0.6228 (m-10) REVERT: A 565 PHE cc_start: 0.7957 (p90) cc_final: 0.7719 (p90) REVERT: A 588 THR cc_start: 0.8996 (m) cc_final: 0.8726 (t) REVERT: A 607 GLN cc_start: 0.8371 (mp10) cc_final: 0.7754 (mp10) REVERT: A 658 ASN cc_start: 0.8305 (t0) cc_final: 0.7790 (p0) REVERT: A 663 ASP cc_start: 0.8408 (t0) cc_final: 0.8184 (t0) REVERT: A 740 MET cc_start: 0.9213 (tpt) cc_final: 0.8966 (tpp) REVERT: A 773 GLU cc_start: 0.8566 (tt0) cc_final: 0.8258 (tp30) REVERT: A 780 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8441 (mm-30) REVERT: A 819 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7943 (mt-10) REVERT: A 820 ASP cc_start: 0.8571 (t70) cc_final: 0.8371 (t0) REVERT: A 823 PHE cc_start: 0.8129 (m-80) cc_final: 0.7494 (t80) REVERT: A 848 ASP cc_start: 0.8434 (t0) cc_final: 0.7694 (p0) REVERT: A 854 LYS cc_start: 0.9463 (tttt) cc_final: 0.9208 (tttt) REVERT: A 867 ASP cc_start: 0.8648 (m-30) cc_final: 0.8444 (m-30) REVERT: A 935 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8647 (tm-30) REVERT: A 1045 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8549 (tptt) REVERT: A 1072 GLU cc_start: 0.8921 (pm20) cc_final: 0.8594 (pm20) REVERT: B 41 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8550 (mtpp) REVERT: B 200 TYR cc_start: 0.8016 (m-80) cc_final: 0.7778 (m-80) REVERT: B 202 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8674 (mmtm) REVERT: B 237 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8145 (ptt90) REVERT: B 297 SER cc_start: 0.9272 (m) cc_final: 0.8843 (p) REVERT: B 354 ASN cc_start: 0.8271 (t0) cc_final: 0.7729 (p0) REVERT: B 355 ARG cc_start: 0.7978 (tpp80) cc_final: 0.7490 (tpp80) REVERT: B 365 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6883 (p90) REVERT: B 388 ASN cc_start: 0.8527 (t0) cc_final: 0.8203 (t0) REVERT: B 466 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7312 (ttp80) REVERT: B 474 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: B 518 LEU cc_start: 0.9300 (mm) cc_final: 0.8960 (tp) REVERT: B 571 ASP cc_start: 0.8899 (t0) cc_final: 0.8299 (t0) REVERT: B 646 ARG cc_start: 0.8431 (ttt90) cc_final: 0.7869 (mtp180) REVERT: B 661 GLU cc_start: 0.8497 (pm20) cc_final: 0.8154 (pm20) REVERT: B 675 GLN cc_start: 0.7624 (pp30) cc_final: 0.7358 (pp30) REVERT: B 755 GLN cc_start: 0.8576 (pt0) cc_final: 0.8228 (mp10) REVERT: B 765 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8409 (mtm110) REVERT: B 780 GLU cc_start: 0.9011 (tp30) cc_final: 0.8680 (tp30) REVERT: B 848 ASP cc_start: 0.7521 (t0) cc_final: 0.7093 (p0) REVERT: B 912 THR cc_start: 0.9211 (m) cc_final: 0.8968 (p) REVERT: B 983 ARG cc_start: 0.8497 (mpp80) cc_final: 0.8278 (ptp90) REVERT: B 1005 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8619 (tp40) REVERT: B 1010 GLN cc_start: 0.8901 (mt0) cc_final: 0.8637 (mm-40) REVERT: B 1091 ARG cc_start: 0.8375 (ttm110) cc_final: 0.8048 (mtm-85) REVERT: C 63 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 114 THR cc_start: 0.8249 (t) cc_final: 0.8014 (m) REVERT: C 129 LYS cc_start: 0.8589 (tttt) cc_final: 0.8356 (ttmt) REVERT: C 191 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7981 (mt-10) REVERT: C 218 GLN cc_start: 0.8338 (tt0) cc_final: 0.8106 (tt0) REVERT: C 224 GLU cc_start: 0.8614 (mp0) cc_final: 0.8218 (mp0) REVERT: C 242 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8429 (mm) REVERT: C 360 ASN cc_start: 0.9069 (t0) cc_final: 0.8616 (t0) REVERT: C 365 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7521 (t80) REVERT: C 377 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 386 LYS cc_start: 0.8815 (mttp) cc_final: 0.8448 (mttm) REVERT: C 428 ASP cc_start: 0.8583 (t0) cc_final: 0.8345 (t0) REVERT: C 516 GLU cc_start: 0.8146 (tp30) cc_final: 0.7764 (tp30) REVERT: C 547 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8715 (mtpp) REVERT: C 564 GLN cc_start: 0.8893 (tp40) cc_final: 0.8582 (tp40) REVERT: C 571 ASP cc_start: 0.8313 (t0) cc_final: 0.7953 (t0) REVERT: C 610 VAL cc_start: 0.9235 (t) cc_final: 0.8946 (m) REVERT: C 613 GLN cc_start: 0.7871 (mt0) cc_final: 0.7623 (mt0) REVERT: C 646 ARG cc_start: 0.9218 (tpp80) cc_final: 0.8596 (ttp80) REVERT: C 661 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 752 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8893 (mm) REVERT: C 755 GLN cc_start: 0.8909 (mp10) cc_final: 0.8613 (mp10) REVERT: C 773 GLU cc_start: 0.8680 (tt0) cc_final: 0.7845 (tm-30) REVERT: C 918 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8638 (mt-10) REVERT: C 950 ASP cc_start: 0.8150 (p0) cc_final: 0.7750 (p0) REVERT: C 979 ASP cc_start: 0.8907 (t0) cc_final: 0.8689 (t0) outliers start: 115 outliers final: 76 residues processed: 628 average time/residue: 0.1947 time to fit residues: 191.6527 Evaluate side-chains 617 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 531 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 203 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B1002 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.098195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076481 restraints weight = 76980.786| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.99 r_work: 0.3081 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28437 Z= 0.157 Angle : 0.737 16.493 38859 Z= 0.356 Chirality : 0.047 0.492 4635 Planarity : 0.005 0.089 4827 Dihedral : 6.130 88.880 3621 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 3.42 % Allowed : 16.60 % Favored : 79.98 % 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: -0.61 (0.14), residues: 3324 helix: 1.28 (0.19), residues: 781 sheet: -0.12 (0.18), residues: 692 loop : -1.30 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 214 TYR 0.028 0.001 TYR C 636 PHE 0.026 0.002 PHE A 898 TRP 0.029 0.001 TRP C 436 HIS 0.008 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (28291) covalent geometry : angle 0.69261 / 0.35 (38466) SS BOND : bond 0.00641 / 0.41 ( 45) SS BOND : angle 1.71908 / 1.09 ( 90) hydrogen bonds : bond 0.04013 / 2.70 ( 1074) hydrogen bonds : angle 5.58215 / 3.80 ( 2982) link_ALPHA1-4 : bond 0.00816 / 0.50 ( 15) link_ALPHA1-4 : angle 1.97571 / 1.30 ( 45) link_BETA1-4 : bond 0.00346 / 0.22 ( 29) link_BETA1-4 : angle 1.38092 / 0.88 ( 87) link_BETA1-6 : bond 0.00571 / 0.28 ( 3) link_BETA1-6 : angle 1.57772 / 0.96 ( 9) link_NAG-ASN : bond 0.00436 / 0.25 ( 54) link_NAG-ASN : angle 3.52135 / 2.30 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 558 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8712 (mmmm) REVERT: A 99 ASN cc_start: 0.8199 (t0) cc_final: 0.7995 (t0) REVERT: A 129 LYS cc_start: 0.8854 (tttt) cc_final: 0.8412 (ttmm) REVERT: A 190 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8031 (mmm-85) REVERT: A 224 GLU cc_start: 0.8335 (mp0) cc_final: 0.7988 (mp0) REVERT: A 228 ASP cc_start: 0.7962 (p0) cc_final: 0.7684 (p0) REVERT: A 266 TYR cc_start: 0.8220 (m-80) cc_final: 0.7724 (m-80) REVERT: A 287 ASP cc_start: 0.8660 (t0) cc_final: 0.8282 (t0) REVERT: A 319 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7705 (tpt170) REVERT: A 421 TYR cc_start: 0.6310 (m-10) cc_final: 0.6091 (m-10) REVERT: A 588 THR cc_start: 0.9010 (m) cc_final: 0.8777 (t) REVERT: A 607 GLN cc_start: 0.8388 (mp10) cc_final: 0.7780 (mp10) REVERT: A 658 ASN cc_start: 0.8268 (t0) cc_final: 0.7926 (p0) REVERT: A 663 ASP cc_start: 0.8437 (t0) cc_final: 0.8194 (t0) REVERT: A 740 MET cc_start: 0.9174 (tpt) cc_final: 0.8973 (tpp) REVERT: A 763 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 780 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8425 (mm-30) REVERT: A 819 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 820 ASP cc_start: 0.8519 (t70) cc_final: 0.8319 (t0) REVERT: A 823 PHE cc_start: 0.8063 (m-80) cc_final: 0.7312 (t80) REVERT: A 848 ASP cc_start: 0.8402 (t0) cc_final: 0.7658 (p0) REVERT: A 854 LYS cc_start: 0.9458 (tttt) cc_final: 0.9229 (tttt) REVERT: A 935 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: A 1041 ASP cc_start: 0.8642 (m-30) cc_final: 0.8189 (m-30) REVERT: A 1045 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8567 (tptt) REVERT: A 1072 GLU cc_start: 0.8877 (pm20) cc_final: 0.8581 (pm20) REVERT: B 41 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8525 (mtpp) REVERT: B 52 GLN cc_start: 0.8715 (tp40) cc_final: 0.8139 (tp40) REVERT: B 176 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.5957 (mt) REVERT: B 191 GLU cc_start: 0.7947 (mp0) cc_final: 0.7574 (pm20) REVERT: B 200 TYR cc_start: 0.7933 (m-80) cc_final: 0.7725 (m-80) REVERT: B 202 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8644 (mmtm) REVERT: B 237 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8101 (ptt90) REVERT: B 274 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8202 (m) REVERT: B 297 SER cc_start: 0.9274 (m) cc_final: 0.8879 (p) REVERT: B 354 ASN cc_start: 0.8147 (t0) cc_final: 0.7684 (p0) REVERT: B 365 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6830 (p90) REVERT: B 452 LEU cc_start: 0.8824 (mp) cc_final: 0.8430 (mt) REVERT: B 474 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: B 518 LEU cc_start: 0.9193 (mm) cc_final: 0.8980 (tp) REVERT: B 571 ASP cc_start: 0.8891 (t0) cc_final: 0.8266 (t0) REVERT: B 646 ARG cc_start: 0.8479 (ttt90) cc_final: 0.7947 (mtp180) REVERT: B 661 GLU cc_start: 0.8415 (pm20) cc_final: 0.8107 (pm20) REVERT: B 675 GLN cc_start: 0.7604 (pp30) cc_final: 0.7367 (pp30) REVERT: B 755 GLN cc_start: 0.8504 (pt0) cc_final: 0.8188 (mp10) REVERT: B 765 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8406 (mtm110) REVERT: B 780 GLU cc_start: 0.9027 (tp30) cc_final: 0.8698 (tp30) REVERT: B 848 ASP cc_start: 0.7474 (t0) cc_final: 0.7134 (p0) REVERT: B 900 MET cc_start: 0.9051 (mmm) cc_final: 0.8582 (mtp) REVERT: B 912 THR cc_start: 0.9167 (m) cc_final: 0.8946 (p) REVERT: B 1002 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8251 (tp40) REVERT: B 1005 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8575 (tp40) REVERT: B 1010 GLN cc_start: 0.8883 (mt0) cc_final: 0.8654 (mm-40) REVERT: B 1091 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8090 (mtm-85) REVERT: C 63 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8566 (p) REVERT: C 129 LYS cc_start: 0.8591 (tttt) cc_final: 0.8239 (ttmt) REVERT: C 191 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7974 (mt-10) REVERT: C 224 GLU cc_start: 0.8567 (mp0) cc_final: 0.8197 (mp0) REVERT: C 242 LEU cc_start: 0.8573 (mm) cc_final: 0.8365 (mm) REVERT: C 298 GLU cc_start: 0.9023 (tp30) cc_final: 0.8802 (tp30) REVERT: C 316 SER cc_start: 0.8832 (m) cc_final: 0.8508 (p) REVERT: C 360 ASN cc_start: 0.8984 (t0) cc_final: 0.8500 (t0) REVERT: C 365 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7360 (t80) REVERT: C 377 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6828 (t80) REVERT: C 386 LYS cc_start: 0.8751 (mttp) cc_final: 0.8465 (mttm) REVERT: C 428 ASP cc_start: 0.8472 (t0) cc_final: 0.8193 (t0) REVERT: C 516 GLU cc_start: 0.7972 (tp30) cc_final: 0.7615 (tp30) REVERT: C 547 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8732 (mtpp) REVERT: C 564 GLN cc_start: 0.8810 (tp40) cc_final: 0.8533 (tp40) REVERT: C 571 ASP cc_start: 0.8276 (t0) cc_final: 0.7934 (t0) REVERT: C 610 VAL cc_start: 0.9241 (t) cc_final: 0.8958 (m) REVERT: C 613 GLN cc_start: 0.7810 (mt0) cc_final: 0.7602 (mt0) REVERT: C 646 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8626 (tpp80) REVERT: C 661 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7358 (tm-30) REVERT: C 663 ASP cc_start: 0.8503 (t0) cc_final: 0.8301 (t0) REVERT: C 773 GLU cc_start: 0.8585 (tt0) cc_final: 0.7746 (tm-30) REVERT: C 811 LYS cc_start: 0.8487 (tppt) cc_final: 0.8092 (ttmm) REVERT: C 918 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8524 (mt-10) REVERT: C 950 ASP cc_start: 0.8085 (p0) cc_final: 0.7774 (p0) REVERT: C 979 ASP cc_start: 0.8876 (t0) cc_final: 0.8644 (t0) REVERT: C 1002 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8603 (tp40) REVERT: C 1019 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8291 (ttm-80) outliers start: 100 outliers final: 69 residues processed: 613 average time/residue: 0.1875 time to fit residues: 180.6219 Evaluate side-chains 610 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 528 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 255 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 328 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 275 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.076374 restraints weight = 76810.698| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.07 r_work: 0.3068 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28437 Z= 0.154 Angle : 0.736 16.272 38859 Z= 0.353 Chirality : 0.047 0.484 4635 Planarity : 0.005 0.082 4827 Dihedral : 5.956 88.866 3619 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 3.52 % Allowed : 17.12 % Favored : 79.36 % 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: -0.53 (0.14), residues: 3324 helix: 1.36 (0.19), residues: 778 sheet: -0.14 (0.18), residues: 715 loop : -1.23 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 102 TYR 0.025 0.001 TYR C 636 PHE 0.034 0.002 PHE B 338 TRP 0.027 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (28291) covalent geometry : angle 0.69516 / 0.34 (38466) SS BOND : bond 0.00566 / 0.36 ( 45) SS BOND : angle 1.58323 / 1.06 ( 90) hydrogen bonds : bond 0.03908 / 2.63 ( 1074) hydrogen bonds : angle 5.49967 / 3.73 ( 2982) link_ALPHA1-4 : bond 0.00782 / 0.47 ( 15) link_ALPHA1-4 : angle 1.92079 / 1.25 ( 45) link_BETA1-4 : bond 0.00334 / 0.21 ( 29) link_BETA1-4 : angle 1.35086 / 0.86 ( 87) link_BETA1-6 : bond 0.00592 / 0.29 ( 3) link_BETA1-6 : angle 1.58043 / 0.96 ( 9) link_NAG-ASN : bond 0.00443 / 0.25 ( 54) link_NAG-ASN : angle 3.41386 / 2.23 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 535 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8997 (mmmm) REVERT: A 99 ASN cc_start: 0.8342 (t0) cc_final: 0.8032 (t0) REVERT: A 129 LYS cc_start: 0.8873 (tttt) cc_final: 0.8391 (ttmm) REVERT: A 177 MET cc_start: 0.6926 (ppp) cc_final: 0.6588 (tmm) REVERT: A 190 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8078 (mmm-85) REVERT: A 224 GLU cc_start: 0.8332 (mp0) cc_final: 0.8113 (mp0) REVERT: A 228 ASP cc_start: 0.8071 (p0) cc_final: 0.7783 (p0) REVERT: A 266 TYR cc_start: 0.8268 (m-80) cc_final: 0.7741 (m-80) REVERT: A 287 ASP cc_start: 0.8708 (t0) cc_final: 0.8327 (t0) REVERT: A 319 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7632 (tpt170) REVERT: A 588 THR cc_start: 0.8988 (m) cc_final: 0.8745 (t) REVERT: A 607 GLN cc_start: 0.8398 (mp10) cc_final: 0.7766 (mp10) REVERT: A 740 MET cc_start: 0.9182 (tpt) cc_final: 0.8979 (tpp) REVERT: A 763 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 780 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 819 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 820 ASP cc_start: 0.8562 (t70) cc_final: 0.8283 (t0) REVERT: A 848 ASP cc_start: 0.8437 (t0) cc_final: 0.7987 (m-30) REVERT: A 854 LYS cc_start: 0.9457 (tttt) cc_final: 0.9221 (tttt) REVERT: A 856 LYS cc_start: 0.9251 (mptt) cc_final: 0.9039 (mptt) REVERT: A 867 ASP cc_start: 0.8661 (m-30) cc_final: 0.8321 (t0) REVERT: A 935 GLN cc_start: 0.9050 (tm130) cc_final: 0.8676 (tm-30) REVERT: A 1005 GLN cc_start: 0.8931 (tp40) cc_final: 0.8568 (tp40) REVERT: A 1072 GLU cc_start: 0.8908 (pm20) cc_final: 0.8602 (pm20) REVERT: B 52 GLN cc_start: 0.8749 (tp40) cc_final: 0.8138 (tp40) REVERT: B 156 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5540 (mm-30) REVERT: B 202 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8597 (mmtm) REVERT: B 237 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8148 (ptt90) REVERT: B 274 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8215 (m) REVERT: B 297 SER cc_start: 0.9271 (m) cc_final: 0.8857 (p) REVERT: B 354 ASN cc_start: 0.8174 (t0) cc_final: 0.7632 (p0) REVERT: B 365 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6769 (p90) REVERT: B 452 LEU cc_start: 0.8833 (mp) cc_final: 0.8499 (mt) REVERT: B 474 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: B 518 LEU cc_start: 0.9231 (mm) cc_final: 0.9027 (tp) REVERT: B 571 ASP cc_start: 0.8922 (t0) cc_final: 0.8317 (t0) REVERT: B 646 ARG cc_start: 0.8451 (ttt90) cc_final: 0.7842 (mtp180) REVERT: B 661 GLU cc_start: 0.8403 (pm20) cc_final: 0.8039 (pm20) REVERT: B 755 GLN cc_start: 0.8568 (pt0) cc_final: 0.8276 (mp10) REVERT: B 765 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8366 (mtm110) REVERT: B 780 GLU cc_start: 0.9012 (tp30) cc_final: 0.8697 (tp30) REVERT: B 848 ASP cc_start: 0.7492 (t0) cc_final: 0.7116 (p0) REVERT: B 900 MET cc_start: 0.9132 (mmm) cc_final: 0.8756 (mtp) REVERT: B 912 THR cc_start: 0.9176 (m) cc_final: 0.8933 (p) REVERT: B 935 GLN cc_start: 0.8763 (pt0) cc_final: 0.8121 (pp30) REVERT: B 936 ASP cc_start: 0.8418 (m-30) cc_final: 0.7596 (m-30) REVERT: B 1005 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8620 (tp40) REVERT: B 1010 GLN cc_start: 0.8856 (mt0) cc_final: 0.8514 (mm-40) REVERT: B 1091 ARG cc_start: 0.8436 (ttm110) cc_final: 0.8082 (mtm-85) REVERT: C 63 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8508 (p) REVERT: C 129 LYS cc_start: 0.8706 (tttt) cc_final: 0.8327 (ttmt) REVERT: C 218 GLN cc_start: 0.8276 (tt0) cc_final: 0.8030 (mt0) REVERT: C 223 LEU cc_start: 0.9091 (mp) cc_final: 0.8838 (mm) REVERT: C 224 GLU cc_start: 0.8605 (mp0) cc_final: 0.8215 (mp0) REVERT: C 242 LEU cc_start: 0.8642 (mm) cc_final: 0.8400 (mm) REVERT: C 298 GLU cc_start: 0.9083 (tp30) cc_final: 0.8878 (tp30) REVERT: C 316 SER cc_start: 0.8857 (m) cc_final: 0.8500 (p) REVERT: C 360 ASN cc_start: 0.9046 (t0) cc_final: 0.8554 (t0) REVERT: C 365 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7286 (t80) REVERT: C 377 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.7027 (t80) REVERT: C 386 LYS cc_start: 0.8817 (mttp) cc_final: 0.8432 (mttm) REVERT: C 428 ASP cc_start: 0.8531 (t0) cc_final: 0.8263 (t0) REVERT: C 516 GLU cc_start: 0.8037 (tp30) cc_final: 0.7593 (tp30) REVERT: C 547 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8707 (mtpp) REVERT: C 564 GLN cc_start: 0.8866 (tp40) cc_final: 0.8560 (tp40) REVERT: C 571 ASP cc_start: 0.8355 (t0) cc_final: 0.8009 (t0) REVERT: C 610 VAL cc_start: 0.9209 (t) cc_final: 0.8926 (m) REVERT: C 613 GLN cc_start: 0.7792 (mt0) cc_final: 0.7568 (mt0) REVERT: C 646 ARG cc_start: 0.9209 (tpp80) cc_final: 0.8574 (ttp80) REVERT: C 661 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 663 ASP cc_start: 0.8582 (t0) cc_final: 0.8321 (t0) REVERT: C 773 GLU cc_start: 0.8635 (tt0) cc_final: 0.7520 (tm-30) REVERT: C 777 ASN cc_start: 0.8675 (m-40) cc_final: 0.7484 (m110) REVERT: C 811 LYS cc_start: 0.8454 (tppt) cc_final: 0.8096 (ttmm) REVERT: C 935 GLN cc_start: 0.8907 (tt0) cc_final: 0.8419 (tm-30) REVERT: C 950 ASP cc_start: 0.8089 (p0) cc_final: 0.7746 (p0) REVERT: C 979 ASP cc_start: 0.8911 (t0) cc_final: 0.8632 (t0) REVERT: C 1019 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8280 (ttm-80) outliers start: 103 outliers final: 76 residues processed: 594 average time/residue: 0.1908 time to fit residues: 179.1552 Evaluate side-chains 604 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 518 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 274 optimal weight: 2.9990 chunk 154 optimal weight: 0.0070 chunk 242 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 316 optimal weight: 0.4980 chunk 204 optimal weight: 0.3980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 207 HIS B 439 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.098378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076702 restraints weight = 76455.853| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.04 r_work: 0.3073 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28437 Z= 0.148 Angle : 0.732 15.982 38859 Z= 0.352 Chirality : 0.047 0.478 4635 Planarity : 0.005 0.104 4827 Dihedral : 5.651 59.909 3615 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 3.55 % Allowed : 17.59 % Favored : 78.85 % 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: -0.44 (0.14), residues: 3324 helix: 1.42 (0.19), residues: 777 sheet: -0.10 (0.18), residues: 703 loop : -1.15 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1091 TYR 0.023 0.001 TYR C 636 PHE 0.032 0.002 PHE C 342 TRP 0.026 0.001 TRP C 436 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (28291) covalent geometry : angle 0.69287 / 0.34 (38466) SS BOND : bond 0.00631 / 0.34 ( 45) SS BOND : angle 1.56584 / 1.00 ( 90) hydrogen bonds : bond 0.03816 / 2.55 ( 1074) hydrogen bonds : angle 5.45208 / 3.70 ( 2982) link_ALPHA1-4 : bond 0.00768 / 0.47 ( 15) link_ALPHA1-4 : angle 1.87125 / 1.22 ( 45) link_BETA1-4 : bond 0.00335 / 0.21 ( 29) link_BETA1-4 : angle 1.32361 / 0.84 ( 87) link_BETA1-6 : bond 0.00614 / 0.30 ( 3) link_BETA1-6 : angle 1.59378 / 0.97 ( 9) link_NAG-ASN : bond 0.00453 / 0.25 ( 54) link_NAG-ASN : angle 3.34646 / 2.19 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 531 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8979 (mmmm) REVERT: A 99 ASN cc_start: 0.8342 (t0) cc_final: 0.8135 (t0) REVERT: A 129 LYS cc_start: 0.8873 (tttt) cc_final: 0.8324 (tttt) REVERT: A 190 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8117 (mmm-85) REVERT: A 224 GLU cc_start: 0.8278 (mp0) cc_final: 0.8057 (mp0) REVERT: A 228 ASP cc_start: 0.8060 (p0) cc_final: 0.7800 (p0) REVERT: A 287 ASP cc_start: 0.8684 (t0) cc_final: 0.8296 (t0) REVERT: A 319 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7620 (tpt170) REVERT: A 588 THR cc_start: 0.8967 (m) cc_final: 0.8724 (t) REVERT: A 607 GLN cc_start: 0.8377 (mp10) cc_final: 0.7747 (mp10) REVERT: A 763 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 773 GLU cc_start: 0.8493 (tt0) cc_final: 0.8279 (tp30) REVERT: A 780 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 819 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7972 (mt-10) REVERT: A 820 ASP cc_start: 0.8511 (t70) cc_final: 0.8273 (t0) REVERT: A 848 ASP cc_start: 0.8419 (t0) cc_final: 0.7993 (m-30) REVERT: A 854 LYS cc_start: 0.9456 (tttt) cc_final: 0.9219 (tttt) REVERT: A 867 ASP cc_start: 0.8670 (m-30) cc_final: 0.8366 (t0) REVERT: A 935 GLN cc_start: 0.9042 (tm130) cc_final: 0.8670 (tm-30) REVERT: A 1041 ASP cc_start: 0.8723 (m-30) cc_final: 0.8229 (m-30) REVERT: A 1045 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8321 (tptt) REVERT: A 1072 GLU cc_start: 0.8903 (pm20) cc_final: 0.8597 (pm20) REVERT: B 52 GLN cc_start: 0.8749 (tp40) cc_final: 0.8141 (tp40) REVERT: B 156 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5698 (tp30) REVERT: B 202 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8597 (mmtm) REVERT: B 237 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8141 (ptt90) REVERT: B 274 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8218 (m) REVERT: B 297 SER cc_start: 0.9268 (m) cc_final: 0.8853 (p) REVERT: B 354 ASN cc_start: 0.8169 (t0) cc_final: 0.7590 (p0) REVERT: B 365 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6745 (p90) REVERT: B 452 LEU cc_start: 0.8864 (mp) cc_final: 0.8533 (mt) REVERT: B 474 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: B 518 LEU cc_start: 0.9211 (mm) cc_final: 0.8996 (tp) REVERT: B 537 LYS cc_start: 0.9217 (mttt) cc_final: 0.8979 (mttp) REVERT: B 571 ASP cc_start: 0.8922 (t0) cc_final: 0.8325 (t0) REVERT: B 661 GLU cc_start: 0.8382 (pm20) cc_final: 0.8015 (pm20) REVERT: B 755 GLN cc_start: 0.8537 (pt0) cc_final: 0.8279 (mp10) REVERT: B 765 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8368 (mtm110) REVERT: B 780 GLU cc_start: 0.9013 (tp30) cc_final: 0.8703 (tp30) REVERT: B 848 ASP cc_start: 0.7529 (t0) cc_final: 0.7151 (p0) REVERT: B 900 MET cc_start: 0.9135 (mmm) cc_final: 0.8757 (mtp) REVERT: B 912 THR cc_start: 0.9164 (m) cc_final: 0.8914 (p) REVERT: B 935 GLN cc_start: 0.8778 (pt0) cc_final: 0.8103 (pp30) REVERT: B 936 ASP cc_start: 0.8416 (m-30) cc_final: 0.7541 (m-30) REVERT: B 1005 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8572 (tp40) REVERT: B 1091 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8124 (mtm-85) REVERT: C 129 LYS cc_start: 0.8713 (tttt) cc_final: 0.8288 (ttmt) REVERT: C 218 GLN cc_start: 0.8322 (tt0) cc_final: 0.8045 (mt0) REVERT: C 223 LEU cc_start: 0.9089 (mp) cc_final: 0.8834 (mm) REVERT: C 224 GLU cc_start: 0.8611 (mp0) cc_final: 0.8227 (mp0) REVERT: C 242 LEU cc_start: 0.8645 (mm) cc_final: 0.8382 (mm) REVERT: C 298 GLU cc_start: 0.9084 (tp30) cc_final: 0.8875 (tp30) REVERT: C 316 SER cc_start: 0.8865 (m) cc_final: 0.8499 (p) REVERT: C 360 ASN cc_start: 0.9031 (t0) cc_final: 0.8518 (t0) REVERT: C 365 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7242 (t80) REVERT: C 377 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6967 (t80) REVERT: C 386 LYS cc_start: 0.8815 (mttp) cc_final: 0.8441 (mttm) REVERT: C 428 ASP cc_start: 0.8493 (t0) cc_final: 0.8233 (t0) REVERT: C 516 GLU cc_start: 0.8034 (tp30) cc_final: 0.7595 (tp30) REVERT: C 547 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8695 (mtpp) REVERT: C 564 GLN cc_start: 0.8853 (tp40) cc_final: 0.8452 (tp40) REVERT: C 571 ASP cc_start: 0.8363 (t0) cc_final: 0.8025 (t0) REVERT: C 610 VAL cc_start: 0.9214 (t) cc_final: 0.8929 (m) REVERT: C 613 GLN cc_start: 0.7762 (mt0) cc_final: 0.7547 (mt0) REVERT: C 646 ARG cc_start: 0.9222 (tpp80) cc_final: 0.8588 (ttp80) REVERT: C 661 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 663 ASP cc_start: 0.8551 (t0) cc_final: 0.8332 (t0) REVERT: C 752 LEU cc_start: 0.9124 (mm) cc_final: 0.8912 (mm) REVERT: C 755 GLN cc_start: 0.8806 (mp10) cc_final: 0.8603 (mp10) REVERT: C 773 GLU cc_start: 0.8634 (tt0) cc_final: 0.7471 (tm-30) REVERT: C 777 ASN cc_start: 0.8662 (m-40) cc_final: 0.7340 (m110) REVERT: C 811 LYS cc_start: 0.8448 (tppt) cc_final: 0.8122 (ttmm) REVERT: C 950 ASP cc_start: 0.8080 (p0) cc_final: 0.7745 (p0) REVERT: C 979 ASP cc_start: 0.8931 (t0) cc_final: 0.8645 (t0) REVERT: C 1019 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8234 (ttm-80) outliers start: 104 outliers final: 81 residues processed: 597 average time/residue: 0.1926 time to fit residues: 180.7203 Evaluate side-chains 603 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 513 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 2 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 293 optimal weight: 0.5980 chunk 320 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 213 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.3690 r_free = 0.3690 target = 0.098273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076555 restraints weight = 77056.495| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.06 r_work: 0.3078 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28437 Z= 0.150 Angle : 0.729 15.795 38859 Z= 0.350 Chirality : 0.047 0.468 4635 Planarity : 0.004 0.071 4827 Dihedral : 5.468 58.593 3612 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 3.35 % Allowed : 18.55 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.41 (0.14), residues: 3324 helix: 1.46 (0.19), residues: 772 sheet: -0.08 (0.18), residues: 711 loop : -1.13 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1091 TYR 0.022 0.001 TYR B 655 PHE 0.033 0.002 PHE B 338 TRP 0.030 0.001 TRP C 436 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (28291) covalent geometry : angle 0.69126 / 0.34 (38466) SS BOND : bond 0.00531 / 0.31 ( 45) SS BOND : angle 1.52076 / 0.98 ( 90) hydrogen bonds : bond 0.03802 / 2.55 ( 1074) hydrogen bonds : angle 5.41276 / 3.67 ( 2982) link_ALPHA1-4 : bond 0.00753 / 0.46 ( 15) link_ALPHA1-4 : angle 1.84989 / 1.20 ( 45) link_BETA1-4 : bond 0.00331 / 0.21 ( 29) link_BETA1-4 : angle 1.30863 / 0.83 ( 87) link_BETA1-6 : bond 0.00618 / 0.31 ( 3) link_BETA1-6 : angle 1.59235 / 0.97 ( 9) link_NAG-ASN : bond 0.00446 / 0.25 ( 54) link_NAG-ASN : angle 3.29312 / 2.16 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 532 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8722 (mmmm) REVERT: A 129 LYS cc_start: 0.8907 (tttt) cc_final: 0.8264 (tttt) REVERT: A 177 MET cc_start: 0.6890 (ppp) cc_final: 0.6549 (tmm) REVERT: A 190 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8118 (mmm-85) REVERT: A 228 ASP cc_start: 0.8071 (p0) cc_final: 0.7800 (p0) REVERT: A 287 ASP cc_start: 0.8705 (t0) cc_final: 0.7995 (m-30) REVERT: A 319 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7621 (tpt170) REVERT: A 392 PHE cc_start: 0.7108 (m-10) cc_final: 0.6535 (m-80) REVERT: A 532 ASN cc_start: 0.7393 (p0) cc_final: 0.6881 (p0) REVERT: A 588 THR cc_start: 0.8956 (m) cc_final: 0.8698 (t) REVERT: A 607 GLN cc_start: 0.8426 (mp10) cc_final: 0.7811 (mp10) REVERT: A 773 GLU cc_start: 0.8495 (tt0) cc_final: 0.8169 (tp30) REVERT: A 780 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8499 (mm-30) REVERT: A 819 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 848 ASP cc_start: 0.8381 (t0) cc_final: 0.7953 (m-30) REVERT: A 854 LYS cc_start: 0.9455 (tttt) cc_final: 0.9223 (tttt) REVERT: A 856 LYS cc_start: 0.9221 (mptt) cc_final: 0.8997 (mptt) REVERT: A 867 ASP cc_start: 0.8664 (m-30) cc_final: 0.8355 (t0) REVERT: A 935 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: A 1005 GLN cc_start: 0.8905 (tp40) cc_final: 0.8637 (tp40) REVERT: A 1041 ASP cc_start: 0.8711 (m-30) cc_final: 0.8217 (m-30) REVERT: A 1045 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8295 (tptt) REVERT: A 1072 GLU cc_start: 0.8906 (pm20) cc_final: 0.8600 (pm20) REVERT: B 52 GLN cc_start: 0.8758 (tp40) cc_final: 0.8230 (tp40) REVERT: B 156 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5495 (mm-30) REVERT: B 202 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8625 (mmtm) REVERT: B 297 SER cc_start: 0.9256 (m) cc_final: 0.8852 (p) REVERT: B 354 ASN cc_start: 0.8175 (t0) cc_final: 0.7622 (p0) REVERT: B 365 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6736 (p90) REVERT: B 452 LEU cc_start: 0.8891 (mp) cc_final: 0.8572 (mt) REVERT: B 474 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7465 (pp30) REVERT: B 537 LYS cc_start: 0.9206 (mttt) cc_final: 0.8974 (mttp) REVERT: B 571 ASP cc_start: 0.8913 (t0) cc_final: 0.8326 (t0) REVERT: B 633 TRP cc_start: 0.8796 (p-90) cc_final: 0.8538 (p-90) REVERT: B 646 ARG cc_start: 0.8389 (ttt90) cc_final: 0.7880 (mtp180) REVERT: B 661 GLU cc_start: 0.8388 (pm20) cc_final: 0.8016 (pm20) REVERT: B 755 GLN cc_start: 0.8518 (pt0) cc_final: 0.8160 (mp10) REVERT: B 765 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8352 (mtm110) REVERT: B 773 GLU cc_start: 0.8883 (tp30) cc_final: 0.8533 (tp30) REVERT: B 780 GLU cc_start: 0.9008 (tp30) cc_final: 0.8695 (tp30) REVERT: B 848 ASP cc_start: 0.7673 (t0) cc_final: 0.7220 (p0) REVERT: B 900 MET cc_start: 0.9140 (mmm) cc_final: 0.8824 (mtp) REVERT: B 912 THR cc_start: 0.9157 (m) cc_final: 0.8901 (p) REVERT: B 935 GLN cc_start: 0.8780 (pt0) cc_final: 0.8109 (pp30) REVERT: B 936 ASP cc_start: 0.8445 (m-30) cc_final: 0.7542 (m-30) REVERT: B 1005 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8586 (tp40) REVERT: B 1091 ARG cc_start: 0.8465 (ttm110) cc_final: 0.8120 (mtm-85) REVERT: C 129 LYS cc_start: 0.8714 (tttt) cc_final: 0.8401 (ttmt) REVERT: C 218 GLN cc_start: 0.8307 (tt0) cc_final: 0.8049 (mt0) REVERT: C 223 LEU cc_start: 0.9088 (mp) cc_final: 0.8825 (mm) REVERT: C 224 GLU cc_start: 0.8607 (mp0) cc_final: 0.8225 (mp0) REVERT: C 242 LEU cc_start: 0.8619 (mm) cc_final: 0.8347 (mm) REVERT: C 298 GLU cc_start: 0.9079 (tp30) cc_final: 0.8869 (tp30) REVERT: C 316 SER cc_start: 0.8856 (m) cc_final: 0.8496 (p) REVERT: C 360 ASN cc_start: 0.9025 (t0) cc_final: 0.8474 (t0) REVERT: C 377 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6858 (t80) REVERT: C 386 LYS cc_start: 0.8830 (mttp) cc_final: 0.8462 (mttm) REVERT: C 428 ASP cc_start: 0.8445 (t0) cc_final: 0.8198 (t0) REVERT: C 516 GLU cc_start: 0.8015 (tp30) cc_final: 0.7614 (tp30) REVERT: C 547 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8688 (mtpp) REVERT: C 564 GLN cc_start: 0.8843 (tp40) cc_final: 0.8452 (tp40) REVERT: C 571 ASP cc_start: 0.8362 (t0) cc_final: 0.8028 (t0) REVERT: C 610 VAL cc_start: 0.9234 (t) cc_final: 0.8942 (m) REVERT: C 613 GLN cc_start: 0.7801 (mt0) cc_final: 0.7600 (mt0) REVERT: C 646 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8589 (ttp80) REVERT: C 661 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 663 ASP cc_start: 0.8559 (t0) cc_final: 0.8309 (t0) REVERT: C 752 LEU cc_start: 0.9112 (mm) cc_final: 0.8879 (mm) REVERT: C 773 GLU cc_start: 0.8606 (tt0) cc_final: 0.7446 (tm-30) REVERT: C 777 ASN cc_start: 0.8680 (m-40) cc_final: 0.7347 (m110) REVERT: C 811 LYS cc_start: 0.8470 (tppt) cc_final: 0.8121 (ttmm) REVERT: C 817 PHE cc_start: 0.8158 (t80) cc_final: 0.7911 (t80) REVERT: C 950 ASP cc_start: 0.8093 (p0) cc_final: 0.7750 (p0) REVERT: C 953 ASN cc_start: 0.8793 (m-40) cc_final: 0.8531 (m-40) REVERT: C 979 ASP cc_start: 0.8933 (t0) cc_final: 0.8596 (t0) REVERT: C 988 GLU cc_start: 0.7929 (tp30) cc_final: 0.7567 (tp30) REVERT: C 1002 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8296 (mp10) REVERT: C 1019 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8246 (ttm-80) outliers start: 98 outliers final: 81 residues processed: 591 average time/residue: 0.1861 time to fit residues: 173.2429 Evaluate side-chains 594 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 505 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 259 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 332 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 197 optimal weight: 0.1980 chunk 158 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 170 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077311 restraints weight = 76578.702| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.05 r_work: 0.3088 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28437 Z= 0.132 Angle : 0.733 15.236 38859 Z= 0.355 Chirality : 0.047 0.468 4635 Planarity : 0.004 0.064 4827 Dihedral : 5.375 57.804 3612 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 3.18 % Allowed : 18.82 % Favored : 78.00 % 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: -0.37 (0.14), residues: 3324 helix: 1.50 (0.19), residues: 771 sheet: -0.06 (0.18), residues: 724 loop : -1.10 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 457 TYR 0.020 0.001 TYR B 655 PHE 0.034 0.001 PHE C 342 TRP 0.034 0.001 TRP B 436 HIS 0.012 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (28291) covalent geometry : angle 0.69753 / 0.35 (38466) SS BOND : bond 0.00507 / 0.29 ( 45) SS BOND : angle 1.47355 / 0.99 ( 90) hydrogen bonds : bond 0.03733 / 2.50 ( 1074) hydrogen bonds : angle 5.34960 / 3.63 ( 2982) link_ALPHA1-4 : bond 0.00725 / 0.44 ( 15) link_ALPHA1-4 : angle 1.76394 / 1.14 ( 45) link_BETA1-4 : bond 0.00374 / 0.24 ( 29) link_BETA1-4 : angle 1.24473 / 0.79 ( 87) link_BETA1-6 : bond 0.00657 / 0.33 ( 3) link_BETA1-6 : angle 1.53240 / 0.94 ( 9) link_NAG-ASN : bond 0.00447 / 0.26 ( 54) link_NAG-ASN : angle 3.19980 / 2.11 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 533 time to evaluate : 1.059 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 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8743 (mmmm) REVERT: A 129 LYS cc_start: 0.8880 (tttt) cc_final: 0.8256 (tttt) REVERT: A 190 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8143 (mmm-85) REVERT: A 224 GLU cc_start: 0.8149 (mp0) cc_final: 0.7733 (mp0) REVERT: A 226 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 228 ASP cc_start: 0.8176 (p0) cc_final: 0.7887 (p0) REVERT: A 287 ASP cc_start: 0.8700 (t0) cc_final: 0.8323 (t0) REVERT: A 306 PHE cc_start: 0.8468 (m-10) cc_final: 0.7808 (m-80) REVERT: A 319 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7645 (tpt170) REVERT: A 392 PHE cc_start: 0.7007 (m-10) cc_final: 0.6422 (m-80) REVERT: A 532 ASN cc_start: 0.7421 (p0) cc_final: 0.6930 (p0) REVERT: A 588 THR cc_start: 0.8936 (m) cc_final: 0.8666 (t) REVERT: A 607 GLN cc_start: 0.8412 (mp10) cc_final: 0.7787 (mp10) REVERT: A 773 GLU cc_start: 0.8529 (tt0) cc_final: 0.8328 (tm-30) REVERT: A 780 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8453 (mm-30) REVERT: A 819 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 820 ASP cc_start: 0.8584 (t70) cc_final: 0.8352 (t0) REVERT: A 848 ASP cc_start: 0.8309 (t0) cc_final: 0.7868 (m-30) REVERT: A 854 LYS cc_start: 0.9438 (tttt) cc_final: 0.9174 (tttt) REVERT: A 867 ASP cc_start: 0.8698 (m-30) cc_final: 0.8421 (t0) REVERT: A 935 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: A 986 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8766 (mmtm) REVERT: A 1005 GLN cc_start: 0.8896 (tp40) cc_final: 0.8617 (tp40) REVERT: A 1045 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8292 (tptt) REVERT: A 1072 GLU cc_start: 0.8882 (pm20) cc_final: 0.8591 (pm20) REVERT: B 52 GLN cc_start: 0.8711 (tp40) cc_final: 0.8176 (tp40) REVERT: B 129 LYS cc_start: 0.8239 (mttt) cc_final: 0.7897 (tptm) REVERT: B 156 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5666 (mm-30) REVERT: B 202 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8657 (mmtm) REVERT: B 297 SER cc_start: 0.9224 (m) cc_final: 0.8834 (p) REVERT: B 354 ASN cc_start: 0.8138 (t0) cc_final: 0.7567 (p0) REVERT: B 365 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6684 (p90) REVERT: B 452 LEU cc_start: 0.8908 (mp) cc_final: 0.8597 (mt) REVERT: B 460 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8687 (t0) REVERT: B 474 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7488 (pp30) REVERT: B 571 ASP cc_start: 0.8909 (t0) cc_final: 0.8328 (t0) REVERT: B 633 TRP cc_start: 0.8800 (p-90) cc_final: 0.8541 (p-90) REVERT: B 646 ARG cc_start: 0.8423 (ttt90) cc_final: 0.7890 (mtp180) REVERT: B 755 GLN cc_start: 0.8519 (pt0) cc_final: 0.8258 (pm20) REVERT: B 765 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8316 (mtm110) REVERT: B 780 GLU cc_start: 0.8990 (tp30) cc_final: 0.8686 (tp30) REVERT: B 848 ASP cc_start: 0.7662 (t0) cc_final: 0.7210 (p0) REVERT: B 900 MET cc_start: 0.9080 (mmm) cc_final: 0.8784 (mtp) REVERT: B 912 THR cc_start: 0.9128 (m) cc_final: 0.8866 (p) REVERT: B 935 GLN cc_start: 0.8768 (pt0) cc_final: 0.8090 (pp30) REVERT: B 936 ASP cc_start: 0.8412 (m-30) cc_final: 0.7502 (m-30) REVERT: B 1005 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8596 (tp40) REVERT: B 1091 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8162 (mtm-85) REVERT: C 129 LYS cc_start: 0.8733 (tttt) cc_final: 0.8273 (ttmt) REVERT: C 218 GLN cc_start: 0.8278 (tt0) cc_final: 0.8012 (mt0) REVERT: C 223 LEU cc_start: 0.9088 (mp) cc_final: 0.8819 (mm) REVERT: C 224 GLU cc_start: 0.8605 (mp0) cc_final: 0.8221 (mp0) REVERT: C 242 LEU cc_start: 0.8615 (mm) cc_final: 0.8303 (mm) REVERT: C 298 GLU cc_start: 0.9067 (tp30) cc_final: 0.8843 (tp30) REVERT: C 316 SER cc_start: 0.8837 (m) cc_final: 0.8459 (p) REVERT: C 360 ASN cc_start: 0.8962 (t0) cc_final: 0.8408 (t0) REVERT: C 386 LYS cc_start: 0.8827 (mttp) cc_final: 0.8457 (mttm) REVERT: C 428 ASP cc_start: 0.8424 (t0) cc_final: 0.8182 (t0) REVERT: C 516 GLU cc_start: 0.7915 (tp30) cc_final: 0.7523 (tp30) REVERT: C 547 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8635 (mtpp) REVERT: C 564 GLN cc_start: 0.8816 (tp40) cc_final: 0.8422 (tp40) REVERT: C 571 ASP cc_start: 0.8332 (t0) cc_final: 0.8004 (t0) REVERT: C 610 VAL cc_start: 0.9216 (t) cc_final: 0.8909 (m) REVERT: C 613 GLN cc_start: 0.7800 (mt0) cc_final: 0.7589 (mt0) REVERT: C 646 ARG cc_start: 0.9228 (tpp80) cc_final: 0.8601 (ttp80) REVERT: C 661 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 663 ASP cc_start: 0.8576 (t0) cc_final: 0.8353 (t0) REVERT: C 773 GLU cc_start: 0.8602 (tt0) cc_final: 0.7395 (tm-30) REVERT: C 777 ASN cc_start: 0.8637 (m-40) cc_final: 0.7321 (m110) REVERT: C 811 LYS cc_start: 0.8446 (tppt) cc_final: 0.8142 (ttmm) REVERT: C 950 ASP cc_start: 0.8077 (p0) cc_final: 0.7763 (p0) REVERT: C 953 ASN cc_start: 0.8791 (m-40) cc_final: 0.8519 (m-40) REVERT: C 979 ASP cc_start: 0.8948 (t0) cc_final: 0.8605 (t0) REVERT: C 1002 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: C 1019 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8410 (ttm-80) REVERT: C 1072 GLU cc_start: 0.8358 (pm20) cc_final: 0.8080 (pm20) outliers start: 93 outliers final: 73 residues processed: 586 average time/residue: 0.1944 time to fit residues: 178.7614 Evaluate side-chains 597 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 515 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 214 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 164 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.098781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077261 restraints weight = 76746.014| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.03 r_work: 0.3086 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.257 28437 Z= 0.211 Angle : 0.848 59.195 38859 Z= 0.441 Chirality : 0.048 0.466 4635 Planarity : 0.005 0.147 4827 Dihedral : 5.337 57.740 3610 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 2.97 % Allowed : 19.51 % Favored : 77.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z 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: -0.36 (0.14), residues: 3324 helix: 1.52 (0.19), residues: 768 sheet: -0.06 (0.18), residues: 724 loop : -1.10 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.001 ARG B 190 TYR 0.041 0.001 TYR C 495 PHE 0.068 0.002 PHE C 374 TRP 0.110 0.003 TRP C 436 HIS 0.011 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (28291) covalent geometry : angle 0.81941 / 0.44 (38466) SS BOND : bond 0.00515 / 0.30 ( 45) SS BOND : angle 1.42210 / 0.95 ( 90) hydrogen bonds : bond 0.03759 / 2.51 ( 1074) hydrogen bonds : angle 5.35577 / 3.63 ( 2982) link_ALPHA1-4 : bond 0.00732 / 0.44 ( 15) link_ALPHA1-4 : angle 1.76571 / 1.14 ( 45) link_BETA1-4 : bond 0.00366 / 0.23 ( 29) link_BETA1-4 : angle 1.25073 / 0.79 ( 87) link_BETA1-6 : bond 0.00636 / 0.32 ( 3) link_BETA1-6 : angle 1.53874 / 0.94 ( 9) link_NAG-ASN : bond 0.00446 / 0.26 ( 54) link_NAG-ASN : angle 3.20250 / 2.11 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6648 Ramachandran restraints generated. 3324 Oldfield, 0 Emsley, 3324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 516 time to evaluate : 1.040 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 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8742 (mmmm) REVERT: A 111 ASP cc_start: 0.8027 (p0) cc_final: 0.7548 (p0) REVERT: A 129 LYS cc_start: 0.8883 (tttt) cc_final: 0.8255 (tttt) REVERT: A 190 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8140 (mmm-85) REVERT: A 224 GLU cc_start: 0.8156 (mp0) cc_final: 0.7722 (mp0) REVERT: A 226 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7845 (mm) REVERT: A 228 ASP cc_start: 0.8149 (p0) cc_final: 0.7862 (p0) REVERT: A 287 ASP cc_start: 0.8714 (t0) cc_final: 0.8326 (t0) REVERT: A 319 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7640 (tpt170) REVERT: A 392 PHE cc_start: 0.7002 (m-10) cc_final: 0.6418 (m-80) REVERT: A 532 ASN cc_start: 0.7414 (p0) cc_final: 0.6921 (p0) REVERT: A 588 THR cc_start: 0.8918 (m) cc_final: 0.8664 (t) REVERT: A 607 GLN cc_start: 0.8422 (mp10) cc_final: 0.7799 (mp10) REVERT: A 780 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8443 (mm-30) REVERT: A 819 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 820 ASP cc_start: 0.8578 (t70) cc_final: 0.8346 (t0) REVERT: A 848 ASP cc_start: 0.8320 (t0) cc_final: 0.7874 (m-30) REVERT: A 854 LYS cc_start: 0.9439 (tttt) cc_final: 0.9176 (tttt) REVERT: A 867 ASP cc_start: 0.8687 (m-30) cc_final: 0.8421 (t0) REVERT: A 935 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8701 (tm-30) REVERT: A 1005 GLN cc_start: 0.8885 (tp40) cc_final: 0.8616 (tp40) REVERT: A 1045 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8308 (tptt) REVERT: A 1072 GLU cc_start: 0.8877 (pm20) cc_final: 0.8578 (pm20) REVERT: B 52 GLN cc_start: 0.8725 (tp40) cc_final: 0.8189 (tp40) REVERT: B 129 LYS cc_start: 0.8231 (mttt) cc_final: 0.7895 (tptm) REVERT: B 156 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5656 (mm-30) REVERT: B 202 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8626 (mmtm) REVERT: B 297 SER cc_start: 0.9230 (m) cc_final: 0.8837 (p) REVERT: B 354 ASN cc_start: 0.8134 (t0) cc_final: 0.7585 (p0) REVERT: B 365 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6684 (p90) REVERT: B 452 LEU cc_start: 0.8904 (mp) cc_final: 0.8593 (mt) REVERT: B 474 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7493 (pp30) REVERT: B 537 LYS cc_start: 0.9193 (mttt) cc_final: 0.8952 (mttp) REVERT: B 571 ASP cc_start: 0.8907 (t0) cc_final: 0.8330 (t0) REVERT: B 633 TRP cc_start: 0.8800 (p-90) cc_final: 0.8556 (p-90) REVERT: B 646 ARG cc_start: 0.8420 (ttt90) cc_final: 0.7894 (mtp180) REVERT: B 755 GLN cc_start: 0.8525 (pt0) cc_final: 0.8263 (pm20) REVERT: B 765 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8318 (mtm110) REVERT: B 780 GLU cc_start: 0.8989 (tp30) cc_final: 0.8684 (tp30) REVERT: B 848 ASP cc_start: 0.7643 (t0) cc_final: 0.7207 (p0) REVERT: B 900 MET cc_start: 0.9090 (mmm) cc_final: 0.8794 (mtp) REVERT: B 912 THR cc_start: 0.9133 (m) cc_final: 0.8873 (p) REVERT: B 935 GLN cc_start: 0.8758 (pt0) cc_final: 0.8083 (pp30) REVERT: B 936 ASP cc_start: 0.8418 (m-30) cc_final: 0.7507 (m-30) REVERT: B 1005 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8582 (tp40) REVERT: B 1091 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8174 (mtm-85) REVERT: C 41 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8731 (mmmm) REVERT: C 129 LYS cc_start: 0.8659 (tttt) cc_final: 0.8282 (ttmt) REVERT: C 218 GLN cc_start: 0.8277 (tt0) cc_final: 0.8021 (mt0) REVERT: C 223 LEU cc_start: 0.9085 (mp) cc_final: 0.8818 (mm) REVERT: C 224 GLU cc_start: 0.8610 (mp0) cc_final: 0.8224 (mp0) REVERT: C 242 LEU cc_start: 0.8624 (mm) cc_final: 0.8313 (mm) REVERT: C 298 GLU cc_start: 0.9059 (tp30) cc_final: 0.8832 (tp30) REVERT: C 316 SER cc_start: 0.8839 (m) cc_final: 0.8465 (p) REVERT: C 360 ASN cc_start: 0.8967 (t0) cc_final: 0.8416 (t0) REVERT: C 386 LYS cc_start: 0.8824 (mttp) cc_final: 0.8450 (mttm) REVERT: C 428 ASP cc_start: 0.8418 (t0) cc_final: 0.8180 (t0) REVERT: C 516 GLU cc_start: 0.7924 (tp30) cc_final: 0.7527 (tp30) REVERT: C 547 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8626 (mtpp) REVERT: C 564 GLN cc_start: 0.8809 (tp40) cc_final: 0.8413 (tp40) REVERT: C 571 ASP cc_start: 0.8330 (t0) cc_final: 0.8000 (t0) REVERT: C 610 VAL cc_start: 0.9222 (t) cc_final: 0.8916 (m) REVERT: C 613 GLN cc_start: 0.7814 (mt0) cc_final: 0.7605 (mt0) REVERT: C 646 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8601 (ttp80) REVERT: C 661 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 663 ASP cc_start: 0.8566 (t0) cc_final: 0.8325 (t0) REVERT: C 773 GLU cc_start: 0.8598 (tt0) cc_final: 0.7397 (tm-30) REVERT: C 777 ASN cc_start: 0.8643 (m-40) cc_final: 0.7328 (m110) REVERT: C 811 LYS cc_start: 0.8444 (tppt) cc_final: 0.8149 (ttmm) REVERT: C 935 GLN cc_start: 0.8491 (tt0) cc_final: 0.8240 (mt0) REVERT: C 950 ASP cc_start: 0.8077 (p0) cc_final: 0.7769 (p0) REVERT: C 953 ASN cc_start: 0.8786 (m-40) cc_final: 0.8510 (m-40) REVERT: C 979 ASP cc_start: 0.8942 (t0) cc_final: 0.8603 (t0) REVERT: C 1002 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: C 1019 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8410 (ttm-80) REVERT: C 1072 GLU cc_start: 0.8361 (pm20) cc_final: 0.8077 (pm20) outliers start: 87 outliers final: 74 residues processed: 569 average time/residue: 0.1802 time to fit residues: 161.2759 Evaluate side-chains 599 residues out of total 2927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 517 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1156 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.096208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074621 restraints weight = 76932.100| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.02 r_work: 0.3033 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28437 Z= 0.248 Angle : 0.820 16.422 38859 Z= 0.397 Chirality : 0.049 0.434 4635 Planarity : 0.005 0.074 4827 Dihedral : 5.664 56.776 3610 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 3.25 % Allowed : 19.13 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.55 (0.14), residues: 3324 helix: 1.33 (0.19), residues: 767 sheet: -0.11 (0.18), residues: 715 loop : -1.24 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 190 TYR 0.019 0.002 TYR C 636 PHE 0.042 0.002 PHE C 375 TRP 0.092 0.003 TRP C 436 HIS 0.018 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (28291) covalent geometry : angle 0.78277 / 0.39 (38466) SS BOND : bond 0.00587 / 0.35 ( 45) SS BOND : angle 1.66540 / 1.09 ( 90) hydrogen bonds : bond 0.04327 / 2.89 ( 1074) hydrogen bonds : angle 5.54690 / 3.76 ( 2982) link_ALPHA1-4 : bond 0.00822 / 0.51 ( 15) link_ALPHA1-4 : angle 2.06545 / 1.35 ( 45) link_BETA1-4 : bond 0.00337 / 0.22 ( 29) link_BETA1-4 : angle 1.53488 / 0.99 ( 87) link_BETA1-6 : bond 0.00522 / 0.25 ( 3) link_BETA1-6 : angle 1.77958 / 1.04 ( 9) link_NAG-ASN : bond 0.00531 / 0.34 ( 54) link_NAG-ASN : angle 3.43375 / 2.23 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7275.90 seconds wall clock time: 125 minutes 51.69 seconds (7551.69 seconds total)