Starting phenix.real_space_refine on Fri Mar 6 01:38:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1w_24125/03_2026/7n1w_24125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1w_24125/03_2026/7n1w_24125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n1w_24125/03_2026/7n1w_24125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1w_24125/03_2026/7n1w_24125.map" model { file = "/net/cci-nas-00/data/ceres_data/7n1w_24125/03_2026/7n1w_24125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1w_24125/03_2026/7n1w_24125.cif" } resolution = 3.33 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= 0.044 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 114 5.16 5 C 17037 2.51 5 N 4338 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26810 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8522 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8554 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 53, 'TRANS': 1038} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.97, per 1000 atoms: 0.22 Number of scatterers: 26810 At special positions: 0 Unit cell: (151.812, 154.288, 216.168, 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 114 16.00 O 5321 8.00 N 4338 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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 T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 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 A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " 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 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 48 sheets defined 27.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.695A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.846A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.312A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.898A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.593A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.826A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.984A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.105A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.586A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.595A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.625A 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: 3.614A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.529A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (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: 3.973A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 3.554A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.254A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.163A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.357A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.612A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.652A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.885A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.566A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.031A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.617A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.544A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.538A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.632A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.770A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.220A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.965A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.526A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.961A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.496A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.607A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.746A 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 919 removed outlier: 3.581A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.096A 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 984 removed outlier: 3.604A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.383A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.702A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.024A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.839A 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: 4.980A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.938A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.163A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.138A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.930A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.542A 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 319 removed outlier: 4.868A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.050A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.115A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.969A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.003A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.394A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.405A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.992A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.741A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.053A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.134A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.485A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.202A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.021A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.634A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.377A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.723A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.507A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.049A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.308A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.572A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.566A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.269A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.058A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.665A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.979A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.733A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.018A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.653A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.653A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.693A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1123 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4335 1.30 - 1.43: 7309 1.43 - 1.56: 15615 1.56 - 1.69: 1 1.69 - 1.83: 144 Bond restraints: 27404 Sorted by residual: bond pdb=" C ARG C 357 " pdb=" O ARG C 357 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.21e-02 6.83e+03 3.14e+01 bond pdb=" C ARG B 765 " pdb=" O ARG B 765 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.16e-02 7.43e+03 2.76e+01 bond pdb=" C ARG C1014 " pdb=" O ARG C1014 " ideal model delta sigma weight residual 1.237 1.175 0.062 1.19e-02 7.06e+03 2.71e+01 bond pdb=" CA ARG B1019 " pdb=" C ARG B1019 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.26e-02 6.30e+03 2.40e+01 bond pdb=" C ARG A 995 " pdb=" O ARG A 995 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.19e-02 7.06e+03 2.40e+01 ... (remaining 27399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 30507 2.36 - 4.72: 6294 4.72 - 7.08: 446 7.08 - 9.44: 24 9.44 - 11.80: 7 Bond angle restraints: 37278 Sorted by residual: angle pdb=" OD1 ASN B1074 " pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 122.60 113.66 8.94 1.00e+00 1.00e+00 8.00e+01 angle pdb=" OD1 ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 122.60 114.08 8.52 1.00e+00 1.00e+00 7.26e+01 angle pdb=" OD1 ASN A 149 " pdb=" CG ASN A 149 " pdb=" ND2 ASN A 149 " ideal model delta sigma weight residual 122.60 114.17 8.43 1.00e+00 1.00e+00 7.10e+01 angle pdb=" CB ASN B1074 " pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 116.40 128.20 -11.80 1.50e+00 4.44e-01 6.19e+01 angle pdb=" OD1 ASN C 149 " pdb=" CG ASN C 149 " pdb=" ND2 ASN C 149 " ideal model delta sigma weight residual 122.60 114.79 7.81 1.00e+00 1.00e+00 6.11e+01 ... (remaining 37273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.24: 16662 24.24 - 48.48: 686 48.48 - 72.72: 123 72.72 - 96.95: 44 96.95 - 121.19: 22 Dihedral angle restraints: 17537 sinusoidal: 8052 harmonic: 9485 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -152.40 66.40 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -151.22 65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 17534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.694: 4481 0.694 - 1.387: 4 1.387 - 2.081: 1 2.081 - 2.774: 0 2.774 - 3.468: 1 Chirality restraints: 4487 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 1.07 -3.47 2.00e-01 2.50e+01 3.01e+02 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.33 -2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.41e+01 ... (remaining 4484 not shown) Planarity restraints: 4744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.117 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN C 616 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.172 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.535 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " -0.315 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " 0.216 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN A 17 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " -0.293 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.068 2.00e-02 2.50e+03 1.95e-01 4.77e+02 pdb=" CG ASN A 603 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.196 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.306 2.00e-02 2.50e+03 pdb=" C1 NAG A1408 " 0.227 2.00e-02 2.50e+03 ... (remaining 4741 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 55 2.54 - 3.13: 19835 3.13 - 3.72: 40345 3.72 - 4.31: 58638 4.31 - 4.90: 94794 Nonbonded interactions: 213667 Sorted by model distance: nonbonded pdb=" ND2 ASN C 616 " pdb=" N2 NAG a 1 " model vdw 1.951 2.560 nonbonded pdb=" NH2 ARG A1107 " pdb=" CE1 TYR B 904 " model vdw 1.973 3.420 nonbonded pdb=" CD ARG A 815 " pdb=" OD1 ASP A 820 " model vdw 2.022 3.440 nonbonded pdb=" ND2 ASN A 234 " pdb=" C1 NAG A1405 " model vdw 2.071 3.550 nonbonded pdb=" O4 NAG F 1 " pdb=" O7 NAG F 2 " model vdw 2.076 3.040 ... (remaining 213662 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 826 or resid 855 through 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' 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: 12.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 26.720 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.482 27538 Z= 0.834 Angle : 1.889 51.463 37638 Z= 1.193 Chirality : 0.123 3.468 4487 Planarity : 0.012 0.127 4690 Dihedral : 14.713 121.193 11309 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.96 % Favored : 93.52 % Rotamer: Outliers : 0.81 % Allowed : 4.92 % Favored : 94.27 % Cbeta Deviations : 0.56 % 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: -1.65 (0.13), residues: 3223 helix: -1.36 (0.16), residues: 734 sheet: 0.46 (0.20), residues: 573 loop : -1.52 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 357 TYR 0.117 0.020 TYR A 495 PHE 0.092 0.013 PHE B1148 TRP 0.171 0.030 TRP C 258 HIS 0.015 0.004 HIS C1159 Details of bonding type rmsd covalent geometry : bond 0.01380 (27404) covalent geometry : angle 1.78872 (37278) SS BOND : bond 0.01212 ( 42) SS BOND : angle 2.29924 ( 84) hydrogen bonds : bond 0.16074 ( 1105) hydrogen bonds : angle 8.50970 ( 3063) link_ALPHA1-4 : bond 0.02904 ( 6) link_ALPHA1-4 : angle 4.47270 ( 18) link_BETA1-4 : bond 0.02146 ( 29) link_BETA1-4 : angle 3.71327 ( 87) link_BETA1-6 : bond 0.03268 ( 3) link_BETA1-6 : angle 3.25455 ( 9) link_NAG-ASN : bond 0.14721 ( 54) link_NAG-ASN : angle 8.94351 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 779 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8572 (m-40) cc_final: 0.8350 (m-40) REVERT: A 92 PHE cc_start: 0.8690 (t80) cc_final: 0.8473 (t80) REVERT: A 96 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 100 ILE cc_start: 0.8742 (mm) cc_final: 0.8491 (mm) REVERT: A 124 THR cc_start: 0.8045 (p) cc_final: 0.7838 (p) REVERT: A 129 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8045 (mmmt) REVERT: A 133 PHE cc_start: 0.7007 (m-80) cc_final: 0.6803 (m-80) REVERT: A 191 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 241 LEU cc_start: 0.8601 (mt) cc_final: 0.8282 (mt) REVERT: A 290 ASP cc_start: 0.8274 (t0) cc_final: 0.8053 (t70) REVERT: A 347 PHE cc_start: 0.7050 (m-10) cc_final: 0.6738 (m-10) REVERT: A 368 LEU cc_start: 0.8437 (tt) cc_final: 0.8080 (tt) REVERT: A 388 ASN cc_start: 0.7906 (m110) cc_final: 0.7443 (p0) REVERT: A 546 LEU cc_start: 0.8694 (tp) cc_final: 0.8440 (tp) REVERT: A 643 PHE cc_start: 0.8240 (t80) cc_final: 0.7759 (t80) REVERT: A 719 THR cc_start: 0.8713 (t) cc_final: 0.8451 (p) REVERT: A 737 ASP cc_start: 0.7413 (t0) cc_final: 0.7175 (t0) REVERT: A 748 GLU cc_start: 0.8282 (mp0) cc_final: 0.8039 (mp0) REVERT: A 751 ASN cc_start: 0.8639 (m110) cc_final: 0.8408 (m-40) REVERT: A 759 PHE cc_start: 0.8194 (m-80) cc_final: 0.7871 (m-80) REVERT: A 764 ASN cc_start: 0.8364 (m-40) cc_final: 0.8085 (m110) REVERT: A 776 LYS cc_start: 0.8230 (tttm) cc_final: 0.7797 (tttm) REVERT: A 884 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8486 (t) REVERT: A 950 ASP cc_start: 0.8059 (t0) cc_final: 0.7422 (t0) REVERT: A 954 GLN cc_start: 0.8091 (mt0) cc_final: 0.7599 (mt0) REVERT: A 957 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7670 (tp40) REVERT: A 985 ASP cc_start: 0.7766 (p0) cc_final: 0.7242 (p0) REVERT: A 1002 GLN cc_start: 0.7823 (tp40) cc_final: 0.7296 (tp40) REVERT: A 1005 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7839 (tp40) REVERT: A 1017 GLU cc_start: 0.7698 (tt0) cc_final: 0.7434 (tp30) REVERT: A 1038 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8826 (mmmm) REVERT: A 1116 THR cc_start: 0.8566 (p) cc_final: 0.8200 (p) REVERT: B 129 LYS cc_start: 0.8390 (mmtp) cc_final: 0.8155 (mmtm) REVERT: B 177 MET cc_start: 0.5935 (ppp) cc_final: 0.5715 (ppp) REVERT: B 270 LEU cc_start: 0.8918 (mt) cc_final: 0.8562 (mt) REVERT: B 271 GLN cc_start: 0.8120 (mp10) cc_final: 0.7512 (mp10) REVERT: B 287 ASP cc_start: 0.8170 (t0) cc_final: 0.7933 (t70) REVERT: B 306 PHE cc_start: 0.7921 (m-80) cc_final: 0.7679 (m-80) REVERT: B 351 TYR cc_start: 0.7266 (p90) cc_final: 0.6759 (p90) REVERT: B 353 TRP cc_start: 0.7552 (p-90) cc_final: 0.6003 (p-90) REVERT: B 396 TYR cc_start: 0.7484 (m-80) cc_final: 0.7198 (m-80) REVERT: B 418 ILE cc_start: 0.8089 (pt) cc_final: 0.7825 (mt) REVERT: B 495 TYR cc_start: 0.6212 (m-80) cc_final: 0.5835 (m-80) REVERT: B 514 SER cc_start: 0.8723 (m) cc_final: 0.8439 (t) REVERT: B 574 ASP cc_start: 0.8090 (p0) cc_final: 0.7874 (p0) REVERT: B 619 GLU cc_start: 0.8065 (tp30) cc_final: 0.7612 (tp30) REVERT: B 737 ASP cc_start: 0.7360 (t0) cc_final: 0.7151 (t0) REVERT: B 779 GLN cc_start: 0.8139 (tp40) cc_final: 0.7799 (mm-40) REVERT: B 804 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7957 (mm110) REVERT: B 921 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8351 (mmmm) REVERT: B 925 ASN cc_start: 0.8561 (m-40) cc_final: 0.8330 (m110) REVERT: B 933 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8047 (mtpp) REVERT: B 1005 GLN cc_start: 0.8274 (tp-100) cc_final: 0.8049 (mm-40) REVERT: B 1031 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 41 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8205 (mmmm) REVERT: C 223 LEU cc_start: 0.8651 (mt) cc_final: 0.8434 (mt) REVERT: C 238 PHE cc_start: 0.8003 (p90) cc_final: 0.7647 (p90) REVERT: C 424 LYS cc_start: 0.7583 (tppt) cc_final: 0.7334 (tppt) REVERT: C 427 ASP cc_start: 0.7774 (m-30) cc_final: 0.7373 (t0) REVERT: C 430 THR cc_start: 0.9131 (m) cc_final: 0.8770 (p) REVERT: C 466 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7473 (ttp-110) REVERT: C 474 GLN cc_start: 0.7567 (pt0) cc_final: 0.7234 (pp30) REVERT: C 643 PHE cc_start: 0.8613 (t80) cc_final: 0.8151 (t80) REVERT: C 655 HIS cc_start: 0.8656 (t-170) cc_final: 0.8308 (t-170) REVERT: C 745 ASP cc_start: 0.6413 (p0) cc_final: 0.6168 (p0) REVERT: C 764 ASN cc_start: 0.8267 (m-40) cc_final: 0.7950 (m-40) REVERT: C 855 PHE cc_start: 0.5594 (t80) cc_final: 0.5200 (t80) REVERT: C 904 TYR cc_start: 0.8150 (m-80) cc_final: 0.7787 (m-10) REVERT: C 918 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 928 ASN cc_start: 0.8773 (m-40) cc_final: 0.8411 (m-40) REVERT: C 960 ASN cc_start: 0.8569 (t0) cc_final: 0.8308 (t0) REVERT: C 993 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 1002 GLN cc_start: 0.8178 (tt0) cc_final: 0.7859 (tt0) REVERT: C 1017 GLU cc_start: 0.7752 (tt0) cc_final: 0.7291 (tt0) REVERT: C 1041 ASP cc_start: 0.7800 (t0) cc_final: 0.7568 (m-30) REVERT: C 1119 ASN cc_start: 0.8043 (m-40) cc_final: 0.7839 (m-40) outliers start: 23 outliers final: 9 residues processed: 795 average time/residue: 0.1885 time to fit residues: 231.3127 Evaluate side-chains 629 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 616 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 658 ASN A 751 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 52 GLN B 388 ASN B 613 GLN B 751 ASN B1118 HIS C 14 GLN C 188 ASN C 271 GLN C 343 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 784 GLN C 804 GLN C 901 GLN C 907 ASN C 926 GLN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081396 restraints weight = 69515.723| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.48 r_work: 0.3144 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27538 Z= 0.178 Angle : 0.827 12.803 37638 Z= 0.403 Chirality : 0.050 0.527 4487 Planarity : 0.004 0.059 4690 Dihedral : 10.795 108.421 5491 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.11 % Allowed : 11.24 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3223 helix: 0.79 (0.19), residues: 728 sheet: 0.25 (0.20), residues: 639 loop : -1.10 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1107 TYR 0.024 0.002 TYR B 265 PHE 0.035 0.002 PHE B1148 TRP 0.020 0.002 TRP C 64 HIS 0.004 0.001 HIS B1118 Details of bonding type rmsd covalent geometry : bond 0.00389 (27404) covalent geometry : angle 0.76400 (37278) SS BOND : bond 0.00722 ( 42) SS BOND : angle 2.50776 ( 84) hydrogen bonds : bond 0.04812 ( 1105) hydrogen bonds : angle 6.35325 ( 3063) link_ALPHA1-4 : bond 0.01736 ( 6) link_ALPHA1-4 : angle 3.19680 ( 18) link_BETA1-4 : bond 0.00425 ( 29) link_BETA1-4 : angle 2.17680 ( 87) link_BETA1-6 : bond 0.01355 ( 3) link_BETA1-6 : angle 2.04879 ( 9) link_NAG-ASN : bond 0.00769 ( 54) link_NAG-ASN : angle 4.15717 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 636 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8240 (mp) cc_final: 0.7976 (tt) REVERT: A 100 ILE cc_start: 0.8728 (mm) cc_final: 0.8320 (mm) REVERT: A 129 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8267 (mmmt) REVERT: A 191 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7861 (mt-10) REVERT: A 200 TYR cc_start: 0.6857 (m-80) cc_final: 0.6522 (m-80) REVERT: A 236 THR cc_start: 0.8739 (p) cc_final: 0.8500 (t) REVERT: A 269 TYR cc_start: 0.8648 (m-10) cc_final: 0.8263 (m-10) REVERT: A 290 ASP cc_start: 0.8486 (t0) cc_final: 0.8211 (t0) REVERT: A 351 TYR cc_start: 0.7490 (p90) cc_final: 0.7288 (p90) REVERT: A 353 TRP cc_start: 0.4140 (p-90) cc_final: 0.3865 (p-90) REVERT: A 389 ASP cc_start: 0.8782 (m-30) cc_final: 0.8270 (p0) REVERT: A 436 TRP cc_start: 0.7285 (p90) cc_final: 0.7027 (p90) REVERT: A 546 LEU cc_start: 0.8833 (tp) cc_final: 0.8596 (tp) REVERT: A 643 PHE cc_start: 0.8539 (t80) cc_final: 0.7977 (t80) REVERT: A 759 PHE cc_start: 0.8425 (m-80) cc_final: 0.8135 (m-80) REVERT: A 764 ASN cc_start: 0.8680 (m-40) cc_final: 0.8359 (m110) REVERT: A 773 GLU cc_start: 0.8151 (tt0) cc_final: 0.7938 (tt0) REVERT: A 950 ASP cc_start: 0.8568 (t0) cc_final: 0.8284 (t0) REVERT: A 1005 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8187 (tp40) REVERT: A 1038 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8950 (mmmm) REVERT: A 1091 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: B 129 LYS cc_start: 0.8383 (mmtp) cc_final: 0.7292 (mmmm) REVERT: B 133 PHE cc_start: 0.7962 (m-80) cc_final: 0.7725 (m-80) REVERT: B 169 GLU cc_start: 0.7676 (mp0) cc_final: 0.6968 (mp0) REVERT: B 270 LEU cc_start: 0.8825 (mt) cc_final: 0.8610 (mt) REVERT: B 271 GLN cc_start: 0.8402 (mp10) cc_final: 0.7950 (mp10) REVERT: B 274 THR cc_start: 0.8882 (m) cc_final: 0.8305 (t) REVERT: B 301 CYS cc_start: 0.7976 (t) cc_final: 0.7752 (t) REVERT: B 353 TRP cc_start: 0.7734 (p-90) cc_final: 0.6898 (p-90) REVERT: B 398 ASP cc_start: 0.7756 (m-30) cc_final: 0.7220 (m-30) REVERT: B 436 TRP cc_start: 0.7200 (p90) cc_final: 0.6979 (p90) REVERT: B 483 VAL cc_start: 0.7414 (m) cc_final: 0.7090 (t) REVERT: B 619 GLU cc_start: 0.8009 (tp30) cc_final: 0.7616 (tp30) REVERT: B 765 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: B 804 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8551 (mm110) REVERT: B 858 LEU cc_start: 0.8918 (mt) cc_final: 0.8697 (mm) REVERT: B 921 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8612 (mmmm) REVERT: B 1041 ASP cc_start: 0.8491 (t70) cc_final: 0.8248 (t0) REVERT: C 14 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5199 (pp30) REVERT: C 96 GLU cc_start: 0.7709 (tp30) cc_final: 0.7490 (tp30) REVERT: C 153 MET cc_start: 0.7139 (ptp) cc_final: 0.6664 (ppp) REVERT: C 206 LYS cc_start: 0.8497 (tppt) cc_final: 0.8111 (tptm) REVERT: C 211 ASN cc_start: 0.7880 (p0) cc_final: 0.7462 (m-40) REVERT: C 238 PHE cc_start: 0.8285 (p90) cc_final: 0.7977 (p90) REVERT: C 304 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8693 (mmmt) REVERT: C 424 LYS cc_start: 0.7567 (tppt) cc_final: 0.7274 (tppt) REVERT: C 455 LEU cc_start: 0.8851 (tp) cc_final: 0.8545 (tp) REVERT: C 516 GLU cc_start: 0.7287 (mp0) cc_final: 0.6803 (mp0) REVERT: C 773 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 960 ASN cc_start: 0.8713 (t0) cc_final: 0.8292 (t0) REVERT: C 988 GLU cc_start: 0.7979 (tt0) cc_final: 0.7743 (tt0) REVERT: C 993 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9088 (mp) REVERT: C 1041 ASP cc_start: 0.8353 (t0) cc_final: 0.8038 (t0) outliers start: 60 outliers final: 30 residues processed: 670 average time/residue: 0.1765 time to fit residues: 184.9414 Evaluate side-chains 609 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 577 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 311 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 872 GLN A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 751 ASN B1005 GLN C 14 GLN C 271 GLN C 343 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 777 ASN C 784 GLN C 787 GLN C 804 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.077734 restraints weight = 70335.504| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.44 r_work: 0.3070 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 27538 Z= 0.333 Angle : 0.880 14.673 37638 Z= 0.426 Chirality : 0.052 0.535 4487 Planarity : 0.005 0.060 4690 Dihedral : 10.362 115.060 5466 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.58 % Allowed : 12.89 % Favored : 83.53 % 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: -0.66 (0.14), residues: 3223 helix: 0.97 (0.19), residues: 747 sheet: -0.12 (0.19), residues: 653 loop : -1.18 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 346 TYR 0.024 0.003 TYR B 351 PHE 0.034 0.003 PHE B1148 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00753 (27404) covalent geometry : angle 0.82537 (37278) SS BOND : bond 0.00701 ( 42) SS BOND : angle 2.47162 ( 84) hydrogen bonds : bond 0.05015 ( 1105) hydrogen bonds : angle 6.27652 ( 3063) link_ALPHA1-4 : bond 0.01987 ( 6) link_ALPHA1-4 : angle 3.35711 ( 18) link_BETA1-4 : bond 0.00539 ( 29) link_BETA1-4 : angle 2.32712 ( 87) link_BETA1-6 : bond 0.01303 ( 3) link_BETA1-6 : angle 2.03330 ( 9) link_NAG-ASN : bond 0.00712 ( 54) link_NAG-ASN : angle 3.93448 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 587 time to evaluate : 0.978 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 18 LEU cc_start: 0.8304 (mp) cc_final: 0.8090 (tt) REVERT: A 128 ILE cc_start: 0.8847 (mp) cc_final: 0.8238 (mp) REVERT: A 129 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8282 (mmpt) REVERT: A 180 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6544 (pp20) REVERT: A 236 THR cc_start: 0.8915 (p) cc_final: 0.8706 (t) REVERT: A 269 TYR cc_start: 0.8687 (m-10) cc_final: 0.8350 (m-10) REVERT: A 290 ASP cc_start: 0.8497 (t0) cc_final: 0.8208 (t70) REVERT: A 351 TYR cc_start: 0.7463 (p90) cc_final: 0.7251 (p90) REVERT: A 538 CYS cc_start: 0.6368 (t) cc_final: 0.6074 (t) REVERT: A 602 THR cc_start: 0.8401 (m) cc_final: 0.7960 (p) REVERT: A 764 ASN cc_start: 0.8752 (m-40) cc_final: 0.8401 (m110) REVERT: A 790 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8159 (mtmt) REVERT: A 950 ASP cc_start: 0.8528 (t0) cc_final: 0.8223 (t0) REVERT: A 1038 LYS cc_start: 0.9299 (mmmt) cc_final: 0.9092 (mmmm) REVERT: B 51 THR cc_start: 0.9009 (t) cc_final: 0.8716 (p) REVERT: B 52 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8248 (tp-100) REVERT: B 270 LEU cc_start: 0.8946 (mt) cc_final: 0.8673 (mt) REVERT: B 271 GLN cc_start: 0.8351 (mp10) cc_final: 0.7627 (mp10) REVERT: B 326 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8150 (mp) REVERT: B 353 TRP cc_start: 0.7716 (p-90) cc_final: 0.7042 (p-90) REVERT: B 604 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8480 (t) REVERT: B 619 GLU cc_start: 0.8155 (tp30) cc_final: 0.7751 (tp30) REVERT: B 921 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8623 (mmmm) REVERT: B 1041 ASP cc_start: 0.8537 (t70) cc_final: 0.8304 (t0) REVERT: C 14 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5170 (pp30) REVERT: C 153 MET cc_start: 0.7184 (ptp) cc_final: 0.6835 (ppp) REVERT: C 211 ASN cc_start: 0.8012 (p0) cc_final: 0.7488 (m-40) REVERT: C 238 PHE cc_start: 0.8348 (p90) cc_final: 0.8007 (p90) REVERT: C 396 TYR cc_start: 0.8325 (m-80) cc_final: 0.7255 (m-80) REVERT: C 430 THR cc_start: 0.9251 (m) cc_final: 0.8906 (p) REVERT: C 455 LEU cc_start: 0.8883 (tp) cc_final: 0.8591 (tp) REVERT: C 515 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7353 (p90) REVERT: C 516 GLU cc_start: 0.7536 (mp0) cc_final: 0.7063 (mp0) REVERT: C 544 ASN cc_start: 0.8488 (m-40) cc_final: 0.8203 (m110) REVERT: C 586 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: C 619 GLU cc_start: 0.7308 (mp0) cc_final: 0.7043 (mp0) REVERT: C 855 PHE cc_start: 0.6347 (t80) cc_final: 0.5854 (t80) REVERT: C 918 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8289 (mt-10) REVERT: C 960 ASN cc_start: 0.8723 (t0) cc_final: 0.8467 (t0) REVERT: C 993 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9087 (mp) outliers start: 102 outliers final: 65 residues processed: 651 average time/residue: 0.1766 time to fit residues: 180.2805 Evaluate side-chains 620 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 547 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 300 optimal weight: 0.5980 chunk 238 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 99 ASN B 196 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 926 GLN B1005 GLN C 14 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 777 ASN C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080033 restraints weight = 69972.410| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.48 r_work: 0.3107 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27538 Z= 0.165 Angle : 0.755 13.141 37638 Z= 0.361 Chirality : 0.048 0.550 4487 Planarity : 0.004 0.043 4690 Dihedral : 9.438 108.606 5465 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.09 % Allowed : 14.89 % Favored : 82.02 % 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: -0.48 (0.14), residues: 3223 helix: 1.30 (0.20), residues: 745 sheet: 0.01 (0.19), residues: 633 loop : -1.15 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 357 TYR 0.029 0.002 TYR B 351 PHE 0.036 0.002 PHE C 497 TRP 0.013 0.001 TRP C 436 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00369 (27404) covalent geometry : angle 0.70673 (37278) SS BOND : bond 0.00597 ( 42) SS BOND : angle 2.09232 ( 84) hydrogen bonds : bond 0.04219 ( 1105) hydrogen bonds : angle 5.98455 ( 3063) link_ALPHA1-4 : bond 0.01740 ( 6) link_ALPHA1-4 : angle 3.24576 ( 18) link_BETA1-4 : bond 0.00396 ( 29) link_BETA1-4 : angle 1.91431 ( 87) link_BETA1-6 : bond 0.01465 ( 3) link_BETA1-6 : angle 2.04984 ( 9) link_NAG-ASN : bond 0.00570 ( 54) link_NAG-ASN : angle 3.46677 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 603 time to evaluate : 0.987 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 18 LEU cc_start: 0.8431 (mp) cc_final: 0.8197 (tt) REVERT: A 129 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8260 (mmmt) REVERT: A 224 GLU cc_start: 0.8373 (mp0) cc_final: 0.8123 (mp0) REVERT: A 236 THR cc_start: 0.8823 (p) cc_final: 0.8610 (t) REVERT: A 244 LEU cc_start: 0.6892 (mt) cc_final: 0.6212 (mm) REVERT: A 265 TYR cc_start: 0.7597 (p90) cc_final: 0.7241 (p90) REVERT: A 269 TYR cc_start: 0.8600 (m-10) cc_final: 0.8163 (m-10) REVERT: A 290 ASP cc_start: 0.8480 (t0) cc_final: 0.8170 (t70) REVERT: A 351 TYR cc_start: 0.7411 (p90) cc_final: 0.7201 (p90) REVERT: A 602 THR cc_start: 0.8321 (m) cc_final: 0.7875 (p) REVERT: A 764 ASN cc_start: 0.8690 (m-40) cc_final: 0.8271 (m110) REVERT: A 790 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7977 (mtmt) REVERT: A 950 ASP cc_start: 0.8490 (t0) cc_final: 0.8218 (t0) REVERT: B 52 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8256 (tp-100) REVERT: B 270 LEU cc_start: 0.8880 (mt) cc_final: 0.8612 (mt) REVERT: B 271 GLN cc_start: 0.8365 (mp10) cc_final: 0.7646 (mp10) REVERT: B 274 THR cc_start: 0.9134 (m) cc_final: 0.8619 (t) REVERT: B 290 ASP cc_start: 0.7741 (t0) cc_final: 0.7411 (t0) REVERT: B 353 TRP cc_start: 0.7773 (p-90) cc_final: 0.7355 (p-90) REVERT: B 408 ARG cc_start: 0.8207 (mpp-170) cc_final: 0.7981 (mmp80) REVERT: B 483 VAL cc_start: 0.7569 (m) cc_final: 0.7220 (t) REVERT: B 495 TYR cc_start: 0.6395 (m-80) cc_final: 0.6131 (m-80) REVERT: B 591 SER cc_start: 0.8762 (t) cc_final: 0.8527 (p) REVERT: B 604 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8397 (t) REVERT: B 921 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8559 (mmmm) REVERT: B 988 GLU cc_start: 0.8061 (pm20) cc_final: 0.7757 (pm20) REVERT: B 1041 ASP cc_start: 0.8518 (t70) cc_final: 0.8259 (t0) REVERT: C 41 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8131 (mmmm) REVERT: C 111 ASP cc_start: 0.7378 (p0) cc_final: 0.7135 (p0) REVERT: C 153 MET cc_start: 0.7108 (ptp) cc_final: 0.6835 (ppp) REVERT: C 211 ASN cc_start: 0.7504 (p0) cc_final: 0.7286 (m-40) REVERT: C 238 PHE cc_start: 0.8290 (p90) cc_final: 0.8075 (p90) REVERT: C 424 LYS cc_start: 0.7525 (tppt) cc_final: 0.7279 (tppt) REVERT: C 430 THR cc_start: 0.9191 (m) cc_final: 0.8981 (p) REVERT: C 455 LEU cc_start: 0.8896 (tp) cc_final: 0.8620 (tp) REVERT: C 516 GLU cc_start: 0.7467 (mp0) cc_final: 0.7022 (mp0) REVERT: C 586 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: C 619 GLU cc_start: 0.7158 (mp0) cc_final: 0.6915 (mp0) REVERT: C 855 PHE cc_start: 0.6314 (t80) cc_final: 0.5864 (t80) REVERT: C 868 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8108 (mm-30) REVERT: C 918 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8263 (mt-10) REVERT: C 960 ASN cc_start: 0.8694 (t0) cc_final: 0.8443 (t0) REVERT: C 993 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9075 (mp) REVERT: C 1126 CYS cc_start: 0.7548 (m) cc_final: 0.7215 (m) REVERT: C 1138 TYR cc_start: 0.8231 (t80) cc_final: 0.7767 (t80) outliers start: 88 outliers final: 49 residues processed: 656 average time/residue: 0.1784 time to fit residues: 183.6961 Evaluate side-chains 621 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 568 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 993 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 229 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 751 ASN A 872 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1135 ASN B 30 ASN B 99 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B1005 GLN C 14 GLN C 271 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079900 restraints weight = 69900.809| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.41 r_work: 0.3113 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27538 Z= 0.179 Angle : 0.753 12.072 37638 Z= 0.361 Chirality : 0.048 0.525 4487 Planarity : 0.004 0.074 4690 Dihedral : 8.959 108.943 5465 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.58 % Allowed : 15.84 % Favored : 80.58 % 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: -0.46 (0.14), residues: 3223 helix: 1.34 (0.19), residues: 752 sheet: -0.06 (0.19), residues: 642 loop : -1.14 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.024 0.002 TYR B 351 PHE 0.032 0.002 PHE C 497 TRP 0.013 0.001 TRP A 353 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00405 (27404) covalent geometry : angle 0.70627 (37278) SS BOND : bond 0.00523 ( 42) SS BOND : angle 2.25816 ( 84) hydrogen bonds : bond 0.04130 ( 1105) hydrogen bonds : angle 5.92606 ( 3063) link_ALPHA1-4 : bond 0.01893 ( 6) link_ALPHA1-4 : angle 3.33260 ( 18) link_BETA1-4 : bond 0.00393 ( 29) link_BETA1-4 : angle 1.87456 ( 87) link_BETA1-6 : bond 0.01475 ( 3) link_BETA1-6 : angle 2.01171 ( 9) link_NAG-ASN : bond 0.00558 ( 54) link_NAG-ASN : angle 3.31316 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 579 time to evaluate : 1.010 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 129 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8203 (mmmt) REVERT: A 236 THR cc_start: 0.8857 (p) cc_final: 0.8596 (t) REVERT: A 244 LEU cc_start: 0.7083 (mt) cc_final: 0.6439 (mm) REVERT: A 290 ASP cc_start: 0.8439 (t0) cc_final: 0.8127 (t70) REVERT: A 387 LEU cc_start: 0.8707 (mp) cc_final: 0.8466 (tp) REVERT: A 436 TRP cc_start: 0.7158 (p90) cc_final: 0.6779 (p90) REVERT: A 495 TYR cc_start: 0.5914 (m-80) cc_final: 0.5645 (m-80) REVERT: A 602 THR cc_start: 0.8336 (m) cc_final: 0.7913 (p) REVERT: A 673 SER cc_start: 0.8439 (m) cc_final: 0.8226 (m) REVERT: A 764 ASN cc_start: 0.8727 (m-40) cc_final: 0.8308 (m110) REVERT: A 790 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7993 (mtmt) REVERT: A 950 ASP cc_start: 0.8463 (t0) cc_final: 0.8232 (t0) REVERT: A 957 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8320 (tp40) REVERT: B 51 THR cc_start: 0.8999 (t) cc_final: 0.8689 (p) REVERT: B 52 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (tp-100) REVERT: B 270 LEU cc_start: 0.8883 (mt) cc_final: 0.8622 (mt) REVERT: B 271 GLN cc_start: 0.8365 (mp10) cc_final: 0.7650 (mp10) REVERT: B 290 ASP cc_start: 0.7803 (t0) cc_final: 0.7526 (t0) REVERT: B 353 TRP cc_start: 0.7787 (p-90) cc_final: 0.7399 (p-90) REVERT: B 591 SER cc_start: 0.8752 (t) cc_final: 0.8517 (p) REVERT: B 604 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (t) REVERT: B 921 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8529 (mmmm) REVERT: B 977 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 1041 ASP cc_start: 0.8523 (t70) cc_final: 0.8262 (t0) REVERT: C 14 GLN cc_start: 0.6274 (OUTLIER) cc_final: 0.6019 (pp30) REVERT: C 153 MET cc_start: 0.7039 (ptp) cc_final: 0.6801 (ppp) REVERT: C 211 ASN cc_start: 0.7643 (p0) cc_final: 0.7424 (m-40) REVERT: C 238 PHE cc_start: 0.8310 (p90) cc_final: 0.7972 (p90) REVERT: C 424 LYS cc_start: 0.7554 (tppt) cc_final: 0.7290 (tppt) REVERT: C 430 THR cc_start: 0.9197 (m) cc_final: 0.8994 (p) REVERT: C 437 ASN cc_start: 0.7180 (m-40) cc_final: 0.6961 (m-40) REVERT: C 453 TYR cc_start: 0.7305 (p90) cc_final: 0.6814 (p90) REVERT: C 516 GLU cc_start: 0.7496 (mp0) cc_final: 0.7165 (mp0) REVERT: C 570 ASP cc_start: 0.7722 (m-30) cc_final: 0.7410 (p0) REVERT: C 586 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: C 619 GLU cc_start: 0.7134 (mp0) cc_final: 0.6883 (mp0) REVERT: C 855 PHE cc_start: 0.6341 (t80) cc_final: 0.5843 (t80) REVERT: C 868 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8124 (mm-30) REVERT: C 918 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8247 (mt-10) REVERT: C 960 ASN cc_start: 0.8695 (t0) cc_final: 0.8483 (t0) REVERT: C 993 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9066 (mp) REVERT: C 1126 CYS cc_start: 0.7466 (m) cc_final: 0.7230 (m) REVERT: C 1138 TYR cc_start: 0.8270 (t80) cc_final: 0.7758 (t80) outliers start: 102 outliers final: 71 residues processed: 641 average time/residue: 0.1754 time to fit residues: 177.6402 Evaluate side-chains 631 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 554 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 112 optimal weight: 0.0020 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1005 GLN B 30 ASN B 99 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B 960 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 544 ASN C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080028 restraints weight = 70614.744| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.47 r_work: 0.3110 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27538 Z= 0.184 Angle : 0.746 11.771 37638 Z= 0.357 Chirality : 0.048 0.504 4487 Planarity : 0.004 0.063 4690 Dihedral : 8.529 108.205 5465 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.58 % Allowed : 16.72 % Favored : 79.70 % 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: -0.44 (0.14), residues: 3223 helix: 1.42 (0.20), residues: 746 sheet: 0.02 (0.19), residues: 634 loop : -1.17 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 102 TYR 0.022 0.002 TYR A 495 PHE 0.026 0.002 PHE A 157 TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00416 (27404) covalent geometry : angle 0.70117 (37278) SS BOND : bond 0.00418 ( 42) SS BOND : angle 2.02623 ( 84) hydrogen bonds : bond 0.04093 ( 1105) hydrogen bonds : angle 5.85008 ( 3063) link_ALPHA1-4 : bond 0.02080 ( 6) link_ALPHA1-4 : angle 3.59556 ( 18) link_BETA1-4 : bond 0.00385 ( 29) link_BETA1-4 : angle 1.85904 ( 87) link_BETA1-6 : bond 0.01659 ( 3) link_BETA1-6 : angle 1.95210 ( 9) link_NAG-ASN : bond 0.00543 ( 54) link_NAG-ASN : angle 3.23726 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 579 time to evaluate : 0.863 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 24 LEU cc_start: 0.6722 (mm) cc_final: 0.6471 (mt) REVERT: A 129 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8156 (mmmt) REVERT: A 191 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 224 GLU cc_start: 0.8329 (mp0) cc_final: 0.8113 (mp0) REVERT: A 236 THR cc_start: 0.8896 (p) cc_final: 0.8641 (t) REVERT: A 244 LEU cc_start: 0.6974 (mt) cc_final: 0.6415 (mm) REVERT: A 290 ASP cc_start: 0.8433 (t0) cc_final: 0.8133 (t0) REVERT: A 436 TRP cc_start: 0.7137 (p90) cc_final: 0.6740 (p90) REVERT: A 591 SER cc_start: 0.9111 (t) cc_final: 0.8739 (p) REVERT: A 602 THR cc_start: 0.8339 (m) cc_final: 0.7925 (p) REVERT: A 673 SER cc_start: 0.8417 (m) cc_final: 0.8202 (m) REVERT: A 764 ASN cc_start: 0.8730 (m-40) cc_final: 0.8306 (m110) REVERT: A 790 LYS cc_start: 0.8507 (mtpt) cc_final: 0.7997 (mtmt) REVERT: A 950 ASP cc_start: 0.8475 (t0) cc_final: 0.8249 (t0) REVERT: A 957 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8326 (tp40) REVERT: B 51 THR cc_start: 0.8998 (t) cc_final: 0.8700 (p) REVERT: B 52 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8276 (tp-100) REVERT: B 204 TYR cc_start: 0.8941 (m-80) cc_final: 0.8677 (m-80) REVERT: B 270 LEU cc_start: 0.8885 (mt) cc_final: 0.8629 (mt) REVERT: B 271 GLN cc_start: 0.8364 (mp10) cc_final: 0.7637 (mp10) REVERT: B 290 ASP cc_start: 0.7808 (t0) cc_final: 0.7534 (t0) REVERT: B 351 TYR cc_start: 0.7806 (p90) cc_final: 0.7603 (p90) REVERT: B 353 TRP cc_start: 0.7824 (p-90) cc_final: 0.7338 (p-90) REVERT: B 408 ARG cc_start: 0.8259 (mpp-170) cc_final: 0.8049 (mmp80) REVERT: B 591 SER cc_start: 0.8715 (t) cc_final: 0.8438 (p) REVERT: B 604 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8405 (t) REVERT: B 921 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8537 (mmmm) REVERT: B 977 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8691 (mp) REVERT: C 238 PHE cc_start: 0.8180 (p90) cc_final: 0.7927 (p90) REVERT: C 424 LYS cc_start: 0.7543 (tppt) cc_final: 0.7282 (tppt) REVERT: C 437 ASN cc_start: 0.7131 (m-40) cc_final: 0.6864 (m-40) REVERT: C 473 TYR cc_start: 0.6603 (t80) cc_final: 0.6301 (t80) REVERT: C 515 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7490 (p90) REVERT: C 516 GLU cc_start: 0.7502 (mp0) cc_final: 0.7178 (mp0) REVERT: C 570 ASP cc_start: 0.7761 (m-30) cc_final: 0.7458 (p0) REVERT: C 586 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: C 619 GLU cc_start: 0.7211 (mp0) cc_final: 0.6976 (mp0) REVERT: C 855 PHE cc_start: 0.6323 (t80) cc_final: 0.5861 (t80) REVERT: C 918 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8233 (mt-10) REVERT: C 960 ASN cc_start: 0.8718 (t0) cc_final: 0.8406 (t0) REVERT: C 1126 CYS cc_start: 0.7542 (m) cc_final: 0.7305 (m) REVERT: C 1138 TYR cc_start: 0.8288 (t80) cc_final: 0.7788 (t80) outliers start: 102 outliers final: 68 residues processed: 642 average time/residue: 0.1726 time to fit residues: 174.9800 Evaluate side-chains 629 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 556 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 chunk 259 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 751 ASN A 872 GLN A1005 GLN B 30 ASN B 99 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1005 GLN C 14 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 544 ASN C 580 GLN C 607 GLN C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080103 restraints weight = 70500.569| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.49 r_work: 0.3112 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27538 Z= 0.147 Angle : 0.725 11.771 37638 Z= 0.348 Chirality : 0.047 0.500 4487 Planarity : 0.004 0.059 4690 Dihedral : 8.018 105.335 5463 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.27 % Allowed : 17.39 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3223 helix: 1.60 (0.20), residues: 737 sheet: 0.17 (0.19), residues: 630 loop : -1.12 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.032 0.002 TYR A 904 PHE 0.038 0.002 PHE C 456 TRP 0.025 0.001 TRP A 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00333 (27404) covalent geometry : angle 0.68355 (37278) SS BOND : bond 0.00376 ( 42) SS BOND : angle 1.70572 ( 84) hydrogen bonds : bond 0.03872 ( 1105) hydrogen bonds : angle 5.75151 ( 3063) link_ALPHA1-4 : bond 0.01786 ( 6) link_ALPHA1-4 : angle 3.56144 ( 18) link_BETA1-4 : bond 0.00402 ( 29) link_BETA1-4 : angle 1.72054 ( 87) link_BETA1-6 : bond 0.01542 ( 3) link_BETA1-6 : angle 1.85542 ( 9) link_NAG-ASN : bond 0.00534 ( 54) link_NAG-ASN : angle 3.12691 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 586 time to evaluate : 0.963 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 24 LEU cc_start: 0.6767 (mm) cc_final: 0.6505 (mt) REVERT: A 129 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7929 (mmmt) REVERT: A 191 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 224 GLU cc_start: 0.8385 (mp0) cc_final: 0.8108 (mp0) REVERT: A 236 THR cc_start: 0.8897 (p) cc_final: 0.8625 (t) REVERT: A 244 LEU cc_start: 0.6801 (mt) cc_final: 0.6347 (mm) REVERT: A 265 TYR cc_start: 0.7494 (p90) cc_final: 0.7236 (p90) REVERT: A 290 ASP cc_start: 0.8454 (t0) cc_final: 0.8151 (t0) REVERT: A 387 LEU cc_start: 0.8802 (mp) cc_final: 0.8557 (tp) REVERT: A 495 TYR cc_start: 0.6049 (m-80) cc_final: 0.5543 (m-80) REVERT: A 591 SER cc_start: 0.9041 (t) cc_final: 0.8588 (p) REVERT: A 602 THR cc_start: 0.8284 (m) cc_final: 0.7896 (p) REVERT: A 673 SER cc_start: 0.8321 (m) cc_final: 0.8117 (m) REVERT: A 764 ASN cc_start: 0.8743 (m-40) cc_final: 0.8311 (m110) REVERT: A 790 LYS cc_start: 0.8554 (mtpt) cc_final: 0.7998 (mtmt) REVERT: A 935 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8513 (tt0) REVERT: A 957 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8367 (tp40) REVERT: A 1107 ARG cc_start: 0.8549 (ttm110) cc_final: 0.6100 (ttm170) REVERT: B 51 THR cc_start: 0.8989 (t) cc_final: 0.8656 (p) REVERT: B 52 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (tp-100) REVERT: B 204 TYR cc_start: 0.8973 (m-80) cc_final: 0.8719 (m-80) REVERT: B 270 LEU cc_start: 0.8860 (mt) cc_final: 0.8601 (mt) REVERT: B 271 GLN cc_start: 0.8373 (mp10) cc_final: 0.7634 (mp10) REVERT: B 290 ASP cc_start: 0.7812 (t0) cc_final: 0.7542 (t0) REVERT: B 304 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8827 (mmmm) REVERT: B 306 PHE cc_start: 0.8452 (m-80) cc_final: 0.8108 (t80) REVERT: B 351 TYR cc_start: 0.7869 (p90) cc_final: 0.7626 (p90) REVERT: B 353 TRP cc_start: 0.7800 (p-90) cc_final: 0.7364 (p-90) REVERT: B 408 ARG cc_start: 0.8267 (mpp-170) cc_final: 0.8039 (mmp80) REVERT: B 591 SER cc_start: 0.8683 (t) cc_final: 0.8187 (p) REVERT: B 604 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8380 (t) REVERT: B 619 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: B 921 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8543 (mmmm) REVERT: B 977 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 1005 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8435 (mm-40) REVERT: B 1041 ASP cc_start: 0.8576 (t70) cc_final: 0.8326 (t0) REVERT: C 424 LYS cc_start: 0.7606 (tppt) cc_final: 0.7329 (tppt) REVERT: C 473 TYR cc_start: 0.6695 (t80) cc_final: 0.6304 (t80) REVERT: C 516 GLU cc_start: 0.7528 (mp0) cc_final: 0.7201 (mp0) REVERT: C 570 ASP cc_start: 0.7791 (m-30) cc_final: 0.7432 (p0) REVERT: C 586 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: C 855 PHE cc_start: 0.6429 (t80) cc_final: 0.5951 (t80) REVERT: C 868 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8153 (mm-30) REVERT: C 1126 CYS cc_start: 0.7485 (m) cc_final: 0.7255 (m) outliers start: 93 outliers final: 68 residues processed: 640 average time/residue: 0.1781 time to fit residues: 179.1432 Evaluate side-chains 640 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 566 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 229 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 872 GLN A1005 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B 804 GLN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 544 ASN C 580 GLN C 777 ASN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079713 restraints weight = 70964.354| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.49 r_work: 0.3107 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27538 Z= 0.170 Angle : 0.743 14.691 37638 Z= 0.357 Chirality : 0.047 0.489 4487 Planarity : 0.004 0.057 4690 Dihedral : 7.853 105.227 5461 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.13 % Allowed : 18.23 % Favored : 78.64 % 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: -0.33 (0.14), residues: 3223 helix: 1.56 (0.20), residues: 733 sheet: 0.10 (0.20), residues: 612 loop : -1.09 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 102 TYR 0.036 0.002 TYR A 904 PHE 0.046 0.002 PHE B 497 TRP 0.023 0.001 TRP A 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00388 (27404) covalent geometry : angle 0.70249 (37278) SS BOND : bond 0.00419 ( 42) SS BOND : angle 1.76113 ( 84) hydrogen bonds : bond 0.03927 ( 1105) hydrogen bonds : angle 5.75157 ( 3063) link_ALPHA1-4 : bond 0.01877 ( 6) link_ALPHA1-4 : angle 3.57834 ( 18) link_BETA1-4 : bond 0.00382 ( 29) link_BETA1-4 : angle 1.74478 ( 87) link_BETA1-6 : bond 0.01433 ( 3) link_BETA1-6 : angle 1.77488 ( 9) link_NAG-ASN : bond 0.00520 ( 54) link_NAG-ASN : angle 3.11646 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 572 time to evaluate : 0.996 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 24 LEU cc_start: 0.6799 (mm) cc_final: 0.6522 (mt) REVERT: A 102 ARG cc_start: 0.7273 (mmm160) cc_final: 0.7051 (mmm160) REVERT: A 129 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7934 (mmmt) REVERT: A 191 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 224 GLU cc_start: 0.8413 (mp0) cc_final: 0.8139 (mp0) REVERT: A 236 THR cc_start: 0.8909 (p) cc_final: 0.8644 (t) REVERT: A 244 LEU cc_start: 0.6795 (mt) cc_final: 0.6337 (mm) REVERT: A 290 ASP cc_start: 0.8444 (t0) cc_final: 0.8122 (t0) REVERT: A 368 LEU cc_start: 0.8266 (pp) cc_final: 0.7803 (mp) REVERT: A 387 LEU cc_start: 0.8789 (mp) cc_final: 0.8549 (tp) REVERT: A 495 TYR cc_start: 0.6073 (m-80) cc_final: 0.5482 (m-80) REVERT: A 591 SER cc_start: 0.9020 (t) cc_final: 0.8616 (p) REVERT: A 602 THR cc_start: 0.8308 (m) cc_final: 0.7910 (p) REVERT: A 673 SER cc_start: 0.8336 (m) cc_final: 0.8132 (m) REVERT: A 764 ASN cc_start: 0.8742 (m-40) cc_final: 0.8329 (m110) REVERT: A 790 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8009 (mtmt) REVERT: A 950 ASP cc_start: 0.8539 (t70) cc_final: 0.8263 (t0) REVERT: A 957 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8332 (tp40) REVERT: B 51 THR cc_start: 0.8982 (t) cc_final: 0.8660 (p) REVERT: B 52 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8290 (tp-100) REVERT: B 204 TYR cc_start: 0.8970 (m-80) cc_final: 0.8724 (m-80) REVERT: B 270 LEU cc_start: 0.8864 (mt) cc_final: 0.8605 (mt) REVERT: B 271 GLN cc_start: 0.8367 (mp10) cc_final: 0.7633 (mp10) REVERT: B 290 ASP cc_start: 0.7859 (t0) cc_final: 0.7599 (t0) REVERT: B 304 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8816 (mmmm) REVERT: B 306 PHE cc_start: 0.8433 (m-80) cc_final: 0.8159 (t80) REVERT: B 351 TYR cc_start: 0.7859 (p90) cc_final: 0.7599 (p90) REVERT: B 353 TRP cc_start: 0.7825 (p-90) cc_final: 0.7508 (p-90) REVERT: B 408 ARG cc_start: 0.8279 (mpp-170) cc_final: 0.8069 (mmp80) REVERT: B 591 SER cc_start: 0.8677 (t) cc_final: 0.8163 (p) REVERT: B 604 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8397 (t) REVERT: B 619 GLU cc_start: 0.7857 (tp30) cc_final: 0.7382 (tt0) REVERT: B 675 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 921 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8562 (mmmm) REVERT: B 977 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8695 (mp) REVERT: B 1041 ASP cc_start: 0.8572 (t70) cc_final: 0.8328 (t0) REVERT: C 424 LYS cc_start: 0.7605 (tppt) cc_final: 0.7331 (tppt) REVERT: C 473 TYR cc_start: 0.6682 (t80) cc_final: 0.6311 (t80) REVERT: C 515 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7533 (p90) REVERT: C 516 GLU cc_start: 0.7527 (mp0) cc_final: 0.7206 (mp0) REVERT: C 570 ASP cc_start: 0.7791 (m-30) cc_final: 0.7438 (p0) REVERT: C 586 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.6968 (m-30) REVERT: C 855 PHE cc_start: 0.6406 (t80) cc_final: 0.5940 (t80) REVERT: C 868 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8174 (mm-30) REVERT: C 912 THR cc_start: 0.8802 (m) cc_final: 0.8547 (p) REVERT: C 1126 CYS cc_start: 0.7535 (m) cc_final: 0.7299 (m) outliers start: 89 outliers final: 74 residues processed: 627 average time/residue: 0.1731 time to fit residues: 170.0403 Evaluate side-chains 646 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 567 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 139 optimal weight: 0.0870 chunk 307 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081033 restraints weight = 70515.450| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.42 r_work: 0.3117 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27538 Z= 0.147 Angle : 0.735 12.576 37638 Z= 0.354 Chirality : 0.047 0.487 4487 Planarity : 0.004 0.041 4690 Dihedral : 7.508 102.263 5461 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.99 % Allowed : 18.72 % Favored : 78.29 % 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: -0.29 (0.14), residues: 3223 helix: 1.56 (0.20), residues: 745 sheet: 0.22 (0.19), residues: 626 loop : -1.12 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 102 TYR 0.032 0.002 TYR B 904 PHE 0.035 0.002 PHE B 497 TRP 0.024 0.001 TRP A 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00338 (27404) covalent geometry : angle 0.69673 (37278) SS BOND : bond 0.00371 ( 42) SS BOND : angle 1.67518 ( 84) hydrogen bonds : bond 0.03824 ( 1105) hydrogen bonds : angle 5.69498 ( 3063) link_ALPHA1-4 : bond 0.01806 ( 6) link_ALPHA1-4 : angle 3.61855 ( 18) link_BETA1-4 : bond 0.00394 ( 29) link_BETA1-4 : angle 1.66583 ( 87) link_BETA1-6 : bond 0.01357 ( 3) link_BETA1-6 : angle 1.75567 ( 9) link_NAG-ASN : bond 0.00519 ( 54) link_NAG-ASN : angle 3.04342 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 585 time to evaluate : 0.897 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 24 LEU cc_start: 0.6816 (mm) cc_final: 0.6546 (mt) REVERT: A 129 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7899 (mmmt) REVERT: A 224 GLU cc_start: 0.8433 (mp0) cc_final: 0.8135 (mp0) REVERT: A 236 THR cc_start: 0.8923 (p) cc_final: 0.8648 (t) REVERT: A 244 LEU cc_start: 0.6716 (mt) cc_final: 0.6291 (mm) REVERT: A 265 TYR cc_start: 0.7507 (p90) cc_final: 0.7208 (p90) REVERT: A 290 ASP cc_start: 0.8424 (t0) cc_final: 0.8098 (t0) REVERT: A 365 TYR cc_start: 0.8339 (m-10) cc_final: 0.7366 (m-10) REVERT: A 368 LEU cc_start: 0.8327 (pp) cc_final: 0.7773 (mp) REVERT: A 369 TYR cc_start: 0.8019 (t80) cc_final: 0.7648 (t80) REVERT: A 387 LEU cc_start: 0.8765 (mp) cc_final: 0.8525 (tp) REVERT: A 495 TYR cc_start: 0.6165 (m-80) cc_final: 0.5476 (m-80) REVERT: A 591 SER cc_start: 0.8959 (t) cc_final: 0.8729 (m) REVERT: A 602 THR cc_start: 0.8236 (m) cc_final: 0.7838 (p) REVERT: A 673 SER cc_start: 0.8242 (m) cc_final: 0.8032 (m) REVERT: A 764 ASN cc_start: 0.8747 (m-40) cc_final: 0.8086 (m110) REVERT: A 790 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8148 (mtmt) REVERT: A 935 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8402 (tt0) REVERT: A 957 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8384 (tp40) REVERT: A 1107 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7423 (tpp80) REVERT: B 52 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8287 (tp-100) REVERT: B 270 LEU cc_start: 0.8896 (mt) cc_final: 0.8637 (mt) REVERT: B 271 GLN cc_start: 0.8393 (mp10) cc_final: 0.7663 (mp10) REVERT: B 306 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 351 TYR cc_start: 0.7897 (p90) cc_final: 0.7636 (p90) REVERT: B 353 TRP cc_start: 0.7799 (p-90) cc_final: 0.7494 (p-90) REVERT: B 408 ARG cc_start: 0.8275 (mpp-170) cc_final: 0.8060 (mmp80) REVERT: B 591 SER cc_start: 0.8630 (t) cc_final: 0.8093 (p) REVERT: B 604 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 619 GLU cc_start: 0.7800 (tp30) cc_final: 0.7328 (tt0) REVERT: B 921 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8561 (mmmm) REVERT: B 977 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8684 (mp) REVERT: B 1041 ASP cc_start: 0.8584 (t70) cc_final: 0.8335 (t0) REVERT: C 238 PHE cc_start: 0.8090 (p90) cc_final: 0.7841 (p90) REVERT: C 424 LYS cc_start: 0.7641 (tppt) cc_final: 0.7347 (tppt) REVERT: C 473 TYR cc_start: 0.6697 (t80) cc_final: 0.6311 (t80) REVERT: C 493 GLN cc_start: 0.7291 (tm-30) cc_final: 0.7046 (tm-30) REVERT: C 516 GLU cc_start: 0.7560 (mp0) cc_final: 0.7244 (mp0) REVERT: C 570 ASP cc_start: 0.7788 (m-30) cc_final: 0.7393 (p0) REVERT: C 586 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: C 633 TRP cc_start: 0.7918 (p-90) cc_final: 0.7679 (p-90) REVERT: C 734 THR cc_start: 0.9214 (m) cc_final: 0.8806 (p) REVERT: C 855 PHE cc_start: 0.6366 (t80) cc_final: 0.5913 (t80) REVERT: C 868 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8182 (mm-30) REVERT: C 912 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8520 (p) outliers start: 85 outliers final: 69 residues processed: 635 average time/residue: 0.1667 time to fit residues: 166.6746 Evaluate side-chains 644 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 569 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 235 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 272 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 580 GLN C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079726 restraints weight = 70663.379| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.39 r_work: 0.3093 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27538 Z= 0.205 Angle : 0.770 11.955 37638 Z= 0.372 Chirality : 0.048 0.478 4487 Planarity : 0.004 0.060 4690 Dihedral : 7.637 103.559 5461 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.02 % Allowed : 19.11 % Favored : 77.87 % 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: -0.43 (0.14), residues: 3223 helix: 1.45 (0.20), residues: 745 sheet: 0.05 (0.19), residues: 634 loop : -1.18 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 102 TYR 0.026 0.002 TYR A 200 PHE 0.038 0.002 PHE B 497 TRP 0.018 0.002 TRP A 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00469 (27404) covalent geometry : angle 0.73036 (37278) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.86069 ( 84) hydrogen bonds : bond 0.04075 ( 1105) hydrogen bonds : angle 5.77809 ( 3063) link_ALPHA1-4 : bond 0.01780 ( 6) link_ALPHA1-4 : angle 3.65944 ( 18) link_BETA1-4 : bond 0.00391 ( 29) link_BETA1-4 : angle 1.83571 ( 87) link_BETA1-6 : bond 0.01247 ( 3) link_BETA1-6 : angle 1.72169 ( 9) link_NAG-ASN : bond 0.00534 ( 54) link_NAG-ASN : angle 3.14683 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 569 time to evaluate : 0.838 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 24 LEU cc_start: 0.6817 (mm) cc_final: 0.6551 (mt) REVERT: A 129 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7934 (mmmt) REVERT: A 236 THR cc_start: 0.8937 (p) cc_final: 0.8666 (t) REVERT: A 290 ASP cc_start: 0.8430 (t0) cc_final: 0.8082 (t70) REVERT: A 365 TYR cc_start: 0.8370 (m-10) cc_final: 0.7588 (m-10) REVERT: A 368 LEU cc_start: 0.8493 (pp) cc_final: 0.7908 (mp) REVERT: A 495 TYR cc_start: 0.6020 (m-80) cc_final: 0.5513 (m-80) REVERT: A 591 SER cc_start: 0.9018 (t) cc_final: 0.8767 (m) REVERT: A 602 THR cc_start: 0.8304 (m) cc_final: 0.7890 (p) REVERT: A 764 ASN cc_start: 0.8737 (m-40) cc_final: 0.8072 (m110) REVERT: A 790 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8125 (mtmt) REVERT: A 950 ASP cc_start: 0.8536 (t70) cc_final: 0.8272 (t0) REVERT: B 51 THR cc_start: 0.8987 (t) cc_final: 0.8668 (p) REVERT: B 52 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8308 (tp-100) REVERT: B 270 LEU cc_start: 0.8899 (mt) cc_final: 0.8638 (mt) REVERT: B 271 GLN cc_start: 0.8399 (mp10) cc_final: 0.7674 (mp10) REVERT: B 287 ASP cc_start: 0.8566 (t0) cc_final: 0.8336 (t0) REVERT: B 304 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8830 (mmmm) REVERT: B 306 PHE cc_start: 0.8421 (m-80) cc_final: 0.8020 (t80) REVERT: B 351 TYR cc_start: 0.7881 (p90) cc_final: 0.7589 (p90) REVERT: B 591 SER cc_start: 0.8649 (t) cc_final: 0.8115 (p) REVERT: B 604 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8422 (t) REVERT: B 619 GLU cc_start: 0.7901 (tp30) cc_final: 0.7554 (tt0) REVERT: B 773 GLU cc_start: 0.8345 (tt0) cc_final: 0.8127 (tt0) REVERT: B 804 GLN cc_start: 0.8631 (mm110) cc_final: 0.8249 (mm-40) REVERT: B 921 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8555 (mmmm) REVERT: B 977 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 1041 ASP cc_start: 0.8558 (t70) cc_final: 0.8297 (t0) REVERT: B 1125 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8721 (p0) REVERT: C 237 ARG cc_start: 0.8295 (ttt90) cc_final: 0.7771 (ptm160) REVERT: C 473 TYR cc_start: 0.6586 (t80) cc_final: 0.6263 (t80) REVERT: C 515 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7552 (p90) REVERT: C 516 GLU cc_start: 0.7503 (mp0) cc_final: 0.7219 (mp0) REVERT: C 570 ASP cc_start: 0.7745 (m-30) cc_final: 0.7405 (p0) REVERT: C 586 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: C 633 TRP cc_start: 0.7929 (p-90) cc_final: 0.7690 (p-90) REVERT: C 734 THR cc_start: 0.9201 (m) cc_final: 0.8808 (p) REVERT: C 784 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8273 (mt0) REVERT: C 855 PHE cc_start: 0.6445 (t80) cc_final: 0.5950 (t80) REVERT: C 868 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8210 (mm-30) REVERT: C 912 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8552 (p) REVERT: C 1148 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7286 (m-80) outliers start: 86 outliers final: 71 residues processed: 622 average time/residue: 0.1668 time to fit residues: 164.0438 Evaluate side-chains 636 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 556 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 95 optimal weight: 0.0770 chunk 270 optimal weight: 0.0770 chunk 79 optimal weight: 0.5980 chunk 271 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 250 optimal weight: 0.6980 chunk 305 optimal weight: 0.0020 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 409 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079392 restraints weight = 70246.385| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.42 r_work: 0.3092 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 27538 Z= 0.205 Angle : 0.868 59.200 37638 Z= 0.450 Chirality : 0.049 0.684 4487 Planarity : 0.004 0.066 4690 Dihedral : 7.634 103.370 5461 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.92 % Allowed : 19.67 % Favored : 77.41 % Cbeta Deviations : 0.03 % 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: -0.43 (0.14), residues: 3223 helix: 1.46 (0.20), residues: 745 sheet: 0.05 (0.19), residues: 634 loop : -1.19 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 102 TYR 0.030 0.002 TYR A 365 PHE 0.031 0.002 PHE C 456 TRP 0.018 0.002 TRP A 353 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00457 (27404) covalent geometry : angle 0.83084 (37278) SS BOND : bond 0.00476 ( 42) SS BOND : angle 2.39774 ( 84) hydrogen bonds : bond 0.04036 ( 1105) hydrogen bonds : angle 5.77999 ( 3063) link_ALPHA1-4 : bond 0.01660 ( 6) link_ALPHA1-4 : angle 3.67620 ( 18) link_BETA1-4 : bond 0.00386 ( 29) link_BETA1-4 : angle 1.82319 ( 87) link_BETA1-6 : bond 0.01315 ( 3) link_BETA1-6 : angle 1.71827 ( 9) link_NAG-ASN : bond 0.00529 ( 54) link_NAG-ASN : angle 3.13977 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6343.84 seconds wall clock time: 109 minutes 31.32 seconds (6571.32 seconds total)