Starting phenix.real_space_refine on Mon Sep 14 01:12:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vv5_21391/09_2026/6vv5_21391.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 111 5.16 5 C 17100 2.51 5 N 4212 2.21 5 O 5415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26838 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "B" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "C" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8480 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 39, 'TRANS': 1057} Chain breaks: 18 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 97 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 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 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 chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 106 Unusual residues: {'NAG': 5, 'PAM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.39, per 1000 atoms: 0.24 Number of scatterers: 26838 At special positions: 0 Unit cell: (141.45, 133.4, 171.35, 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 111 16.00 O 5415 8.00 N 4212 7.00 C 17100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.04 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.07 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.06 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.09 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.10 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.02 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.04 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.07 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.06 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.09 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.10 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.02 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.07 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.09 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.10 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.02 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.04 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA N 3 " - " MAN N 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " MAN D 6 " - " MAN D 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " BETA1-2 " MAN D 6 " - " NAG D 7 " " MAN N 6 " - " NAG N 7 " " MAN X 6 " - " NAG X 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 2 " - " BMA H 3 " " 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 N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " 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 X 2 " - " BMA X 3 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " 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-ASN " NAG A1401 " - " ASN A 216 " " NAG A1402 " - " ASN A 300 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 781 " " NAG A1405 " - " ASN A1249 " " NAG B1401 " - " ASN B 216 " " NAG B1402 " - " ASN B 300 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 781 " " NAG B1405 " - " ASN B1249 " " NAG C1401 " - " ASN C 216 " " NAG C1402 " - " ASN C 300 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 781 " " NAG C1405 " - " ASN C1249 " " NAG D 1 " - " ASN A 264 " " NAG E 1 " - " ASN A 344 " " NAG F 1 " - " ASN A 514 " " NAG G 1 " - " ASN A 556 " " NAG H 1 " - " ASN A 688 " " NAG I 1 " - " ASN A 726 " " NAG J 1 " - " ASN A 743 " " NAG K 1 " - " ASN A 787 " " NAG L 1 " - " ASN A 873 " " NAG M 1 " - " ASN A1232 " " NAG N 1 " - " ASN B 264 " " NAG O 1 " - " ASN B 344 " " NAG P 1 " - " ASN B 514 " " NAG Q 1 " - " ASN B 556 " " NAG R 1 " - " ASN B 688 " " NAG S 1 " - " ASN B 726 " " NAG T 1 " - " ASN B 743 " " NAG U 1 " - " ASN B 787 " " NAG V 1 " - " ASN B 873 " " NAG W 1 " - " ASN B1232 " " NAG X 1 " - " ASN C 264 " " NAG Y 1 " - " ASN C 344 " " NAG Z 1 " - " ASN C 514 " " NAG a 1 " - " ASN C 556 " " NAG b 1 " - " ASN C 688 " " NAG c 1 " - " ASN C 726 " " NAG d 1 " - " ASN C 743 " " NAG e 1 " - " ASN C 787 " " NAG f 1 " - " ASN C 873 " " NAG g 1 " - " ASN C1232 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 24.0% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 826 through 852 Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 993 through 1014 removed outlier: 3.936A pdb=" N GLN A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1020 Processing helix chain 'A' and resid 1030 through 1044 Processing helix chain 'A' and resid 1048 through 1055 Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1072 Processing helix chain 'A' and resid 1075 through 1123 Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1237 through 1241 Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 826 through 852 Processing helix chain 'B' and resid 855 through 860 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 960 Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 973 through 986 Processing helix chain 'B' and resid 993 through 1014 removed outlier: 3.936A pdb=" N GLN B 997 " --> pdb=" O GLN B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1020 Processing helix chain 'B' and resid 1030 through 1044 Processing helix chain 'B' and resid 1048 through 1055 Processing helix chain 'B' and resid 1056 through 1058 No H-bonds generated for 'chain 'B' and resid 1056 through 1058' Processing helix chain 'B' and resid 1066 through 1072 Processing helix chain 'B' and resid 1075 through 1123 Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1237 through 1241 Processing helix chain 'B' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 826 through 852 Processing helix chain 'C' and resid 855 through 860 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 946 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 973 through 986 Processing helix chain 'C' and resid 993 through 1014 removed outlier: 3.936A pdb=" N GLN C 997 " --> pdb=" O GLN C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1020 Processing helix chain 'C' and resid 1030 through 1044 Processing helix chain 'C' and resid 1048 through 1055 Processing helix chain 'C' and resid 1056 through 1058 No H-bonds generated for 'chain 'C' and resid 1056 through 1058' Processing helix chain 'C' and resid 1066 through 1072 Processing helix chain 'C' and resid 1075 through 1123 Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1241 Processing helix chain 'C' and resid 1247 through 1254 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 154 removed outlier: 3.524A pdb=" N ARG A 191 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN A 322 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 441 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 320 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A 443 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 318 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 452 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG A 460 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN A 454 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.989A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 5.284A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU A 627 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N LEU A 583 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS A 614 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 605 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 786 Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 798 removed outlier: 7.157A pdb=" N GLY A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA A1146 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A1152 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A1144 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A1154 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A1142 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR A1156 " --> pdb=" O ILE A1140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 3.520A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 180 through 184 Processing sheet with id=AC1, first strand: chain 'B' and resid 148 through 154 removed outlier: 3.524A pdb=" N ARG B 191 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 322 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 441 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG B 320 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER B 443 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 318 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 452 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG B 460 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 296 through 298 removed outlier: 6.990A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 499 through 502 removed outlier: 5.284A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER B 511 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER B 552 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 513 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE B 554 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 515 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN B 556 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 517 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR B 558 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 519 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY B 625 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU B 627 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N LEU B 583 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 536 removed outlier: 6.832A pdb=" N SER B 511 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER B 552 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 513 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N PHE B 554 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 515 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN B 556 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 517 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR B 558 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA B 519 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS B 614 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY B 605 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD1, first strand: chain 'B' and resid 780 through 786 Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 798 removed outlier: 7.157A pdb=" N GLY B1150 " --> pdb=" O ALA B1146 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA B1146 " --> pdb=" O GLY B1150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B1152 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B1144 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1154 " --> pdb=" O SER B1142 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B1142 " --> pdb=" O LEU B1154 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR B1156 " --> pdb=" O ILE B1140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD4, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.520A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 51 Processing sheet with id=AD7, first strand: chain 'C' and resid 180 through 184 Processing sheet with id=AD8, first strand: chain 'C' and resid 148 through 154 removed outlier: 3.524A pdb=" N ARG C 191 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN C 322 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 441 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 320 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER C 443 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA C 318 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 270 through 286 removed outlier: 5.576A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU C 452 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ARG C 460 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.989A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.549A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 709 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE C 713 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 499 through 502 removed outlier: 5.283A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 531 through 536 removed outlier: 6.833A pdb=" N SER C 511 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER C 552 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 513 " --> pdb=" O SER C 552 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE C 554 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 515 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASN C 556 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 517 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 558 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 519 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C 625 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU C 627 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N LEU C 583 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 531 through 536 removed outlier: 6.833A pdb=" N SER C 511 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N SER C 552 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 513 " --> pdb=" O SER C 552 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE C 554 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 515 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ASN C 556 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 517 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 558 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 519 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AE8, first strand: chain 'C' and resid 780 through 786 Processing sheet with id=AE9, first strand: chain 'C' and resid 789 through 798 removed outlier: 7.157A pdb=" N GLY C1150 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA C1146 " --> pdb=" O GLY C1150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C1152 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL C1144 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C1154 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER C1142 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C1156 " --> pdb=" O ILE C1140 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF2, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.520A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1187 through 1190 1129 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: 8.39 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5483 1.32 - 1.45: 8317 1.45 - 1.58: 13386 1.58 - 1.71: 12 1.71 - 1.84: 138 Bond restraints: 27336 Sorted by residual: bond pdb=" C10 PAM B1406 " pdb=" C9 PAM B1406 " ideal model delta sigma weight residual 1.332 1.526 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C10 PAM C1406 " pdb=" C9 PAM C1406 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.34e+01 bond pdb=" C10 PAM C1407 " pdb=" C9 PAM C1407 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" C10 PAM A1406 " pdb=" C9 PAM A1406 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" C10 PAM A1407 " pdb=" C9 PAM A1407 " ideal model delta sigma weight residual 1.332 1.525 -0.193 2.00e-02 2.50e+03 9.29e+01 ... (remaining 27331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 34197 2.90 - 5.79: 2651 5.79 - 8.69: 247 8.69 - 11.58: 9 11.58 - 14.48: 12 Bond angle restraints: 37116 Sorted by residual: angle pdb=" C CYS C 572 " pdb=" N PRO C 573 " pdb=" CA PRO C 573 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C CYS A 572 " pdb=" N PRO A 573 " pdb=" CA PRO A 573 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C CYS B 572 " pdb=" N PRO B 573 " pdb=" CA PRO B 573 " ideal model delta sigma weight residual 119.82 127.71 -7.89 9.80e-01 1.04e+00 6.48e+01 angle pdb=" C TYR A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta sigma weight residual 119.56 127.35 -7.79 1.01e+00 9.80e-01 5.94e+01 angle pdb=" C TYR C 606 " pdb=" N PRO C 607 " pdb=" CA PRO C 607 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.91e+01 ... (remaining 37111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 14764 17.84 - 35.68: 449 35.68 - 53.51: 150 53.51 - 71.35: 66 71.35 - 89.19: 15 Dihedral angle restraints: 15444 sinusoidal: 5868 harmonic: 9576 Sorted by residual: dihedral pdb=" CB CYS B1173 " pdb=" SG CYS B1173 " pdb=" SG CYS B1226 " pdb=" CB CYS B1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.35 49.35 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS C1173 " pdb=" SG CYS C1173 " pdb=" SG CYS C1226 " pdb=" CB CYS C1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.34 49.34 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CB CYS A1173 " pdb=" SG CYS A1173 " pdb=" SG CYS A1226 " pdb=" CB CYS A1226 " ideal model delta sinusoidal sigma weight residual -86.00 -135.33 49.33 1 1.00e+01 1.00e-02 3.34e+01 ... (remaining 15441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3180 0.088 - 0.176: 1185 0.176 - 0.263: 231 0.263 - 0.351: 21 0.351 - 0.439: 3 Chirality restraints: 4620 Sorted by residual: chirality pdb=" C1 NAG D 7 " pdb=" O2 MAN D 6 " pdb=" C2 NAG D 7 " pdb=" O5 NAG D 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" C1 NAG N 7 " pdb=" O2 MAN N 6 " pdb=" C2 NAG N 7 " pdb=" O5 NAG N 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 chirality pdb=" C1 NAG X 7 " pdb=" O2 MAN X 6 " pdb=" C2 NAG X 7 " pdb=" O5 NAG X 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 4617 not shown) Planarity restraints: 4629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG N 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG D 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG X 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.149 2.00e-02 2.50e+03 ... (remaining 4626 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6522 2.79 - 3.32: 24512 3.32 - 3.84: 44904 3.84 - 4.37: 53060 4.37 - 4.90: 88789 Nonbonded interactions: 217787 Sorted by model distance: nonbonded pdb=" O3 NAG b 1 " pdb=" O7 NAG b 1 " model vdw 2.262 3.040 nonbonded pdb=" O3 NAG R 1 " pdb=" O7 NAG R 1 " model vdw 2.263 3.040 nonbonded pdb=" O3 NAG H 1 " pdb=" O7 NAG H 1 " model vdw 2.263 3.040 nonbonded pdb=" O4 BMA X 3 " pdb=" O2 MAN X 8 " model vdw 2.296 3.040 nonbonded pdb=" O4 BMA D 3 " pdb=" O2 MAN D 8 " model vdw 2.297 3.040 ... (remaining 217782 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'R' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.260 Find NCS groups from input model: 0.890 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: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.017 0.194 27474 Z= 0.940 Angle : 1.679 14.477 37488 Z= 1.104 Chirality : 0.089 0.439 4620 Planarity : 0.026 0.301 4584 Dihedral : 11.246 89.190 9132 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.30 % Rotamer: Outliers : 1.26 % Allowed : 1.26 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3177 helix: 0.72 (0.17), residues: 678 sheet: 1.53 (0.18), residues: 705 loop : 0.22 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1112 TYR 0.083 0.008 TYR A 676 PHE 0.036 0.005 PHE A 185 TRP 0.020 0.005 TRP C 439 HIS 0.007 0.002 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.01741 / 0.94 (27336) covalent geometry : angle 1.67576 / 1.11 (37116) SS BOND : bond 0.02788 / 1.88 ( 42) SS BOND : angle 2.59710 / 1.88 ( 84) hydrogen bonds : bond 0.17105 / 11.08 ( 1099) hydrogen bonds : angle 7.67282 / 5.35 ( 3063) link_ALPHA1-2 : bond 0.00059 / 0.03 ( 3) link_ALPHA1-2 : angle 0.58301 / 0.42 ( 9) link_ALPHA1-3 : bond 0.00799 / 0.40 ( 3) link_ALPHA1-3 : angle 1.95184 / 1.44 ( 9) link_ALPHA1-6 : bond 0.00128 / 0.06 ( 6) link_ALPHA1-6 : angle 1.33015 / 0.90 ( 18) link_BETA1-2 : bond 0.00049 / 0.02 ( 3) link_BETA1-2 : angle 1.91459 / 1.41 ( 9) link_BETA1-4 : bond 0.00292 / 0.14 ( 36) link_BETA1-4 : angle 1.62131 / 1.30 ( 108) link_NAG-ASN : bond 0.00225 / 0.13 ( 45) link_NAG-ASN : angle 1.81841 / 1.26 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 598 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.6123 (m-80) cc_final: 0.5643 (m-10) REVERT: A 263 SER cc_start: 0.9264 (t) cc_final: 0.9038 (p) REVERT: A 303 ILE cc_start: 0.9195 (pt) cc_final: 0.8951 (pt) REVERT: A 850 SER cc_start: 0.8970 (t) cc_final: 0.8704 (m) REVERT: A 899 ASP cc_start: 0.8453 (t70) cc_final: 0.8071 (t0) REVERT: A 1059 ASN cc_start: 0.8051 (t0) cc_final: 0.7843 (p0) REVERT: A 1104 LYS cc_start: 0.8805 (tptt) cc_final: 0.8574 (mtpt) REVERT: B 397 GLU cc_start: 0.8234 (tt0) cc_final: 0.7767 (tt0) REVERT: B 850 SER cc_start: 0.8968 (t) cc_final: 0.8689 (m) REVERT: B 899 ASP cc_start: 0.8526 (t70) cc_final: 0.8050 (t0) REVERT: B 1059 ASN cc_start: 0.8252 (t0) cc_final: 0.8042 (p0) REVERT: B 1104 LYS cc_start: 0.8626 (tptt) cc_final: 0.8302 (mtpt) REVERT: C 38 LYS cc_start: 0.8017 (mttm) cc_final: 0.7778 (mtpt) REVERT: C 303 ILE cc_start: 0.9223 (pt) cc_final: 0.8919 (pt) REVERT: C 758 LYS cc_start: 0.8244 (pttt) cc_final: 0.8031 (tptt) REVERT: C 850 SER cc_start: 0.8983 (t) cc_final: 0.8585 (m) REVERT: C 899 ASP cc_start: 0.8394 (t70) cc_final: 0.8084 (t0) REVERT: C 1059 ASN cc_start: 0.8085 (t0) cc_final: 0.7796 (p0) REVERT: C 1104 LYS cc_start: 0.8797 (tptt) cc_final: 0.8537 (mtpt) outliers start: 36 outliers final: 14 residues processed: 620 average time/residue: 0.1889 time to fit residues: 184.3968 Evaluate side-chains 276 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 714 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN A 356 HIS A 445 ASN A1045 GLN A1139 HIS B 110 HIS B 282 ASN B 295 GLN B 445 ASN B1045 GLN B1051 GLN B1061 GLN B1139 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS C 282 ASN C 356 HIS C 445 ASN C 816 ASN C 821 GLN C 988 GLN C1045 GLN C1058 HIS ** C1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115655 restraints weight = 35840.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118503 restraints weight = 22731.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120326 restraints weight = 17057.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121396 restraints weight = 14242.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122223 restraints weight = 12743.898| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27474 Z= 0.164 Angle : 0.760 23.149 37488 Z= 0.366 Chirality : 0.050 0.583 4620 Planarity : 0.004 0.040 4584 Dihedral : 6.754 58.744 3583 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.33 % Allowed : 7.78 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3177 helix: 1.88 (0.19), residues: 714 sheet: 1.18 (0.18), residues: 729 loop : -0.17 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 33 TYR 0.016 0.002 TYR B 227 PHE 0.025 0.002 PHE A 39 TRP 0.008 0.002 TRP A 168 HIS 0.007 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (27336) covalent geometry : angle 0.70774 / 0.35 (37116) SS BOND : bond 0.00481 / 0.34 ( 42) SS BOND : angle 1.33079 / 0.94 ( 84) hydrogen bonds : bond 0.05873 / 3.82 ( 1099) hydrogen bonds : angle 5.95146 / 4.18 ( 3063) link_ALPHA1-2 : bond 0.00421 / 0.21 ( 3) link_ALPHA1-2 : angle 1.72859 / 1.15 ( 9) link_ALPHA1-3 : bond 0.01689 / 0.85 ( 3) link_ALPHA1-3 : angle 1.03755 / 0.62 ( 9) link_ALPHA1-6 : bond 0.01178 / 0.61 ( 6) link_ALPHA1-6 : angle 2.37915 / 1.45 ( 18) link_BETA1-2 : bond 0.00095 / 0.05 ( 3) link_BETA1-2 : angle 2.64328 / 1.89 ( 9) link_BETA1-4 : bond 0.00598 / 0.42 ( 36) link_BETA1-4 : angle 1.66409 / 1.23 ( 108) link_NAG-ASN : bond 0.00585 / 0.38 ( 45) link_NAG-ASN : angle 4.20385 / 2.73 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: A 263 SER cc_start: 0.9126 (t) cc_final: 0.8820 (p) REVERT: A 704 GLU cc_start: 0.7692 (pt0) cc_final: 0.7443 (pt0) REVERT: A 850 SER cc_start: 0.8878 (t) cc_final: 0.8634 (m) REVERT: A 899 ASP cc_start: 0.8160 (t70) cc_final: 0.7656 (t0) REVERT: A 1057 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 1124 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8804 (mttp) REVERT: B 49 LEU cc_start: 0.8563 (mp) cc_final: 0.8298 (mp) REVERT: B 215 LEU cc_start: 0.8051 (mp) cc_final: 0.7790 (mt) REVERT: B 397 GLU cc_start: 0.8351 (tt0) cc_final: 0.7754 (tt0) REVERT: B 850 SER cc_start: 0.9009 (t) cc_final: 0.8750 (m) REVERT: B 899 ASP cc_start: 0.8202 (t70) cc_final: 0.7670 (t0) REVERT: B 1051 GLN cc_start: 0.8016 (mm110) cc_final: 0.7543 (mt0) REVERT: C 38 LYS cc_start: 0.8134 (mttm) cc_final: 0.7720 (mtpt) REVERT: C 303 ILE cc_start: 0.9155 (pt) cc_final: 0.8928 (pt) REVERT: C 372 TYR cc_start: 0.7978 (m-10) cc_final: 0.7673 (m-80) REVERT: C 704 GLU cc_start: 0.7640 (pt0) cc_final: 0.7430 (pt0) REVERT: C 850 SER cc_start: 0.8902 (t) cc_final: 0.8593 (m) REVERT: C 899 ASP cc_start: 0.7996 (t70) cc_final: 0.7545 (t0) REVERT: C 1051 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7684 (mt0) outliers start: 38 outliers final: 30 residues processed: 352 average time/residue: 0.1657 time to fit residues: 96.8632 Evaluate side-chains 260 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1124 LYS Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 235 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS A 571 ASN A 821 GLN A1059 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B 571 ASN B1061 GLN C 147 ASN C 979 GLN C 996 GLN C1051 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.110249 restraints weight = 36030.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112921 restraints weight = 23151.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114653 restraints weight = 17531.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115581 restraints weight = 14754.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116371 restraints weight = 13321.949| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27474 Z= 0.222 Angle : 0.683 10.157 37488 Z= 0.338 Chirality : 0.048 0.453 4620 Planarity : 0.004 0.040 4584 Dihedral : 6.365 59.753 3568 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.23 % Allowed : 8.62 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3177 helix: 1.70 (0.19), residues: 723 sheet: 0.79 (0.18), residues: 747 loop : -0.49 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1090 TYR 0.019 0.002 TYR A 652 PHE 0.022 0.002 PHE B 39 TRP 0.007 0.001 TRP A 259 HIS 0.008 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (27336) covalent geometry : angle 0.65190 / 0.33 (37116) SS BOND : bond 0.00482 / 0.32 ( 42) SS BOND : angle 1.37195 / 0.96 ( 84) hydrogen bonds : bond 0.05459 / 3.55 ( 1099) hydrogen bonds : angle 5.50677 / 3.85 ( 3063) link_ALPHA1-2 : bond 0.00313 / 0.16 ( 3) link_ALPHA1-2 : angle 1.57831 / 1.00 ( 9) link_ALPHA1-3 : bond 0.00797 / 0.39 ( 3) link_ALPHA1-3 : angle 1.22549 / 0.70 ( 9) link_ALPHA1-6 : bond 0.01133 / 0.61 ( 6) link_ALPHA1-6 : angle 2.47669 / 1.52 ( 18) link_BETA1-2 : bond 0.00455 / 0.23 ( 3) link_BETA1-2 : angle 2.76347 / 2.07 ( 9) link_BETA1-4 : bond 0.00482 / 0.29 ( 36) link_BETA1-4 : angle 1.44508 / 1.05 ( 108) link_NAG-ASN : bond 0.00350 / 0.23 ( 45) link_NAG-ASN : angle 2.84743 / 1.96 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8158 (mttm) cc_final: 0.7596 (mtpt) REVERT: A 39 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: A 214 MET cc_start: 0.7757 (tmm) cc_final: 0.6835 (tmm) REVERT: A 263 SER cc_start: 0.9261 (t) cc_final: 0.8906 (p) REVERT: A 899 ASP cc_start: 0.8222 (t70) cc_final: 0.7783 (t0) REVERT: A 1051 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7298 (mt0) REVERT: A 1057 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 1162 ASP cc_start: 0.7987 (m-30) cc_final: 0.7591 (m-30) REVERT: B 157 HIS cc_start: 0.3141 (t-90) cc_final: 0.2909 (t70) REVERT: B 214 MET cc_start: 0.7680 (ttp) cc_final: 0.7448 (ttp) REVERT: B 850 SER cc_start: 0.9154 (t) cc_final: 0.8936 (m) REVERT: B 899 ASP cc_start: 0.8221 (t70) cc_final: 0.7716 (t0) REVERT: B 984 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7288 (t80) REVERT: B 1051 GLN cc_start: 0.7887 (mm110) cc_final: 0.7431 (mt0) REVERT: C 38 LYS cc_start: 0.8173 (mttm) cc_final: 0.7766 (mtpt) REVERT: C 303 ILE cc_start: 0.9258 (pt) cc_final: 0.9029 (pt) REVERT: C 397 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: C 899 ASP cc_start: 0.8100 (t70) cc_final: 0.7619 (t0) outliers start: 64 outliers final: 44 residues processed: 303 average time/residue: 0.1656 time to fit residues: 83.0514 Evaluate side-chains 256 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain B residue 1229 THR Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1191 THR Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 188 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 271 optimal weight: 0.4980 chunk 176 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 HIS A 571 ASN A 979 GLN A 996 GLN A1029 ASN A1059 ASN B 356 HIS B 571 ASN B1192 HIS C 270 HIS C 571 ASN C1029 ASN C1045 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117236 restraints weight = 35154.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120014 restraints weight = 22569.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121805 restraints weight = 17058.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122838 restraints weight = 14313.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123628 restraints weight = 12845.545| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27474 Z= 0.108 Angle : 0.548 9.812 37488 Z= 0.274 Chirality : 0.044 0.342 4620 Planarity : 0.003 0.039 4584 Dihedral : 5.909 59.952 3566 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.64 % Allowed : 10.44 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3177 helix: 2.13 (0.19), residues: 747 sheet: 0.74 (0.19), residues: 732 loop : -0.48 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 924 TYR 0.030 0.001 TYR C 407 PHE 0.013 0.001 PHE C 296 TRP 0.005 0.001 TRP A 168 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (27336) covalent geometry : angle 0.52182 / 0.27 (37116) SS BOND : bond 0.00349 / 0.26 ( 42) SS BOND : angle 0.84070 / 0.60 ( 84) hydrogen bonds : bond 0.04336 / 2.83 ( 1099) hydrogen bonds : angle 5.14864 / 3.61 ( 3063) link_ALPHA1-2 : bond 0.00296 / 0.15 ( 3) link_ALPHA1-2 : angle 1.37189 / 0.92 ( 9) link_ALPHA1-3 : bond 0.01025 / 0.51 ( 3) link_ALPHA1-3 : angle 1.08006 / 0.67 ( 9) link_ALPHA1-6 : bond 0.01265 / 0.68 ( 6) link_ALPHA1-6 : angle 1.92115 / 1.17 ( 18) link_BETA1-2 : bond 0.00312 / 0.16 ( 3) link_BETA1-2 : angle 1.49677 / 1.06 ( 9) link_BETA1-4 : bond 0.00464 / 0.31 ( 36) link_BETA1-4 : angle 1.19874 / 0.89 ( 108) link_NAG-ASN : bond 0.00780 / 0.57 ( 45) link_NAG-ASN : angle 2.46884 / 1.73 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 1.016 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 38 LYS cc_start: 0.8257 (mttm) cc_final: 0.7733 (mtpt) REVERT: A 214 MET cc_start: 0.8082 (tmm) cc_final: 0.6935 (tmm) REVERT: A 899 ASP cc_start: 0.8063 (t70) cc_final: 0.7682 (t0) REVERT: A 1057 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 1162 ASP cc_start: 0.7856 (m-30) cc_final: 0.7523 (m-30) REVERT: B 111 LYS cc_start: 0.6228 (pttp) cc_final: 0.5887 (tptt) REVERT: B 790 MET cc_start: 0.8276 (mtt) cc_final: 0.7972 (mtt) REVERT: B 899 ASP cc_start: 0.8031 (t70) cc_final: 0.7558 (t0) REVERT: B 961 MET cc_start: 0.8959 (mtt) cc_final: 0.8714 (mtp) REVERT: B 984 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7197 (t80) REVERT: B 1026 LYS cc_start: 0.8833 (ptpp) cc_final: 0.8388 (ttpp) REVERT: B 1051 GLN cc_start: 0.7692 (mm110) cc_final: 0.7450 (mt0) REVERT: C 38 LYS cc_start: 0.8194 (mttm) cc_final: 0.7772 (mtpt) REVERT: C 303 ILE cc_start: 0.9203 (pt) cc_final: 0.9002 (pt) REVERT: C 899 ASP cc_start: 0.7877 (t70) cc_final: 0.7536 (t0) REVERT: C 1071 TYR cc_start: 0.8855 (m-80) cc_final: 0.8379 (m-80) outliers start: 47 outliers final: 31 residues processed: 289 average time/residue: 0.1655 time to fit residues: 79.4368 Evaluate side-chains 254 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1078 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 170 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 270 HIS A 988 GLN B 187 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1061 GLN C1045 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109837 restraints weight = 35950.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112411 restraints weight = 23288.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114085 restraints weight = 17778.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115153 restraints weight = 15014.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115805 restraints weight = 13509.963| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 27474 Z= 0.250 Angle : 0.659 9.971 37488 Z= 0.329 Chirality : 0.047 0.386 4620 Planarity : 0.004 0.041 4584 Dihedral : 5.953 58.305 3562 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.41 % Allowed : 9.84 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3177 helix: 1.74 (0.19), residues: 744 sheet: 0.47 (0.18), residues: 768 loop : -0.70 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1090 TYR 0.022 0.002 TYR A 652 PHE 0.018 0.002 PHE C 39 TRP 0.008 0.002 TRP B 259 HIS 0.008 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (27336) covalent geometry : angle 0.62996 / 0.32 (37116) SS BOND : bond 0.00451 / 0.29 ( 42) SS BOND : angle 1.29797 / 0.93 ( 84) hydrogen bonds : bond 0.05230 / 3.42 ( 1099) hydrogen bonds : angle 5.38275 / 3.76 ( 3063) link_ALPHA1-2 : bond 0.00279 / 0.14 ( 3) link_ALPHA1-2 : angle 1.48693 / 1.02 ( 9) link_ALPHA1-3 : bond 0.00727 / 0.36 ( 3) link_ALPHA1-3 : angle 1.49007 / 0.85 ( 9) link_ALPHA1-6 : bond 0.01184 / 0.67 ( 6) link_ALPHA1-6 : angle 2.41895 / 1.50 ( 18) link_BETA1-2 : bond 0.00646 / 0.33 ( 3) link_BETA1-2 : angle 3.13986 / 2.38 ( 9) link_BETA1-4 : bond 0.00457 / 0.29 ( 36) link_BETA1-4 : angle 1.25866 / 0.91 ( 108) link_NAG-ASN : bond 0.00628 / 0.41 ( 45) link_NAG-ASN : angle 2.74099 / 1.92 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 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 214 MET cc_start: 0.7963 (tmm) cc_final: 0.6750 (tmm) REVERT: A 624 LYS cc_start: 0.6735 (mmtm) cc_final: 0.6361 (mmtm) REVERT: A 899 ASP cc_start: 0.8281 (t70) cc_final: 0.7759 (t0) REVERT: A 1057 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 38 LYS cc_start: 0.7974 (mttm) cc_final: 0.7383 (mttm) REVERT: B 111 LYS cc_start: 0.5988 (pttp) cc_final: 0.5704 (pttm) REVERT: B 899 ASP cc_start: 0.8239 (t70) cc_final: 0.7768 (t0) REVERT: B 984 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B 1051 GLN cc_start: 0.7710 (mm110) cc_final: 0.7478 (mt0) REVERT: C 38 LYS cc_start: 0.8223 (mttm) cc_final: 0.7733 (mtpt) REVERT: C 157 HIS cc_start: 0.3299 (t-90) cc_final: 0.3078 (t-90) REVERT: C 899 ASP cc_start: 0.8238 (t70) cc_final: 0.7973 (t0) REVERT: C 984 TYR cc_start: 0.7715 (m-80) cc_final: 0.7275 (t80) REVERT: C 1082 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7397 (mt0) outliers start: 69 outliers final: 52 residues processed: 294 average time/residue: 0.1685 time to fit residues: 81.7674 Evaluate side-chains 274 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1068 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 356 HIS Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 905 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1229 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 272 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1059 ASN C 276 ASN C 571 ASN C1192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110954 restraints weight = 35938.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113623 restraints weight = 22977.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115387 restraints weight = 17342.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116473 restraints weight = 14492.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117205 restraints weight = 12932.592| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27474 Z= 0.113 Angle : 0.534 9.374 37488 Z= 0.268 Chirality : 0.043 0.337 4620 Planarity : 0.003 0.042 4584 Dihedral : 5.556 59.738 3562 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.78 % Allowed : 10.89 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3177 helix: 2.08 (0.19), residues: 747 sheet: 0.60 (0.18), residues: 738 loop : -0.69 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1085 TYR 0.018 0.001 TYR C 407 PHE 0.012 0.001 PHE C 296 TRP 0.006 0.001 TRP C 168 HIS 0.002 0.001 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (27336) covalent geometry : angle 0.50935 / 0.26 (37116) SS BOND : bond 0.00260 / 0.17 ( 42) SS BOND : angle 0.92820 / 0.66 ( 84) hydrogen bonds : bond 0.04241 / 2.77 ( 1099) hydrogen bonds : angle 5.08275 / 3.56 ( 3063) link_ALPHA1-2 : bond 0.00296 / 0.15 ( 3) link_ALPHA1-2 : angle 1.33737 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00934 / 0.47 ( 3) link_ALPHA1-3 : angle 1.09797 / 0.70 ( 9) link_ALPHA1-6 : bond 0.01252 / 0.68 ( 6) link_ALPHA1-6 : angle 1.89428 / 1.16 ( 18) link_BETA1-2 : bond 0.00141 / 0.07 ( 3) link_BETA1-2 : angle 1.61549 / 1.17 ( 9) link_BETA1-4 : bond 0.00428 / 0.28 ( 36) link_BETA1-4 : angle 1.10756 / 0.82 ( 108) link_NAG-ASN : bond 0.00520 / 0.33 ( 45) link_NAG-ASN : angle 2.35164 / 1.67 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 1.054 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 214 MET cc_start: 0.7991 (tmm) cc_final: 0.6753 (tmm) REVERT: A 899 ASP cc_start: 0.8070 (t70) cc_final: 0.7756 (t0) REVERT: A 1057 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 899 ASP cc_start: 0.7987 (t70) cc_final: 0.7541 (t0) REVERT: B 984 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7154 (t80) REVERT: C 38 LYS cc_start: 0.8007 (mttm) cc_final: 0.7646 (mtpt) REVERT: C 157 HIS cc_start: 0.3630 (t-90) cc_final: 0.3384 (t-90) REVERT: C 214 MET cc_start: 0.7539 (ttp) cc_final: 0.7265 (tmm) REVERT: C 899 ASP cc_start: 0.7940 (t70) cc_final: 0.7566 (t0) REVERT: C 984 TYR cc_start: 0.7601 (m-80) cc_final: 0.7183 (t80) REVERT: C 1071 TYR cc_start: 0.8818 (m-80) cc_final: 0.8379 (m-80) outliers start: 51 outliers final: 38 residues processed: 268 average time/residue: 0.1738 time to fit residues: 76.5647 Evaluate side-chains 256 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 80 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 306 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 HIS B1051 GLN B1058 HIS B1059 ASN C 270 HIS C1059 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111752 restraints weight = 35801.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114355 restraints weight = 23032.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116069 restraints weight = 17532.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117086 restraints weight = 14703.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117836 restraints weight = 13189.691| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27474 Z= 0.132 Angle : 0.545 9.316 37488 Z= 0.273 Chirality : 0.044 0.320 4620 Planarity : 0.003 0.041 4584 Dihedral : 5.390 57.402 3562 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.06 % Allowed : 11.48 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3177 helix: 2.11 (0.19), residues: 747 sheet: 0.56 (0.19), residues: 720 loop : -0.71 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1090 TYR 0.021 0.001 TYR A 407 PHE 0.012 0.001 PHE C 39 TRP 0.007 0.001 TRP C 259 HIS 0.004 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (27336) covalent geometry : angle 0.51824 / 0.27 (37116) SS BOND : bond 0.00298 / 0.20 ( 42) SS BOND : angle 0.99385 / 0.73 ( 84) hydrogen bonds : bond 0.04257 / 2.78 ( 1099) hydrogen bonds : angle 5.04065 / 3.53 ( 3063) link_ALPHA1-2 : bond 0.00286 / 0.14 ( 3) link_ALPHA1-2 : angle 1.36878 / 0.93 ( 9) link_ALPHA1-3 : bond 0.00758 / 0.38 ( 3) link_ALPHA1-3 : angle 1.26805 / 0.78 ( 9) link_ALPHA1-6 : bond 0.01161 / 0.63 ( 6) link_ALPHA1-6 : angle 1.94881 / 1.20 ( 18) link_BETA1-2 : bond 0.00135 / 0.07 ( 3) link_BETA1-2 : angle 1.94588 / 1.46 ( 9) link_BETA1-4 : bond 0.00434 / 0.29 ( 36) link_BETA1-4 : angle 1.14506 / 0.85 ( 108) link_NAG-ASN : bond 0.00670 / 0.48 ( 45) link_NAG-ASN : angle 2.44643 / 1.72 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.918 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 176 PHE cc_start: 0.7867 (m-80) cc_final: 0.7631 (m-80) REVERT: A 214 MET cc_start: 0.7988 (tmm) cc_final: 0.6720 (tmm) REVERT: A 899 ASP cc_start: 0.8130 (t70) cc_final: 0.7731 (t0) REVERT: A 1057 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 899 ASP cc_start: 0.8065 (t70) cc_final: 0.7752 (t0) REVERT: B 984 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.7137 (t80) REVERT: C 38 LYS cc_start: 0.8196 (mttm) cc_final: 0.7733 (mtpp) REVERT: C 545 ASP cc_start: 0.7257 (t0) cc_final: 0.7050 (t0) REVERT: C 899 ASP cc_start: 0.7984 (t70) cc_final: 0.7553 (t0) REVERT: C 984 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7214 (t80) REVERT: C 1071 TYR cc_start: 0.8815 (m-80) cc_final: 0.8374 (m-80) outliers start: 59 outliers final: 48 residues processed: 268 average time/residue: 0.1656 time to fit residues: 72.8924 Evaluate side-chains 261 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 83 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 146 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 187 ASN A 270 HIS A 445 ASN A1058 HIS ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B 996 GLN C 270 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109681 restraints weight = 36027.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112295 restraints weight = 23166.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114019 restraints weight = 17518.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115010 restraints weight = 14687.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115749 restraints weight = 13193.498| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27474 Z= 0.176 Angle : 0.591 11.631 37488 Z= 0.297 Chirality : 0.045 0.313 4620 Planarity : 0.003 0.042 4584 Dihedral : 5.474 57.859 3562 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.06 % Allowed : 11.76 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3177 helix: 1.96 (0.19), residues: 744 sheet: 0.39 (0.19), residues: 729 loop : -0.75 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 547 TYR 0.017 0.001 TYR A 407 PHE 0.022 0.001 PHE A 35 TRP 0.008 0.001 TRP C 259 HIS 0.005 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (27336) covalent geometry : angle 0.56381 / 0.29 (37116) SS BOND : bond 0.00472 / 0.28 ( 42) SS BOND : angle 1.42146 / 1.14 ( 84) hydrogen bonds : bond 0.04577 / 2.99 ( 1099) hydrogen bonds : angle 5.12156 / 3.58 ( 3063) link_ALPHA1-2 : bond 0.00232 / 0.12 ( 3) link_ALPHA1-2 : angle 1.36491 / 0.92 ( 9) link_ALPHA1-3 : bond 0.00712 / 0.36 ( 3) link_ALPHA1-3 : angle 1.35164 / 0.79 ( 9) link_ALPHA1-6 : bond 0.01118 / 0.62 ( 6) link_ALPHA1-6 : angle 2.05687 / 1.27 ( 18) link_BETA1-2 : bond 0.00310 / 0.16 ( 3) link_BETA1-2 : angle 2.23753 / 1.69 ( 9) link_BETA1-4 : bond 0.00397 / 0.26 ( 36) link_BETA1-4 : angle 1.14100 / 0.84 ( 108) link_NAG-ASN : bond 0.00542 / 0.35 ( 45) link_NAG-ASN : angle 2.46952 / 1.74 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.941 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 176 PHE cc_start: 0.7899 (m-80) cc_final: 0.7677 (m-80) REVERT: A 214 MET cc_start: 0.8011 (tmm) cc_final: 0.6726 (tmm) REVERT: A 899 ASP cc_start: 0.8234 (t70) cc_final: 0.7802 (t0) REVERT: A 1057 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 899 ASP cc_start: 0.8208 (t70) cc_final: 0.7726 (t0) REVERT: B 984 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.7150 (t80) REVERT: C 214 MET cc_start: 0.7666 (tmm) cc_final: 0.7259 (tmm) REVERT: C 397 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: C 899 ASP cc_start: 0.8122 (t70) cc_final: 0.7624 (t0) REVERT: C 984 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7258 (t80) outliers start: 59 outliers final: 52 residues processed: 268 average time/residue: 0.1639 time to fit residues: 72.0451 Evaluate side-chains 269 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 223 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108846 restraints weight = 36145.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111407 restraints weight = 23367.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113111 restraints weight = 17669.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114138 restraints weight = 14836.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114846 restraints weight = 13323.458| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27474 Z= 0.157 Angle : 0.572 12.911 37488 Z= 0.287 Chirality : 0.044 0.310 4620 Planarity : 0.003 0.042 4584 Dihedral : 5.419 57.727 3562 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.02 % Allowed : 11.76 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3177 helix: 1.99 (0.19), residues: 747 sheet: 0.39 (0.19), residues: 714 loop : -0.80 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.016 0.001 TYR C 407 PHE 0.020 0.001 PHE B 35 TRP 0.007 0.001 TRP C 259 HIS 0.004 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (27336) covalent geometry : angle 0.54617 / 0.28 (37116) SS BOND : bond 0.00513 / 0.29 ( 42) SS BOND : angle 1.42956 / 1.19 ( 84) hydrogen bonds : bond 0.04418 / 2.89 ( 1099) hydrogen bonds : angle 5.07821 / 3.55 ( 3063) link_ALPHA1-2 : bond 0.00255 / 0.13 ( 3) link_ALPHA1-2 : angle 1.31217 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00752 / 0.38 ( 3) link_ALPHA1-3 : angle 1.31005 / 0.79 ( 9) link_ALPHA1-6 : bond 0.01186 / 0.66 ( 6) link_ALPHA1-6 : angle 1.93689 / 1.20 ( 18) link_BETA1-2 : bond 0.00146 / 0.07 ( 3) link_BETA1-2 : angle 1.91641 / 1.43 ( 9) link_BETA1-4 : bond 0.00428 / 0.29 ( 36) link_BETA1-4 : angle 1.13792 / 0.84 ( 108) link_NAG-ASN : bond 0.00527 / 0.34 ( 45) link_NAG-ASN : angle 2.35304 / 1.66 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 MET cc_start: 0.8007 (tmm) cc_final: 0.6933 (tmm) REVERT: A 899 ASP cc_start: 0.8194 (t70) cc_final: 0.7756 (t0) REVERT: A 1061 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7970 (mm-40) REVERT: B 38 LYS cc_start: 0.7961 (mttm) cc_final: 0.7356 (mttm) REVERT: B 111 LYS cc_start: 0.5946 (pttm) cc_final: 0.5564 (tptt) REVERT: B 899 ASP cc_start: 0.8134 (t70) cc_final: 0.7626 (t0) REVERT: B 984 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.7086 (t80) REVERT: C 397 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7800 (tp30) REVERT: C 984 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7249 (t80) REVERT: C 1071 TYR cc_start: 0.8808 (m-80) cc_final: 0.8454 (m-80) outliers start: 58 outliers final: 53 residues processed: 263 average time/residue: 0.1627 time to fit residues: 70.3676 Evaluate side-chains 266 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1082 GLN Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 119 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 HIS C 110 HIS C1061 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109419 restraints weight = 35997.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112017 restraints weight = 23294.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113534 restraints weight = 17647.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114674 restraints weight = 14988.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115298 restraints weight = 13430.214| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27474 Z= 0.107 Angle : 0.532 11.747 37488 Z= 0.267 Chirality : 0.043 0.307 4620 Planarity : 0.003 0.042 4584 Dihedral : 5.114 53.986 3562 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.75 % Allowed : 12.25 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3177 helix: 2.24 (0.20), residues: 747 sheet: 0.47 (0.19), residues: 714 loop : -0.75 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 894 TYR 0.014 0.001 TYR B 407 PHE 0.022 0.001 PHE A 35 TRP 0.006 0.001 TRP C 259 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (27336) covalent geometry : angle 0.50836 / 0.26 (37116) SS BOND : bond 0.00481 / 0.26 ( 42) SS BOND : angle 1.20266 / 0.99 ( 84) hydrogen bonds : bond 0.03939 / 2.58 ( 1099) hydrogen bonds : angle 4.92182 / 3.45 ( 3063) link_ALPHA1-2 : bond 0.00346 / 0.17 ( 3) link_ALPHA1-2 : angle 1.28673 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00811 / 0.41 ( 3) link_ALPHA1-3 : angle 1.23269 / 0.81 ( 9) link_ALPHA1-6 : bond 0.01173 / 0.64 ( 6) link_ALPHA1-6 : angle 1.71654 / 1.06 ( 18) link_BETA1-2 : bond 0.00084 / 0.04 ( 3) link_BETA1-2 : angle 1.44894 / 1.05 ( 9) link_BETA1-4 : bond 0.00461 / 0.30 ( 36) link_BETA1-4 : angle 1.06814 / 0.80 ( 108) link_NAG-ASN : bond 0.00529 / 0.34 ( 45) link_NAG-ASN : angle 2.20235 / 1.56 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.6499 (pttm) cc_final: 0.5815 (tptt) REVERT: A 214 MET cc_start: 0.8047 (tmm) cc_final: 0.6958 (tmm) REVERT: A 263 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8772 (p) REVERT: A 899 ASP cc_start: 0.7912 (t70) cc_final: 0.7672 (t0) REVERT: A 1061 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7980 (mm-40) REVERT: A 1184 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6803 (mt-10) REVERT: B 111 LYS cc_start: 0.6017 (pttm) cc_final: 0.5705 (tptt) REVERT: B 899 ASP cc_start: 0.7978 (t70) cc_final: 0.7558 (t0) REVERT: C 111 LYS cc_start: 0.6188 (pttm) cc_final: 0.5825 (tptt) REVERT: C 372 TYR cc_start: 0.8015 (m-10) cc_final: 0.7765 (m-80) REVERT: C 397 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7826 (tp30) REVERT: C 899 ASP cc_start: 0.7994 (t0) cc_final: 0.7541 (t0) REVERT: C 984 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.7160 (t80) REVERT: C 1071 TYR cc_start: 0.8746 (m-80) cc_final: 0.8373 (m-80) outliers start: 50 outliers final: 40 residues processed: 262 average time/residue: 0.1725 time to fit residues: 74.0720 Evaluate side-chains 253 residues out of total 2865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 1010 ILE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 722 SER Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 945 VAL Chi-restraints excluded: chain C residue 984 TYR Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1191 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 125 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 150 optimal weight: 0.0570 chunk 85 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 286 optimal weight: 0.0970 chunk 175 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108820 restraints weight = 35852.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111390 restraints weight = 23167.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.113066 restraints weight = 17630.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.114093 restraints weight = 14843.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114781 restraints weight = 13309.180| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27474 Z= 0.164 Angle : 0.576 12.309 37488 Z= 0.288 Chirality : 0.044 0.308 4620 Planarity : 0.003 0.042 4584 Dihedral : 5.225 53.085 3562 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.71 % Allowed : 12.29 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3177 helix: 2.04 (0.19), residues: 747 sheet: 0.46 (0.19), residues: 735 loop : -0.81 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1090 TYR 0.016 0.001 TYR B 413 PHE 0.016 0.001 PHE A 35 TRP 0.008 0.001 TRP C 259 HIS 0.005 0.001 HIS C1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (27336) covalent geometry : angle 0.55178 / 0.28 (37116) SS BOND : bond 0.00523 / 0.29 ( 42) SS BOND : angle 1.33291 / 1.08 ( 84) hydrogen bonds : bond 0.04406 / 2.89 ( 1099) hydrogen bonds : angle 5.01777 / 3.51 ( 3063) link_ALPHA1-2 : bond 0.00251 / 0.13 ( 3) link_ALPHA1-2 : angle 1.35502 / 0.91 ( 9) link_ALPHA1-3 : bond 0.00643 / 0.32 ( 3) link_ALPHA1-3 : angle 1.41032 / 0.83 ( 9) link_ALPHA1-6 : bond 0.01137 / 0.62 ( 6) link_ALPHA1-6 : angle 1.90536 / 1.18 ( 18) link_BETA1-2 : bond 0.00287 / 0.14 ( 3) link_BETA1-2 : angle 2.04563 / 1.55 ( 9) link_BETA1-4 : bond 0.00419 / 0.28 ( 36) link_BETA1-4 : angle 1.11571 / 0.82 ( 108) link_NAG-ASN : bond 0.00504 / 0.32 ( 45) link_NAG-ASN : angle 2.28089 / 1.62 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4157.66 seconds wall clock time: 73 minutes 8.71 seconds (4388.71 seconds total)