Starting phenix.real_space_refine on Thu Mar 5 07:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oro_20176/03_2026/6oro_20176.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oro_20176/03_2026/6oro_20176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oro_20176/03_2026/6oro_20176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oro_20176/03_2026/6oro_20176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oro_20176/03_2026/6oro_20176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oro_20176/03_2026/6oro_20176.map" } resolution = 3.9 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= -0.001 sd= 0.213 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12543 2.51 5 N 3345 2.21 5 O 4077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20085 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.75, per 1000 atoms: 0.24 Number of scatterers: 20085 At special positions: 0 Unit cell: (143.6, 132.112, 153.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4077 8.00 N 3345 7.00 C 12543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=3, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 620 " - " ASN B 88 " " NAG B 625 " - " ASN B 339 " " NAG B 626 " - " ASN B 355 " " NAG B 629 " - " ASN B 276 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 620 " - " ASN G 88 " " NAG G 625 " - " ASN G 339 " " NAG G 626 " - " ASN G 355 " " NAG G 629 " - " ASN G 276 " " NAG I 620 " - " ASN I 88 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 629 " - " ASN I 276 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 448 " " NAG Q 1 " - " ASN B 295 " " NAG R 1 " - " ASN B 197 " " NAG S 1 " - " ASN B 392 " " NAG T 1 " - " ASN B 386 " " NAG U 1 " - " ASN B 301 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN G 332 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 295 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN G 392 " " NAG c 1 " - " ASN G 386 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN I 160 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 262 " " NAG h 1 " - " ASN I 448 " " NAG i 1 " - " ASN I 295 " " NAG j 1 " - " ASN I 197 " " NAG k 1 " - " ASN I 392 " " NAG l 1 " - " ASN I 386 " " NAG m 1 " - " ASN I 301 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 42 sheets defined 15.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.724A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.774A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.730A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS B 117 " --> pdb=" O GLN B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP B 477 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.776A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.528A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.731A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 624' Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.527A pdb=" N LYS C 655 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.775A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.618A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.438A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 113 removed outlier: 3.739A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 117 removed outlier: 3.535A pdb=" N LYS G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.134A pdb=" N MET G 150 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG G 151 " --> pdb=" O SER G 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 151' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 353 removed outlier: 3.570A pdb=" N PHE G 353 " --> pdb=" O ARG G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 350 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS I 117 " --> pdb=" O GLN I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 348 " --> pdb=" O LYS I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE I 353 " --> pdb=" O ARG I 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 350 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.616A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'I' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.590A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.124A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 239 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.281A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 308 removed outlier: 3.510A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 307 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.573A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 81 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER E 67 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.970A pdb=" N CYS E 88 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 90 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU E 97 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.575A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY I 495 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 removed outlier: 3.740A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.511A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 307 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 329 through 333 removed outlier: 3.883A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.506A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.511A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE I 307 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR J 68 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.902A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.910A pdb=" N SER K 67 " --> pdb=" O THR K 70 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 88 through 91 removed outlier: 3.969A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL K 90 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU K 97 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER L 67 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.968A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL L 90 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 936 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: 2.92 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3214 1.26 - 1.40: 4782 1.40 - 1.54: 12093 1.54 - 1.68: 230 1.68 - 1.82: 162 Bond restraints: 20481 Sorted by residual: bond pdb=" C ASN F 618 " pdb=" O ASN F 618 " ideal model delta sigma weight residual 1.233 1.118 0.115 1.36e-02 5.41e+03 7.13e+01 bond pdb=" C ASN F 618 " pdb=" N LEU F 619 " ideal model delta sigma weight residual 1.332 1.218 0.114 1.40e-02 5.10e+03 6.62e+01 bond pdb=" C ILE B 309 " pdb=" O ILE B 309 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.19e-02 7.06e+03 4.17e+01 bond pdb=" C ILE G 309 " pdb=" O ILE G 309 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C ALA I 316 " pdb=" O ALA I 316 " ideal model delta sigma weight residual 1.233 1.163 0.071 1.28e-02 6.10e+03 3.05e+01 ... (remaining 20476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 27098 3.50 - 6.99: 597 6.99 - 10.49: 77 10.49 - 13.99: 22 13.99 - 17.48: 4 Bond angle restraints: 27798 Sorted by residual: angle pdb=" CA PRO G 313 " pdb=" N PRO G 313 " pdb=" CD PRO G 313 " ideal model delta sigma weight residual 111.50 96.11 15.39 1.40e+00 5.10e-01 1.21e+02 angle pdb=" CA PRO B 313 " pdb=" N PRO B 313 " pdb=" CD PRO B 313 " ideal model delta sigma weight residual 111.50 99.17 12.33 1.40e+00 5.10e-01 7.76e+01 angle pdb=" CA PRO I 313 " pdb=" N PRO I 313 " pdb=" CD PRO I 313 " ideal model delta sigma weight residual 111.50 99.85 11.65 1.40e+00 5.10e-01 6.92e+01 angle pdb=" N PRO B 136 " pdb=" CA PRO B 136 " pdb=" C PRO B 136 " ideal model delta sigma weight residual 113.47 101.67 11.80 1.43e+00 4.89e-01 6.81e+01 angle pdb=" N PRO I 136 " pdb=" CA PRO I 136 " pdb=" C PRO I 136 " ideal model delta sigma weight residual 113.47 102.44 11.03 1.43e+00 4.89e-01 5.95e+01 ... (remaining 27793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 12560 21.75 - 43.51: 571 43.51 - 65.26: 182 65.26 - 87.01: 94 87.01 - 108.76: 51 Dihedral angle restraints: 13458 sinusoidal: 6549 harmonic: 6909 Sorted by residual: dihedral pdb=" CA ASN C 637 " pdb=" C ASN C 637 " pdb=" N TYR C 638 " pdb=" CA TYR C 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN A 637 " pdb=" C ASN A 637 " pdb=" N TYR A 638 " pdb=" CA TYR A 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN F 637 " pdb=" C ASN F 637 " pdb=" N TYR F 638 " pdb=" CA TYR F 638 " ideal model delta harmonic sigma weight residual 180.00 130.99 49.01 0 5.00e+00 4.00e-02 9.61e+01 ... (remaining 13455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 3355 0.302 - 0.604: 15 0.604 - 0.907: 3 0.907 - 1.209: 0 1.209 - 1.511: 2 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 618 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.71e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.70e+01 chirality pdb=" C1 NAG B 629 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 629 " pdb=" O5 NAG B 629 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3372 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 617 " -0.030 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C ARG F 617 " 0.106 2.00e-02 2.50e+03 pdb=" O ARG F 617 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN F 618 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 309 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ILE B 309 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE B 309 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY B 312 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.049 2.00e-02 2.50e+03 4.05e-02 2.05e+01 pdb=" C7 NAG F 703 " 0.000 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.068 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.012 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 313 2.62 - 3.19: 16485 3.19 - 3.76: 27050 3.76 - 4.33: 35037 4.33 - 4.90: 58333 Nonbonded interactions: 137218 Sorted by model distance: nonbonded pdb=" O4 NAG F 703 " pdb=" O6 NAG F 703 " model vdw 2.048 3.040 nonbonded pdb=" OE2 GLU C 621 " pdb=" C5 NAG C 702 " model vdw 2.220 3.470 nonbonded pdb=" OE2 GLU A 621 " pdb=" C5 NAG A 702 " model vdw 2.220 3.470 nonbonded pdb=" O VAL H 12 " pdb=" OG SER H 112 " model vdw 2.263 3.040 nonbonded pdb=" O VAL J 12 " pdb=" OG SER J 112 " model vdw 2.263 3.040 ... (remaining 137213 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.470 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.009 0.115 20613 Z= 0.448 Angle : 1.425 23.895 28152 Z= 0.727 Chirality : 0.087 1.511 3375 Planarity : 0.008 0.084 3432 Dihedral : 16.518 108.762 8919 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.05 % Favored : 86.35 % Rotamer: Outliers : 2.93 % Allowed : 2.64 % Favored : 94.44 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.92 % 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: -5.30 (0.13), residues: 2367 helix: -4.63 (0.15), residues: 330 sheet: -3.26 (0.20), residues: 465 loop : -3.56 (0.12), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 308 TYR 0.043 0.003 TYR I 134 PHE 0.039 0.003 PHE J 100C TRP 0.035 0.004 TRP H 47 HIS 0.011 0.002 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00911 (20481) covalent geometry : angle 1.31879 (27798) SS BOND : bond 0.00665 ( 33) SS BOND : angle 1.57935 ( 66) hydrogen bonds : bond 0.30203 ( 367) hydrogen bonds : angle 10.02526 ( 936) Misc. bond : bond 0.00040 ( 3) link_ALPHA1-2 : bond 0.01588 ( 6) link_ALPHA1-2 : angle 3.52757 ( 18) link_ALPHA1-3 : bond 0.00222 ( 3) link_ALPHA1-3 : angle 4.14878 ( 9) link_ALPHA1-6 : bond 0.00262 ( 3) link_ALPHA1-6 : angle 1.73647 ( 9) link_BETA1-4 : bond 0.01456 ( 36) link_BETA1-4 : angle 4.43551 ( 108) link_NAG-ASN : bond 0.01474 ( 48) link_NAG-ASN : angle 6.50333 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 580 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9189 (mttp) cc_final: 0.8868 (mtmm) REVERT: A 640 GLN cc_start: 0.9037 (mm110) cc_final: 0.8825 (mm-40) REVERT: B 92 GLU cc_start: 0.5024 (pt0) cc_final: 0.4754 (pt0) REVERT: B 95 MET cc_start: 0.8690 (ptm) cc_final: 0.8424 (ptt) REVERT: B 114 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: B 161 MET cc_start: 0.8354 (tpp) cc_final: 0.7879 (tpt) REVERT: B 356 ASN cc_start: 0.9183 (t0) cc_final: 0.8980 (t0) REVERT: B 432 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8479 (tp-100) REVERT: B 466 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: C 625 ASN cc_start: 0.8945 (m-40) cc_final: 0.8733 (m-40) REVERT: C 635 ILE cc_start: 0.9296 (tt) cc_final: 0.9000 (tt) REVERT: C 647 GLU cc_start: 0.9068 (pp20) cc_final: 0.8769 (pp20) REVERT: D 19 LYS cc_start: 0.8877 (tttt) cc_final: 0.8674 (tttm) REVERT: D 38 ARG cc_start: 0.7661 (ptm160) cc_final: 0.7184 (ttp-170) REVERT: E 33 VAL cc_start: 0.8233 (p) cc_final: 0.6967 (p) REVERT: E 66 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8360 (tttp) REVERT: E 97 LEU cc_start: 0.8553 (tp) cc_final: 0.8228 (tp) REVERT: E 106 VAL cc_start: 0.6327 (m) cc_final: 0.6016 (m) REVERT: F 616 ASN cc_start: 0.9345 (t0) cc_final: 0.9089 (t0) REVERT: F 640 GLN cc_start: 0.8997 (mm110) cc_final: 0.8758 (mm-40) REVERT: G 104 MET cc_start: 0.8905 (tpp) cc_final: 0.8265 (tpp) REVERT: G 129 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8341 (pp) REVERT: G 180 ASP cc_start: 0.9203 (m-30) cc_final: 0.8585 (m-30) REVERT: G 189 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8024 (mmmt) REVERT: G 308 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8099 (ttm170) REVERT: G 356 ASN cc_start: 0.9092 (t0) cc_final: 0.8678 (t0) REVERT: G 427 TRP cc_start: 0.8377 (m-90) cc_final: 0.7590 (m-90) REVERT: G 466 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: H 72 ASP cc_start: 0.8941 (t0) cc_final: 0.8599 (t0) REVERT: H 75 LYS cc_start: 0.8589 (pttt) cc_final: 0.8160 (pttm) REVERT: H 99 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8548 (tp40) REVERT: I 104 MET cc_start: 0.9048 (tpp) cc_final: 0.8698 (tpp) REVERT: I 150 MET cc_start: 0.9364 (mmm) cc_final: 0.9048 (mmm) REVERT: I 466 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: J 19 LYS cc_start: 0.8954 (tttt) cc_final: 0.8642 (tttm) REVERT: J 67 PHE cc_start: 0.6524 (m-80) cc_final: 0.6013 (m-80) REVERT: K 33 VAL cc_start: 0.8233 (p) cc_final: 0.7623 (p) REVERT: L 33 VAL cc_start: 0.7953 (p) cc_final: 0.6594 (p) REVERT: L 60 ASP cc_start: 0.8750 (p0) cc_final: 0.8511 (t0) REVERT: L 66 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8436 (ttpp) outliers start: 61 outliers final: 18 residues processed: 610 average time/residue: 0.1454 time to fit residues: 133.8765 Evaluate side-chains 418 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 394 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 313 PRO Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain J residue 83 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 300 ASN B 330 HIS B 428 GLN C 543 ASN C 575 GLN C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 76 ASN D 81 GLN D 99 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 300 ASN G 330 HIS G 440 GLN H 81 GLN H 99 GLN I 258 GLN I 300 ASN I 330 HIS J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108917 restraints weight = 32362.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112313 restraints weight = 17671.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114592 restraints weight = 12116.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116089 restraints weight = 9491.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117027 restraints weight = 8068.505| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20613 Z= 0.157 Angle : 0.939 19.527 28152 Z= 0.434 Chirality : 0.054 0.655 3375 Planarity : 0.005 0.050 3432 Dihedral : 14.888 102.394 4606 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.11 % Favored : 88.72 % Rotamer: Outliers : 2.69 % Allowed : 11.08 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -4.84 (0.14), residues: 2367 helix: -3.83 (0.18), residues: 372 sheet: -2.75 (0.18), residues: 591 loop : -3.38 (0.14), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 151 TYR 0.013 0.001 TYR J 100E PHE 0.036 0.002 PHE J 100C TRP 0.026 0.002 TRP G 69 HIS 0.006 0.001 HIS K 95B Details of bonding type rmsd covalent geometry : bond 0.00328 (20481) covalent geometry : angle 0.87385 (27798) SS BOND : bond 0.00283 ( 33) SS BOND : angle 0.70604 ( 66) hydrogen bonds : bond 0.04908 ( 367) hydrogen bonds : angle 7.19245 ( 936) Misc. bond : bond 0.00045 ( 3) link_ALPHA1-2 : bond 0.01475 ( 6) link_ALPHA1-2 : angle 3.24707 ( 18) link_ALPHA1-3 : bond 0.00533 ( 3) link_ALPHA1-3 : angle 2.31442 ( 9) link_ALPHA1-6 : bond 0.01971 ( 3) link_ALPHA1-6 : angle 2.87666 ( 9) link_BETA1-4 : bond 0.00989 ( 36) link_BETA1-4 : angle 2.99053 ( 108) link_NAG-ASN : bond 0.00637 ( 48) link_NAG-ASN : angle 4.00212 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 475 time to evaluate : 0.637 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 601 LYS cc_start: 0.9162 (mttp) cc_final: 0.8789 (mtmm) REVERT: B 114 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: B 134 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.4715 (m-10) REVERT: B 154 LEU cc_start: 0.8315 (mt) cc_final: 0.7821 (mm) REVERT: B 432 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8033 (mm-40) REVERT: C 635 ILE cc_start: 0.8920 (tt) cc_final: 0.8537 (tt) REVERT: D 38 ARG cc_start: 0.7741 (ptm160) cc_final: 0.7124 (ttp-170) REVERT: D 82 MET cc_start: 0.7581 (mmt) cc_final: 0.7290 (mmp) REVERT: E 66 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8199 (tttm) REVERT: F 635 ILE cc_start: 0.8914 (tt) cc_final: 0.8656 (tt) REVERT: G 129 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8544 (pp) REVERT: G 180 ASP cc_start: 0.9035 (m-30) cc_final: 0.8427 (m-30) REVERT: G 308 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8035 (mtt90) REVERT: G 356 ASN cc_start: 0.8973 (t0) cc_final: 0.8762 (t0) REVERT: G 432 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8197 (mp10) REVERT: G 475 MET cc_start: 0.8466 (tpp) cc_final: 0.8216 (tpp) REVERT: H 72 ASP cc_start: 0.8838 (t0) cc_final: 0.8452 (t0) REVERT: H 75 LYS cc_start: 0.8511 (pttt) cc_final: 0.8172 (ptmt) REVERT: H 83 ARG cc_start: 0.7529 (pmt170) cc_final: 0.6719 (ptm160) REVERT: I 46 LYS cc_start: 0.4995 (mttm) cc_final: 0.4229 (mmtm) REVERT: I 104 MET cc_start: 0.9108 (tpp) cc_final: 0.8430 (tpp) REVERT: I 432 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8196 (mm110) REVERT: J 19 LYS cc_start: 0.8931 (tttt) cc_final: 0.8668 (tttm) REVERT: J 83 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6724 (ttm-80) REVERT: J 97 TRP cc_start: 0.8946 (m100) cc_final: 0.8513 (m100) REVERT: K 18 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7997 (t) REVERT: L 31 GLU cc_start: 0.7795 (tp30) cc_final: 0.7309 (tp30) outliers start: 56 outliers final: 31 residues processed: 504 average time/residue: 0.1289 time to fit residues: 103.0437 Evaluate side-chains 430 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 393 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 chunk 205 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107753 restraints weight = 32588.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111143 restraints weight = 17876.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113435 restraints weight = 12298.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114931 restraints weight = 9641.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115913 restraints weight = 8211.950| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20613 Z= 0.150 Angle : 0.872 17.831 28152 Z= 0.403 Chirality : 0.052 0.367 3375 Planarity : 0.004 0.044 3432 Dihedral : 12.863 99.194 4586 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.36 % Favored : 88.47 % Rotamer: Outliers : 3.12 % Allowed : 14.15 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.38 (0.15), residues: 2367 helix: -3.06 (0.22), residues: 354 sheet: -2.40 (0.20), residues: 597 loop : -3.23 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.015 0.001 TYR K 49 PHE 0.037 0.002 PHE D 100C TRP 0.025 0.002 TRP G 69 HIS 0.002 0.001 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00325 (20481) covalent geometry : angle 0.82106 (27798) SS BOND : bond 0.00238 ( 33) SS BOND : angle 0.67862 ( 66) hydrogen bonds : bond 0.04144 ( 367) hydrogen bonds : angle 6.29400 ( 936) Misc. bond : bond 0.00036 ( 3) link_ALPHA1-2 : bond 0.01467 ( 6) link_ALPHA1-2 : angle 3.24130 ( 18) link_ALPHA1-3 : bond 0.00663 ( 3) link_ALPHA1-3 : angle 1.50484 ( 9) link_ALPHA1-6 : bond 0.01952 ( 3) link_ALPHA1-6 : angle 2.98314 ( 9) link_BETA1-4 : bond 0.00851 ( 36) link_BETA1-4 : angle 2.77211 ( 108) link_NAG-ASN : bond 0.00606 ( 48) link_NAG-ASN : angle 3.22386 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 419 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9155 (mttp) cc_final: 0.8874 (mtmm) REVERT: B 104 MET cc_start: 0.8677 (tpp) cc_final: 0.8192 (tpp) REVERT: B 114 GLN cc_start: 0.8544 (tm130) cc_final: 0.8340 (tm-30) REVERT: B 134 TYR cc_start: 0.6745 (OUTLIER) cc_final: 0.4462 (m-10) REVERT: B 154 LEU cc_start: 0.8320 (mt) cc_final: 0.8109 (mm) REVERT: B 356 ASN cc_start: 0.8862 (t0) cc_final: 0.8614 (t0) REVERT: B 432 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8074 (mm-40) REVERT: C 571 TRP cc_start: 0.8330 (m100) cc_final: 0.8047 (m100) REVERT: C 635 ILE cc_start: 0.8909 (tt) cc_final: 0.8540 (tt) REVERT: D 13 GLN cc_start: 0.8013 (mp10) cc_final: 0.7694 (mp10) REVERT: D 34 MET cc_start: 0.8990 (mmm) cc_final: 0.8780 (mmm) REVERT: D 38 ARG cc_start: 0.7983 (ptm160) cc_final: 0.7293 (ttp-170) REVERT: D 67 PHE cc_start: 0.6635 (m-80) cc_final: 0.5863 (m-10) REVERT: D 82 MET cc_start: 0.7432 (mmt) cc_final: 0.7122 (mmt) REVERT: D 99 GLN cc_start: 0.8846 (tp40) cc_final: 0.8438 (tp-100) REVERT: E 66 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8152 (tttm) REVERT: F 635 ILE cc_start: 0.8920 (tt) cc_final: 0.8702 (tt) REVERT: G 69 TRP cc_start: 0.6434 (p-90) cc_final: 0.6220 (p-90) REVERT: G 129 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8687 (pp) REVERT: G 180 ASP cc_start: 0.8981 (m-30) cc_final: 0.8483 (m-30) REVERT: G 265 LEU cc_start: 0.9051 (mm) cc_final: 0.8767 (mt) REVERT: G 308 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7922 (mtt90) REVERT: G 356 ASN cc_start: 0.8998 (t0) cc_final: 0.8777 (t0) REVERT: G 427 TRP cc_start: 0.8198 (m-90) cc_final: 0.7705 (m-90) REVERT: G 432 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8171 (mp10) REVERT: H 72 ASP cc_start: 0.8771 (t0) cc_final: 0.8419 (t0) REVERT: H 83 ARG cc_start: 0.7465 (pmt170) cc_final: 0.6767 (ptm160) REVERT: H 99 GLN cc_start: 0.8594 (tp40) cc_final: 0.8046 (tp40) REVERT: I 46 LYS cc_start: 0.5032 (mttm) cc_final: 0.4334 (mmtp) REVERT: I 104 MET cc_start: 0.9121 (tpp) cc_final: 0.8655 (tpp) REVERT: I 150 MET cc_start: 0.9280 (mmm) cc_final: 0.9048 (tpp) REVERT: I 432 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8157 (mm110) REVERT: J 82 MET cc_start: 0.7524 (mmp) cc_final: 0.7172 (mmp) REVERT: J 83 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6871 (ttm-80) REVERT: J 97 TRP cc_start: 0.8951 (m100) cc_final: 0.8615 (m100) REVERT: J 99 GLN cc_start: 0.8625 (tp40) cc_final: 0.8404 (tp-100) REVERT: K 97 LEU cc_start: 0.8630 (tp) cc_final: 0.8177 (tt) REVERT: L 6 GLN cc_start: 0.7455 (pm20) cc_final: 0.7239 (pm20) REVERT: L 66 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8001 (tttp) outliers start: 65 outliers final: 45 residues processed: 453 average time/residue: 0.1364 time to fit residues: 96.8781 Evaluate side-chains 434 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 167 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 258 GLN C 543 ASN C 640 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN G 258 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108829 restraints weight = 32562.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112268 restraints weight = 17910.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114592 restraints weight = 12299.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116092 restraints weight = 9610.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117125 restraints weight = 8168.651| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20613 Z= 0.132 Angle : 0.814 17.370 28152 Z= 0.376 Chirality : 0.050 0.363 3375 Planarity : 0.004 0.051 3432 Dihedral : 11.530 91.292 4578 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.44 % Favored : 89.40 % Rotamer: Outliers : 2.73 % Allowed : 16.59 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.97 (0.15), residues: 2367 helix: -2.35 (0.27), residues: 306 sheet: -2.25 (0.20), residues: 633 loop : -3.01 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.017 0.001 TYR B 134 PHE 0.032 0.002 PHE H 100C TRP 0.026 0.001 TRP B 69 HIS 0.002 0.000 HIS L 95B Details of bonding type rmsd covalent geometry : bond 0.00279 (20481) covalent geometry : angle 0.77095 (27798) SS BOND : bond 0.00195 ( 33) SS BOND : angle 0.46854 ( 66) hydrogen bonds : bond 0.03401 ( 367) hydrogen bonds : angle 5.85397 ( 936) Misc. bond : bond 0.00027 ( 3) link_ALPHA1-2 : bond 0.01482 ( 6) link_ALPHA1-2 : angle 3.04168 ( 18) link_ALPHA1-3 : bond 0.00818 ( 3) link_ALPHA1-3 : angle 1.38872 ( 9) link_ALPHA1-6 : bond 0.01919 ( 3) link_ALPHA1-6 : angle 2.91178 ( 9) link_BETA1-4 : bond 0.00762 ( 36) link_BETA1-4 : angle 2.45003 ( 108) link_NAG-ASN : bond 0.00576 ( 48) link_NAG-ASN : angle 2.89274 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 399 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9057 (mttp) cc_final: 0.8638 (mtmm) REVERT: B 103 GLN cc_start: 0.7981 (pt0) cc_final: 0.7628 (tt0) REVERT: B 114 GLN cc_start: 0.8567 (tm130) cc_final: 0.8315 (tm-30) REVERT: B 134 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.4687 (m-80) REVERT: B 356 ASN cc_start: 0.8938 (t0) cc_final: 0.8651 (t0) REVERT: B 432 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8065 (mm-40) REVERT: C 635 ILE cc_start: 0.8841 (tt) cc_final: 0.8555 (tt) REVERT: D 34 MET cc_start: 0.8874 (mmm) cc_final: 0.8618 (mmm) REVERT: D 72 ASP cc_start: 0.8797 (t0) cc_final: 0.8495 (t0) REVERT: D 80 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (tt) REVERT: D 99 GLN cc_start: 0.8665 (tp40) cc_final: 0.8285 (tp-100) REVERT: E 66 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8063 (tttm) REVERT: F 635 ILE cc_start: 0.8790 (tt) cc_final: 0.8538 (tt) REVERT: G 129 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8351 (pp) REVERT: G 180 ASP cc_start: 0.9063 (m-30) cc_final: 0.8554 (m-30) REVERT: G 265 LEU cc_start: 0.9072 (mm) cc_final: 0.8758 (mt) REVERT: G 308 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7911 (mtt90) REVERT: G 356 ASN cc_start: 0.8991 (t0) cc_final: 0.8749 (t0) REVERT: G 427 TRP cc_start: 0.8114 (m-90) cc_final: 0.7486 (m-90) REVERT: G 432 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8152 (mp10) REVERT: H 72 ASP cc_start: 0.8778 (t0) cc_final: 0.8479 (t0) REVERT: H 81 GLN cc_start: 0.8854 (tt0) cc_final: 0.8494 (tt0) REVERT: H 83 ARG cc_start: 0.7560 (pmt170) cc_final: 0.6781 (ptm160) REVERT: H 99 GLN cc_start: 0.8525 (tp40) cc_final: 0.8032 (tp40) REVERT: I 46 LYS cc_start: 0.4810 (mttm) cc_final: 0.4208 (mmtp) REVERT: I 104 MET cc_start: 0.9070 (tpp) cc_final: 0.8723 (tpp) REVERT: I 150 MET cc_start: 0.9231 (mmm) cc_final: 0.8664 (mpp) REVERT: I 432 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8210 (mm110) REVERT: J 83 ARG cc_start: 0.7507 (pmt-80) cc_final: 0.7054 (ttm-80) REVERT: J 97 TRP cc_start: 0.8895 (m100) cc_final: 0.8475 (m100) REVERT: K 97 LEU cc_start: 0.8606 (tp) cc_final: 0.8178 (tt) REVERT: L 31 GLU cc_start: 0.8110 (tp30) cc_final: 0.7462 (tp30) REVERT: L 66 LYS cc_start: 0.8648 (ttpp) cc_final: 0.7926 (tttp) outliers start: 57 outliers final: 42 residues processed: 434 average time/residue: 0.1353 time to fit residues: 92.3589 Evaluate side-chains 432 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 386 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105588 restraints weight = 32757.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108887 restraints weight = 18195.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111098 restraints weight = 12630.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112556 restraints weight = 9976.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113432 restraints weight = 8533.536| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20613 Z= 0.186 Angle : 0.842 17.088 28152 Z= 0.392 Chirality : 0.051 0.375 3375 Planarity : 0.004 0.045 3432 Dihedral : 11.056 82.831 4563 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.32 % Favored : 88.51 % Rotamer: Outliers : 4.27 % Allowed : 15.97 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.83 (0.15), residues: 2367 helix: -2.00 (0.28), residues: 318 sheet: -1.96 (0.20), residues: 600 loop : -3.09 (0.14), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 71 TYR 0.018 0.001 TYR B 134 PHE 0.028 0.002 PHE H 100C TRP 0.029 0.002 TRP G 69 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00430 (20481) covalent geometry : angle 0.79931 (27798) SS BOND : bond 0.00265 ( 33) SS BOND : angle 0.68929 ( 66) hydrogen bonds : bond 0.03914 ( 367) hydrogen bonds : angle 5.83888 ( 936) Misc. bond : bond 0.00042 ( 3) link_ALPHA1-2 : bond 0.01278 ( 6) link_ALPHA1-2 : angle 3.16579 ( 18) link_ALPHA1-3 : bond 0.00696 ( 3) link_ALPHA1-3 : angle 1.55547 ( 9) link_ALPHA1-6 : bond 0.01834 ( 3) link_ALPHA1-6 : angle 2.97599 ( 9) link_BETA1-4 : bond 0.00757 ( 36) link_BETA1-4 : angle 2.40457 ( 108) link_NAG-ASN : bond 0.00589 ( 48) link_NAG-ASN : angle 2.98467 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 393 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9065 (mttp) cc_final: 0.8684 (mtmm) REVERT: B 103 GLN cc_start: 0.8336 (pt0) cc_final: 0.7940 (tt0) REVERT: B 114 GLN cc_start: 0.8646 (tm130) cc_final: 0.8250 (tm-30) REVERT: B 134 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.4763 (m-10) REVERT: B 432 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8090 (mm-40) REVERT: C 571 TRP cc_start: 0.8107 (m100) cc_final: 0.7801 (m100) REVERT: C 635 ILE cc_start: 0.8994 (tt) cc_final: 0.8645 (tt) REVERT: C 650 GLN cc_start: 0.7418 (mm110) cc_final: 0.7172 (mm110) REVERT: D 34 MET cc_start: 0.8889 (mmm) cc_final: 0.8611 (mmm) REVERT: D 67 PHE cc_start: 0.7029 (m-10) cc_final: 0.6624 (m-10) REVERT: D 99 GLN cc_start: 0.8757 (tp40) cc_final: 0.8371 (tp-100) REVERT: E 66 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8127 (tttm) REVERT: F 650 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7348 (mm110) REVERT: G 80 ASN cc_start: 0.8385 (m-40) cc_final: 0.8055 (p0) REVERT: G 129 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8373 (pp) REVERT: G 134 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.5038 (m-80) REVERT: G 180 ASP cc_start: 0.9077 (m-30) cc_final: 0.8499 (m-30) REVERT: G 265 LEU cc_start: 0.9115 (mm) cc_final: 0.8814 (mt) REVERT: G 308 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7957 (mtt90) REVERT: G 356 ASN cc_start: 0.9034 (t0) cc_final: 0.8776 (t0) REVERT: G 427 TRP cc_start: 0.8150 (m-90) cc_final: 0.7501 (m-90) REVERT: G 432 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8161 (mp10) REVERT: H 72 ASP cc_start: 0.8759 (t0) cc_final: 0.8462 (t0) REVERT: H 81 GLN cc_start: 0.8893 (tt0) cc_final: 0.8551 (tt0) REVERT: H 83 ARG cc_start: 0.7456 (pmt170) cc_final: 0.6717 (ptm160) REVERT: H 99 GLN cc_start: 0.8621 (tp40) cc_final: 0.8158 (tp40) REVERT: I 432 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8041 (mp10) REVERT: J 72 ASP cc_start: 0.8929 (t0) cc_final: 0.8651 (t0) REVERT: J 97 TRP cc_start: 0.8943 (m100) cc_final: 0.8543 (m100) REVERT: K 20 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7560 (mmt90) REVERT: K 97 LEU cc_start: 0.8683 (tp) cc_final: 0.8262 (tt) REVERT: L 31 GLU cc_start: 0.8061 (tp30) cc_final: 0.7525 (tp30) outliers start: 89 outliers final: 67 residues processed: 447 average time/residue: 0.1315 time to fit residues: 94.0991 Evaluate side-chains 455 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 384 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 177 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 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 = 0.3533 r_free = 0.3533 target = 0.131132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103213 restraints weight = 32870.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106440 restraints weight = 18781.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108601 restraints weight = 13228.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110042 restraints weight = 10546.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110904 restraints weight = 9072.141| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20613 Z= 0.207 Angle : 0.861 16.073 28152 Z= 0.402 Chirality : 0.052 0.388 3375 Planarity : 0.004 0.070 3432 Dihedral : 10.586 68.805 4554 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.83 % Favored : 88.00 % Rotamer: Outliers : 4.65 % Allowed : 16.64 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.78 (0.16), residues: 2367 helix: -1.71 (0.29), residues: 318 sheet: -2.09 (0.20), residues: 633 loop : -3.04 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 83 TYR 0.020 0.002 TYR B 134 PHE 0.028 0.002 PHE D 100C TRP 0.024 0.002 TRP B 69 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00479 (20481) covalent geometry : angle 0.81764 (27798) SS BOND : bond 0.00295 ( 33) SS BOND : angle 0.75261 ( 66) hydrogen bonds : bond 0.04118 ( 367) hydrogen bonds : angle 5.84634 ( 936) Misc. bond : bond 0.00053 ( 3) link_ALPHA1-2 : bond 0.01189 ( 6) link_ALPHA1-2 : angle 3.20054 ( 18) link_ALPHA1-3 : bond 0.00581 ( 3) link_ALPHA1-3 : angle 1.57723 ( 9) link_ALPHA1-6 : bond 0.02316 ( 3) link_ALPHA1-6 : angle 3.12857 ( 9) link_BETA1-4 : bond 0.00740 ( 36) link_BETA1-4 : angle 2.31147 ( 108) link_NAG-ASN : bond 0.00602 ( 48) link_NAG-ASN : angle 3.06720 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 387 time to evaluate : 0.724 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 577 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8231 (tp40) REVERT: A 601 LYS cc_start: 0.9087 (mttp) cc_final: 0.8702 (mtmm) REVERT: B 114 GLN cc_start: 0.8691 (tm130) cc_final: 0.8284 (tm-30) REVERT: B 134 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.5533 (m-10) REVERT: B 432 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8361 (tp-100) REVERT: C 635 ILE cc_start: 0.9052 (tt) cc_final: 0.8775 (tt) REVERT: D 34 MET cc_start: 0.8840 (mmm) cc_final: 0.8543 (mmm) REVERT: D 61 ASP cc_start: 0.8933 (t0) cc_final: 0.8722 (t0) REVERT: D 99 GLN cc_start: 0.8711 (tp40) cc_final: 0.8276 (tp-100) REVERT: E 66 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8067 (tttp) REVERT: F 650 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7319 (mm110) REVERT: G 80 ASN cc_start: 0.8495 (m-40) cc_final: 0.8194 (p0) REVERT: G 129 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8423 (pp) REVERT: G 134 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.5417 (m-80) REVERT: G 180 ASP cc_start: 0.9086 (m-30) cc_final: 0.8522 (m-30) REVERT: G 265 LEU cc_start: 0.9141 (mm) cc_final: 0.8843 (mt) REVERT: G 308 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7944 (mtt90) REVERT: G 356 ASN cc_start: 0.9092 (t0) cc_final: 0.8832 (t0) REVERT: G 427 TRP cc_start: 0.8174 (m-90) cc_final: 0.7519 (m-90) REVERT: G 432 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8175 (mp10) REVERT: H 72 ASP cc_start: 0.8762 (t0) cc_final: 0.8450 (t0) REVERT: H 81 GLN cc_start: 0.8928 (tt0) cc_final: 0.8440 (tt0) REVERT: H 99 GLN cc_start: 0.8610 (tp40) cc_final: 0.8117 (tp40) REVERT: I 46 LYS cc_start: 0.5196 (mmtt) cc_final: 0.4457 (mmtt) REVERT: I 432 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8041 (mp10) REVERT: J 72 ASP cc_start: 0.8836 (t0) cc_final: 0.8572 (t0) REVERT: K 66 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8015 (tttp) REVERT: K 97 LEU cc_start: 0.8703 (tp) cc_final: 0.8295 (tt) REVERT: L 79 GLU cc_start: 0.7739 (tp30) cc_final: 0.7452 (mm-30) REVERT: L 89 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8451 (tm-30) outliers start: 97 outliers final: 76 residues processed: 451 average time/residue: 0.1314 time to fit residues: 95.1101 Evaluate side-chains 456 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 375 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 193 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 156 optimal weight: 0.3980 chunk 128 optimal weight: 0.0570 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 GLN C 651 ASN G 99 ASN H 81 GLN ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108085 restraints weight = 32311.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111389 restraints weight = 17868.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113619 restraints weight = 12358.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115106 restraints weight = 9726.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116008 restraints weight = 8294.440| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20613 Z= 0.126 Angle : 0.789 15.243 28152 Z= 0.367 Chirality : 0.049 0.357 3375 Planarity : 0.004 0.048 3432 Dihedral : 9.706 59.841 4554 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.60 % Favored : 89.23 % Rotamer: Outliers : 3.65 % Allowed : 18.03 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.59 (0.16), residues: 2367 helix: -1.62 (0.29), residues: 318 sheet: -1.96 (0.20), residues: 618 loop : -2.89 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.020 0.001 TYR B 134 PHE 0.026 0.002 PHE D 100C TRP 0.032 0.001 TRP B 69 HIS 0.003 0.000 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00260 (20481) covalent geometry : angle 0.74918 (27798) SS BOND : bond 0.00314 ( 33) SS BOND : angle 0.55990 ( 66) hydrogen bonds : bond 0.03131 ( 367) hydrogen bonds : angle 5.46880 ( 936) Misc. bond : bond 0.00021 ( 3) link_ALPHA1-2 : bond 0.01303 ( 6) link_ALPHA1-2 : angle 2.90524 ( 18) link_ALPHA1-3 : bond 0.00701 ( 3) link_ALPHA1-3 : angle 1.48189 ( 9) link_ALPHA1-6 : bond 0.02640 ( 3) link_ALPHA1-6 : angle 3.30453 ( 9) link_BETA1-4 : bond 0.00682 ( 36) link_BETA1-4 : angle 2.05712 ( 108) link_NAG-ASN : bond 0.00576 ( 48) link_NAG-ASN : angle 2.85023 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 410 time to evaluate : 0.680 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 601 LYS cc_start: 0.8947 (mttp) cc_final: 0.8595 (mtmm) REVERT: B 114 GLN cc_start: 0.8545 (tm130) cc_final: 0.8257 (tm-30) REVERT: B 134 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: B 432 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8026 (mm-40) REVERT: C 635 ILE cc_start: 0.8863 (tt) cc_final: 0.8538 (tt) REVERT: D 28 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8449 (p) REVERT: D 34 MET cc_start: 0.8595 (mmm) cc_final: 0.8324 (mmm) REVERT: D 67 PHE cc_start: 0.7738 (m-10) cc_final: 0.7513 (m-10) REVERT: D 80 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8665 (tt) REVERT: D 99 GLN cc_start: 0.8450 (tp40) cc_final: 0.8041 (tp-100) REVERT: E 66 LYS cc_start: 0.8778 (ttpt) cc_final: 0.7962 (tttp) REVERT: F 650 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7236 (mm110) REVERT: G 80 ASN cc_start: 0.8500 (m-40) cc_final: 0.8190 (p0) REVERT: G 129 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8409 (pp) REVERT: G 134 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.5821 (m-80) REVERT: G 180 ASP cc_start: 0.9071 (m-30) cc_final: 0.8566 (m-30) REVERT: G 265 LEU cc_start: 0.9061 (mm) cc_final: 0.8715 (mt) REVERT: G 308 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7868 (mtt90) REVERT: G 356 ASN cc_start: 0.9072 (t0) cc_final: 0.8803 (t0) REVERT: G 427 TRP cc_start: 0.8110 (m-90) cc_final: 0.7517 (m-90) REVERT: G 432 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8139 (mp10) REVERT: H 72 ASP cc_start: 0.8730 (t0) cc_final: 0.8439 (t0) REVERT: H 81 GLN cc_start: 0.8874 (tt0) cc_final: 0.8416 (tt0) REVERT: H 83 ARG cc_start: 0.7340 (pmt170) cc_final: 0.6967 (ttm-80) REVERT: I 46 LYS cc_start: 0.4933 (mmtt) cc_final: 0.4385 (mmtt) REVERT: I 69 TRP cc_start: 0.6313 (p-90) cc_final: 0.5981 (p-90) REVERT: I 80 ASN cc_start: 0.8731 (m-40) cc_final: 0.8128 (p0) REVERT: I 432 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8032 (mp10) REVERT: J 72 ASP cc_start: 0.8802 (t0) cc_final: 0.8512 (t0) REVERT: J 97 TRP cc_start: 0.8880 (m100) cc_final: 0.8637 (m100) REVERT: L 31 GLU cc_start: 0.8532 (tp30) cc_final: 0.8254 (tp30) REVERT: L 66 LYS cc_start: 0.8675 (ttpp) cc_final: 0.7932 (tttm) REVERT: L 79 GLU cc_start: 0.7647 (tp30) cc_final: 0.7424 (mm-30) outliers start: 76 outliers final: 53 residues processed: 455 average time/residue: 0.1368 time to fit residues: 98.2741 Evaluate side-chains 443 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105331 restraints weight = 32850.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108632 restraints weight = 18585.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110826 restraints weight = 12960.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112272 restraints weight = 10278.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113207 restraints weight = 8821.258| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20613 Z= 0.163 Angle : 0.816 15.285 28152 Z= 0.381 Chirality : 0.050 0.374 3375 Planarity : 0.004 0.051 3432 Dihedral : 9.495 59.877 4552 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.45 % Favored : 88.38 % Rotamer: Outliers : 4.27 % Allowed : 17.99 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.50 (0.16), residues: 2367 helix: -1.48 (0.30), residues: 321 sheet: -1.94 (0.20), residues: 615 loop : -2.82 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 71 TYR 0.021 0.001 TYR B 134 PHE 0.020 0.002 PHE D 100C TRP 0.028 0.002 TRP B 69 HIS 0.010 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00369 (20481) covalent geometry : angle 0.77507 (27798) SS BOND : bond 0.00288 ( 33) SS BOND : angle 1.02264 ( 66) hydrogen bonds : bond 0.03534 ( 367) hydrogen bonds : angle 5.49220 ( 936) Misc. bond : bond 0.00035 ( 3) link_ALPHA1-2 : bond 0.01246 ( 6) link_ALPHA1-2 : angle 3.01591 ( 18) link_ALPHA1-3 : bond 0.00479 ( 3) link_ALPHA1-3 : angle 1.63962 ( 9) link_ALPHA1-6 : bond 0.02743 ( 3) link_ALPHA1-6 : angle 3.37837 ( 9) link_BETA1-4 : bond 0.00712 ( 36) link_BETA1-4 : angle 2.09341 ( 108) link_NAG-ASN : bond 0.00560 ( 48) link_NAG-ASN : angle 2.88392 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 383 time to evaluate : 0.670 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 601 LYS cc_start: 0.8926 (mttp) cc_final: 0.8598 (mtmm) REVERT: B 46 LYS cc_start: 0.6426 (mmtm) cc_final: 0.6086 (mmtm) REVERT: B 114 GLN cc_start: 0.8575 (tm130) cc_final: 0.8208 (tm-30) REVERT: B 134 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.5950 (m-80) REVERT: B 432 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8363 (tp-100) REVERT: C 635 ILE cc_start: 0.8941 (tt) cc_final: 0.8658 (tt) REVERT: D 18 LEU cc_start: 0.8811 (mt) cc_final: 0.8554 (mt) REVERT: D 34 MET cc_start: 0.8739 (mmm) cc_final: 0.8534 (mmm) REVERT: D 67 PHE cc_start: 0.8039 (m-10) cc_final: 0.7808 (m-10) REVERT: D 80 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8764 (tt) REVERT: D 99 GLN cc_start: 0.8535 (tp40) cc_final: 0.8097 (tp-100) REVERT: E 66 LYS cc_start: 0.8849 (ttpt) cc_final: 0.7981 (tttm) REVERT: F 650 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7369 (mm110) REVERT: G 80 ASN cc_start: 0.8620 (m-40) cc_final: 0.8277 (p0) REVERT: G 102 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7970 (mm-30) REVERT: G 125 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8704 (tt) REVERT: G 129 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8398 (pp) REVERT: G 134 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: G 180 ASP cc_start: 0.9073 (m-30) cc_final: 0.8554 (m-30) REVERT: G 308 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7799 (mtt90) REVERT: G 356 ASN cc_start: 0.9075 (t0) cc_final: 0.8809 (t0) REVERT: G 427 TRP cc_start: 0.8125 (m-90) cc_final: 0.7571 (m-90) REVERT: G 432 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8159 (mp10) REVERT: H 28 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (p) REVERT: H 72 ASP cc_start: 0.8747 (t0) cc_final: 0.8442 (t0) REVERT: H 81 GLN cc_start: 0.8858 (tt0) cc_final: 0.8427 (tt0) REVERT: I 46 LYS cc_start: 0.5517 (mmtt) cc_final: 0.4301 (mmtp) REVERT: I 69 TRP cc_start: 0.6337 (p-90) cc_final: 0.5928 (p-90) REVERT: I 328 MET cc_start: 0.8046 (mmm) cc_final: 0.7814 (tpt) REVERT: I 432 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8033 (mp10) REVERT: J 72 ASP cc_start: 0.8822 (t0) cc_final: 0.8515 (t0) REVERT: K 66 LYS cc_start: 0.8968 (ttpp) cc_final: 0.7760 (tttp) REVERT: K 97 LEU cc_start: 0.8782 (tp) cc_final: 0.8557 (tt) REVERT: L 31 GLU cc_start: 0.8413 (tp30) cc_final: 0.8079 (tp30) REVERT: L 66 LYS cc_start: 0.8681 (ttpp) cc_final: 0.7892 (tttm) REVERT: L 89 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8170 (tm-30) outliers start: 89 outliers final: 68 residues processed: 440 average time/residue: 0.1348 time to fit residues: 93.8624 Evaluate side-chains 448 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 373 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 95 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 83 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 203 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS B 80 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107745 restraints weight = 32539.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111124 restraints weight = 18242.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113368 restraints weight = 12670.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114851 restraints weight = 10009.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115748 restraints weight = 8563.404| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20613 Z= 0.130 Angle : 0.776 14.717 28152 Z= 0.362 Chirality : 0.049 0.365 3375 Planarity : 0.004 0.049 3432 Dihedral : 9.043 59.994 4552 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.86 % Favored : 88.97 % Rotamer: Outliers : 4.08 % Allowed : 18.13 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -3.40 (0.16), residues: 2367 helix: -1.35 (0.30), residues: 321 sheet: -1.90 (0.20), residues: 615 loop : -2.76 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 71 TYR 0.020 0.001 TYR B 134 PHE 0.020 0.001 PHE D 100C TRP 0.034 0.001 TRP B 69 HIS 0.009 0.001 HIS A 570 Details of bonding type rmsd covalent geometry : bond 0.00276 (20481) covalent geometry : angle 0.73847 (27798) SS BOND : bond 0.00237 ( 33) SS BOND : angle 0.88593 ( 66) hydrogen bonds : bond 0.03065 ( 367) hydrogen bonds : angle 5.31567 ( 936) Misc. bond : bond 0.00017 ( 3) link_ALPHA1-2 : bond 0.01297 ( 6) link_ALPHA1-2 : angle 2.79607 ( 18) link_ALPHA1-3 : bond 0.00559 ( 3) link_ALPHA1-3 : angle 1.61717 ( 9) link_ALPHA1-6 : bond 0.02798 ( 3) link_ALPHA1-6 : angle 3.53447 ( 9) link_BETA1-4 : bond 0.00705 ( 36) link_BETA1-4 : angle 1.96330 ( 108) link_NAG-ASN : bond 0.00562 ( 48) link_NAG-ASN : angle 2.70900 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 406 time to evaluate : 0.695 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 601 LYS cc_start: 0.8842 (mttp) cc_final: 0.8516 (mtmm) REVERT: B 46 LYS cc_start: 0.6220 (mmtm) cc_final: 0.6008 (mmtp) REVERT: B 114 GLN cc_start: 0.8540 (tm130) cc_final: 0.8208 (tm-30) REVERT: B 134 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: B 432 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8347 (tp-100) REVERT: C 635 ILE cc_start: 0.8787 (tt) cc_final: 0.8461 (tt) REVERT: D 18 LEU cc_start: 0.8753 (mt) cc_final: 0.8538 (mt) REVERT: D 99 GLN cc_start: 0.8308 (tp40) cc_final: 0.7887 (tp-100) REVERT: E 66 LYS cc_start: 0.8802 (ttpt) cc_final: 0.7935 (tttm) REVERT: G 80 ASN cc_start: 0.8648 (m-40) cc_final: 0.8284 (p0) REVERT: G 102 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7976 (mm-30) REVERT: G 125 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8739 (tt) REVERT: G 129 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8324 (pp) REVERT: G 134 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: G 180 ASP cc_start: 0.9087 (m-30) cc_final: 0.8560 (m-30) REVERT: G 308 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7765 (mtt90) REVERT: G 356 ASN cc_start: 0.9076 (t0) cc_final: 0.8802 (t0) REVERT: G 427 TRP cc_start: 0.8116 (m-90) cc_final: 0.7573 (m-90) REVERT: G 432 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8138 (mp10) REVERT: H 28 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8508 (p) REVERT: H 72 ASP cc_start: 0.8804 (t0) cc_final: 0.8478 (t0) REVERT: H 81 GLN cc_start: 0.8755 (tt0) cc_final: 0.8286 (tt0) REVERT: I 69 TRP cc_start: 0.6259 (p-90) cc_final: 0.5998 (p-90) REVERT: I 80 ASN cc_start: 0.8757 (m-40) cc_final: 0.8136 (p0) REVERT: I 432 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8006 (mp10) REVERT: J 72 ASP cc_start: 0.8825 (t0) cc_final: 0.8560 (t0) REVERT: K 97 LEU cc_start: 0.8760 (tp) cc_final: 0.8536 (tt) REVERT: L 31 GLU cc_start: 0.8320 (tp30) cc_final: 0.7899 (tp30) REVERT: L 66 LYS cc_start: 0.8723 (ttpp) cc_final: 0.7870 (tttp) REVERT: L 79 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7135 (mm-30) REVERT: L 89 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8064 (pp30) outliers start: 85 outliers final: 67 residues processed: 457 average time/residue: 0.1312 time to fit residues: 94.7585 Evaluate side-chains 455 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 383 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 TYR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 137 ASN Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 93 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 221 optimal weight: 0.0870 chunk 231 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 570 HIS ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107841 restraints weight = 32769.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111198 restraints weight = 18308.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113460 restraints weight = 12722.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114931 restraints weight = 10039.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115950 restraints weight = 8581.084| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20613 Z= 0.130 Angle : 0.778 14.586 28152 Z= 0.363 Chirality : 0.049 0.360 3375 Planarity : 0.004 0.045 3432 Dihedral : 8.867 59.974 4548 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.03 % Favored : 88.80 % Rotamer: Outliers : 3.26 % Allowed : 19.52 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -3.32 (0.16), residues: 2367 helix: -1.25 (0.30), residues: 321 sheet: -1.85 (0.21), residues: 576 loop : -2.70 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 71 TYR 0.019 0.001 TYR B 134 PHE 0.018 0.001 PHE D 100C TRP 0.034 0.001 TRP B 69 HIS 0.010 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00279 (20481) covalent geometry : angle 0.74201 (27798) SS BOND : bond 0.00303 ( 33) SS BOND : angle 0.92678 ( 66) hydrogen bonds : bond 0.03042 ( 367) hydrogen bonds : angle 5.26402 ( 936) Misc. bond : bond 0.00015 ( 3) link_ALPHA1-2 : bond 0.01253 ( 6) link_ALPHA1-2 : angle 2.76764 ( 18) link_ALPHA1-3 : bond 0.00485 ( 3) link_ALPHA1-3 : angle 1.62748 ( 9) link_ALPHA1-6 : bond 0.02873 ( 3) link_ALPHA1-6 : angle 3.56375 ( 9) link_BETA1-4 : bond 0.00682 ( 36) link_BETA1-4 : angle 1.93937 ( 108) link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 2.64951 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 390 time to evaluate : 0.493 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 601 LYS cc_start: 0.8789 (mttp) cc_final: 0.8440 (mtmm) REVERT: B 46 LYS cc_start: 0.6171 (mmtm) cc_final: 0.5521 (mmtt) REVERT: B 114 GLN cc_start: 0.8547 (tm130) cc_final: 0.8203 (tm-30) REVERT: B 134 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: B 432 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8363 (tp-100) REVERT: C 635 ILE cc_start: 0.8818 (tt) cc_final: 0.8502 (tt) REVERT: D 18 LEU cc_start: 0.8741 (mt) cc_final: 0.8523 (mt) REVERT: D 83 ARG cc_start: 0.7587 (pmt-80) cc_final: 0.6597 (ptm160) REVERT: D 99 GLN cc_start: 0.8300 (tp40) cc_final: 0.7896 (tp-100) REVERT: E 60 ASP cc_start: 0.8943 (t0) cc_final: 0.8557 (t0) REVERT: E 66 LYS cc_start: 0.8781 (ttpt) cc_final: 0.7916 (tttm) REVERT: F 617 ARG cc_start: 0.8757 (mtt-85) cc_final: 0.8524 (mtt-85) REVERT: G 80 ASN cc_start: 0.8606 (m-40) cc_final: 0.8230 (p0) REVERT: G 102 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7980 (mm-30) REVERT: G 125 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8729 (tt) REVERT: G 129 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8314 (pp) REVERT: G 134 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: G 180 ASP cc_start: 0.9080 (m-30) cc_final: 0.8601 (m-30) REVERT: G 308 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7764 (mtt90) REVERT: G 356 ASN cc_start: 0.9068 (t0) cc_final: 0.8787 (t0) REVERT: G 432 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8076 (mp10) REVERT: H 28 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8525 (p) REVERT: H 72 ASP cc_start: 0.8817 (t0) cc_final: 0.8498 (t0) REVERT: H 81 GLN cc_start: 0.8766 (tt0) cc_final: 0.8313 (tt0) REVERT: I 69 TRP cc_start: 0.6247 (p-90) cc_final: 0.6000 (p-90) REVERT: I 432 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8006 (mp10) REVERT: J 13 GLN cc_start: 0.7750 (mp10) cc_final: 0.7322 (mp10) REVERT: J 72 ASP cc_start: 0.8826 (t0) cc_final: 0.8540 (t0) REVERT: K 97 LEU cc_start: 0.8695 (tp) cc_final: 0.8486 (tt) REVERT: L 31 GLU cc_start: 0.8267 (tp30) cc_final: 0.7833 (tp30) REVERT: L 66 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8090 (tttp) REVERT: L 79 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7070 (mm-30) REVERT: L 89 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7949 (pp30) outliers start: 68 outliers final: 59 residues processed: 434 average time/residue: 0.1304 time to fit residues: 89.8912 Evaluate side-chains 449 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 385 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 570 HIS I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109594 restraints weight = 32561.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112987 restraints weight = 18136.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115248 restraints weight = 12503.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116756 restraints weight = 9821.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117661 restraints weight = 8358.606| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20613 Z= 0.125 Angle : 0.759 14.694 28152 Z= 0.354 Chirality : 0.048 0.357 3375 Planarity : 0.004 0.047 3432 Dihedral : 8.601 59.925 4548 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.03 % Favored : 88.80 % Rotamer: Outliers : 3.31 % Allowed : 19.52 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.33 (0.16), residues: 2367 helix: -1.39 (0.28), residues: 357 sheet: -1.71 (0.22), residues: 558 loop : -2.76 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 71 TYR 0.019 0.001 TYR B 134 PHE 0.017 0.001 PHE D 100C TRP 0.036 0.001 TRP B 69 HIS 0.010 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00261 (20481) covalent geometry : angle 0.72449 (27798) SS BOND : bond 0.00215 ( 33) SS BOND : angle 0.82377 ( 66) hydrogen bonds : bond 0.02851 ( 367) hydrogen bonds : angle 5.15662 ( 936) Misc. bond : bond 0.00011 ( 3) link_ALPHA1-2 : bond 0.01280 ( 6) link_ALPHA1-2 : angle 2.63798 ( 18) link_ALPHA1-3 : bond 0.00499 ( 3) link_ALPHA1-3 : angle 1.60471 ( 9) link_ALPHA1-6 : bond 0.02950 ( 3) link_ALPHA1-6 : angle 3.59554 ( 9) link_BETA1-4 : bond 0.00664 ( 36) link_BETA1-4 : angle 1.88192 ( 108) link_NAG-ASN : bond 0.00541 ( 48) link_NAG-ASN : angle 2.53830 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.47 seconds wall clock time: 57 minutes 16.14 seconds (3436.14 seconds total)