Starting phenix.real_space_refine on Thu Sep 18 20:43:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euu_28617/09_2025/8euu_28617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euu_28617/09_2025/8euu_28617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8euu_28617/09_2025/8euu_28617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euu_28617/09_2025/8euu_28617.map" model { file = "/net/cci-nas-00/data/ceres_data/8euu_28617/09_2025/8euu_28617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euu_28617/09_2025/8euu_28617.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 129 5.16 5 C 12468 2.51 5 N 3339 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19926 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "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: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.28, per 1000 atoms: 0.26 Number of scatterers: 19926 At special positions: 0 Unit cell: (144.42, 151.89, 121.18, 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 129 16.00 O 3990 8.00 N 3339 7.00 C 12468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 731.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 45 sheets defined 20.3% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.992A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.814A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.258A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.164A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.615A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.620A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.773A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.959A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.696A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.251A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.115A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.647A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.552A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 663 removed outlier: 3.782A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.974A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.658A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.913A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.529A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.716A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.784A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.293A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 97 through 100A removed outlier: 3.501A pdb=" N ASN G 100 " --> pdb=" O TYR G 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.901A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.157A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 97 through 100A Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.018A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.256A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 97 through 100A Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.877A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.530A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.018A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.416A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.489A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.679A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.466A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.626A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.808A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.455A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.502A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.761A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.451A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.657A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.992A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.910A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.507A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.698A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.472A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.611A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.855A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 12.065A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.272A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.883A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.861A pdb=" N THR H 97 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.650A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.797A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.596A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.880A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.860A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.201A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.816A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.071A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.913A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.870A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2025 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: 4.29 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6290 1.35 - 1.47: 5225 1.47 - 1.60: 8633 1.60 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 20322 Sorted by residual: bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.67e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" N GLN K 1 " pdb=" CA GLN K 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.56e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.53e+00 bond pdb=" N ALA B 512 " pdb=" CA ALA B 512 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 ... (remaining 20317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26754 1.79 - 3.57: 681 3.57 - 5.36: 136 5.36 - 7.14: 16 7.14 - 8.93: 1 Bond angle restraints: 27588 Sorted by residual: angle pdb=" CB MET F 535 " pdb=" CG MET F 535 " pdb=" SD MET F 535 " ideal model delta sigma weight residual 112.70 121.63 -8.93 3.00e+00 1.11e-01 8.86e+00 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG2 ILE B 635 " ideal model delta sigma weight residual 110.50 114.72 -4.22 1.70e+00 3.46e-01 6.16e+00 angle pdb=" CA GLN A 114 " pdb=" CB GLN A 114 " pdb=" CG GLN A 114 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA ILE F 635 " pdb=" CB ILE F 635 " pdb=" CG2 ILE F 635 " ideal model delta sigma weight residual 110.50 114.54 -4.04 1.70e+00 3.46e-01 5.66e+00 angle pdb=" CA ILE D 635 " pdb=" CB ILE D 635 " pdb=" CG2 ILE D 635 " ideal model delta sigma weight residual 110.50 114.44 -3.94 1.70e+00 3.46e-01 5.38e+00 ... (remaining 27583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 11930 21.51 - 43.02: 985 43.02 - 64.52: 272 64.52 - 86.03: 57 86.03 - 107.54: 28 Dihedral angle restraints: 13272 sinusoidal: 6387 harmonic: 6885 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -152.23 66.23 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.31 62.31 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 -147.00 61.00 1 1.00e+01 1.00e-02 4.95e+01 ... (remaining 13269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2796 0.055 - 0.111: 405 0.111 - 0.166: 141 0.166 - 0.222: 3 0.222 - 0.277: 9 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3351 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 24 " -0.138 9.50e-02 1.11e+02 6.22e-02 2.69e+00 pdb=" NE ARG J 24 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG J 24 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 24 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 635 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE D 635 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE D 635 " 0.010 2.00e-02 2.50e+03 pdb=" N SER D 636 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 444 " 0.127 9.50e-02 1.11e+02 5.73e-02 2.15e+00 pdb=" NE ARG A 444 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 444 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 444 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 444 " 0.002 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 161 2.59 - 3.17: 15684 3.17 - 3.74: 29963 3.74 - 4.32: 44876 4.32 - 4.90: 73331 Nonbonded interactions: 164015 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.012 3.040 nonbonded pdb=" O7 NAG Z 2 " pdb=" O6 NAG f 1 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.158 3.040 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.203 3.040 ... (remaining 164010 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 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.070 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.880 Find NCS groups from input model: 0.500 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:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.005 0.039 20451 Z= 0.213 Angle : 0.693 8.930 27933 Z= 0.320 Chirality : 0.049 0.277 3354 Planarity : 0.003 0.062 3402 Dihedral : 17.088 107.540 8712 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.48 % Allowed : 15.83 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 2352 helix: 1.87 (0.29), residues: 393 sheet: 0.93 (0.18), residues: 819 loop : 0.43 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 24 TYR 0.014 0.001 TYR J 36 PHE 0.023 0.001 PHE C 53 TRP 0.010 0.001 TRP I 47 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00451 (20322) covalent geometry : angle 0.67483 (27588) SS BOND : bond 0.00264 ( 42) SS BOND : angle 1.05337 ( 84) hydrogen bonds : bond 0.12000 ( 732) hydrogen bonds : angle 5.73306 ( 2025) link_ALPHA1-2 : bond 0.00356 ( 3) link_ALPHA1-2 : angle 1.73246 ( 9) link_ALPHA1-3 : bond 0.00420 ( 3) link_ALPHA1-3 : angle 1.67511 ( 9) link_BETA1-4 : bond 0.00466 ( 36) link_BETA1-4 : angle 1.12532 ( 108) link_NAG-ASN : bond 0.00247 ( 45) link_NAG-ASN : angle 2.08203 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.9058 (mmp) cc_final: 0.8585 (mmp) REVERT: E 95 MET cc_start: 0.8576 (ptm) cc_final: 0.8315 (ptm) REVERT: F 530 MET cc_start: 0.8384 (mtp) cc_final: 0.7910 (mtp) REVERT: F 655 LYS cc_start: 0.6671 (mtpt) cc_final: 0.5742 (pttm) REVERT: I 34 LEU cc_start: 0.8530 (tp) cc_final: 0.8160 (mt) REVERT: K 77 THR cc_start: 0.6727 (p) cc_final: 0.6500 (p) outliers start: 10 outliers final: 9 residues processed: 262 average time/residue: 0.6038 time to fit residues: 178.8271 Evaluate side-chains 232 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain L residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 440 GLN E 137 ASN G 32 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 105 GLN J 90 HIS K 32 ASN L 6 GLN L 90 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.201450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144930 restraints weight = 21098.195| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.40 r_work: 0.3425 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20451 Z= 0.116 Angle : 0.555 6.375 27933 Z= 0.274 Chirality : 0.043 0.255 3354 Planarity : 0.003 0.035 3402 Dihedral : 9.658 71.291 4366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.06 % Allowed : 14.53 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2352 helix: 2.37 (0.29), residues: 375 sheet: 1.13 (0.19), residues: 753 loop : 0.40 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 38 TYR 0.025 0.001 TYR H 49 PHE 0.011 0.001 PHE C 53 TRP 0.010 0.001 TRP C 96 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00256 (20322) covalent geometry : angle 0.52194 (27588) SS BOND : bond 0.00276 ( 42) SS BOND : angle 0.84353 ( 84) hydrogen bonds : bond 0.03584 ( 732) hydrogen bonds : angle 4.79995 ( 2025) link_ALPHA1-2 : bond 0.00463 ( 3) link_ALPHA1-2 : angle 1.80458 ( 9) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 2.04599 ( 9) link_BETA1-4 : bond 0.00588 ( 36) link_BETA1-4 : angle 1.40102 ( 108) link_NAG-ASN : bond 0.00255 ( 45) link_NAG-ASN : angle 2.36186 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7948 (ptt-90) REVERT: B 658 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: C 46 LYS cc_start: 0.7895 (tttp) cc_final: 0.7586 (mmtp) REVERT: C 151 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7425 (mtt-85) REVERT: C 189 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7838 (tttm) REVERT: C 444 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7415 (tmm-80) REVERT: E 327 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7965 (ptt-90) REVERT: F 530 MET cc_start: 0.8393 (mtp) cc_final: 0.8030 (mtp) REVERT: I 34 LEU cc_start: 0.7932 (tp) cc_final: 0.7660 (mt) REVERT: K 69 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: K 77 THR cc_start: 0.6837 (p) cc_final: 0.6613 (p) outliers start: 43 outliers final: 14 residues processed: 256 average time/residue: 0.6305 time to fit residues: 180.9589 Evaluate side-chains 235 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN K 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.198969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141386 restraints weight = 21008.525| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.41 r_work: 0.3377 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20451 Z= 0.134 Angle : 0.568 7.961 27933 Z= 0.280 Chirality : 0.043 0.245 3354 Planarity : 0.003 0.036 3402 Dihedral : 7.952 59.994 4356 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.69 % Allowed : 14.68 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.18), residues: 2352 helix: 1.62 (0.28), residues: 414 sheet: 1.07 (0.19), residues: 777 loop : 0.57 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.021 0.001 TYR A 173 PHE 0.014 0.001 PHE E 383 TRP 0.010 0.001 TRP E 427 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00306 (20322) covalent geometry : angle 0.53205 (27588) SS BOND : bond 0.00291 ( 42) SS BOND : angle 0.82581 ( 84) hydrogen bonds : bond 0.03679 ( 732) hydrogen bonds : angle 4.73961 ( 2025) link_ALPHA1-2 : bond 0.00304 ( 3) link_ALPHA1-2 : angle 1.57336 ( 9) link_ALPHA1-3 : bond 0.00978 ( 3) link_ALPHA1-3 : angle 1.26762 ( 9) link_BETA1-4 : bond 0.00456 ( 36) link_BETA1-4 : angle 1.42675 ( 108) link_NAG-ASN : bond 0.00299 ( 45) link_NAG-ASN : angle 2.57367 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: A 327 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7929 (ptt-90) REVERT: A 502 LYS cc_start: 0.8086 (tttm) cc_final: 0.7691 (tttm) REVERT: B 658 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: C 46 LYS cc_start: 0.7898 (tttp) cc_final: 0.7583 (mmtp) REVERT: C 189 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7937 (tttm) REVERT: C 327 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7843 (ptt-90) REVERT: C 444 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7449 (tmm-80) REVERT: C 502 LYS cc_start: 0.8208 (tttp) cc_final: 0.7885 (tttp) REVERT: D 635 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6961 (mm) REVERT: D 658 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: E 327 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7998 (ptt-90) REVERT: F 530 MET cc_start: 0.8378 (mtp) cc_final: 0.8021 (mtp) REVERT: F 660 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7118 (tp) REVERT: I 34 LEU cc_start: 0.7883 (tp) cc_final: 0.7552 (tp) REVERT: K 62 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5715 (pptt) REVERT: K 69 MET cc_start: 0.7477 (mtm) cc_final: 0.7016 (mtt) REVERT: L 46 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6709 (tt) outliers start: 56 outliers final: 20 residues processed: 258 average time/residue: 0.6496 time to fit residues: 187.9345 Evaluate side-chains 244 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 184 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 139 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN B 607 ASN B 653 GLN H 90 HIS I 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.196915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140126 restraints weight = 20934.415| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.36 r_work: 0.3365 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20451 Z= 0.163 Angle : 0.601 8.756 27933 Z= 0.296 Chirality : 0.044 0.251 3354 Planarity : 0.004 0.035 3402 Dihedral : 6.920 55.619 4356 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.12 % Allowed : 15.73 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.18), residues: 2352 helix: 1.54 (0.28), residues: 414 sheet: 0.99 (0.18), residues: 777 loop : 0.43 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.021 0.002 TYR A 173 PHE 0.014 0.002 PHE E 383 TRP 0.013 0.002 TRP E 427 HIS 0.004 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00378 (20322) covalent geometry : angle 0.56039 (27588) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.06070 ( 84) hydrogen bonds : bond 0.03941 ( 732) hydrogen bonds : angle 4.78361 ( 2025) link_ALPHA1-2 : bond 0.00222 ( 3) link_ALPHA1-2 : angle 1.65562 ( 9) link_ALPHA1-3 : bond 0.00927 ( 3) link_ALPHA1-3 : angle 1.20529 ( 9) link_BETA1-4 : bond 0.00445 ( 36) link_BETA1-4 : angle 1.46279 ( 108) link_NAG-ASN : bond 0.00379 ( 45) link_NAG-ASN : angle 2.81280 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6529 (tm-30) REVERT: A 327 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7895 (ptt-90) REVERT: A 444 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7229 (tpt90) REVERT: A 502 LYS cc_start: 0.8199 (tttm) cc_final: 0.7811 (tttm) REVERT: C 46 LYS cc_start: 0.7919 (tttp) cc_final: 0.7630 (mmtp) REVERT: C 67 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8360 (t0) REVERT: C 189 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7976 (tttt) REVERT: C 327 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7834 (ptt-90) REVERT: C 444 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7512 (tmm-80) REVERT: C 502 LYS cc_start: 0.8215 (tttp) cc_final: 0.7869 (tttp) REVERT: D 635 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7068 (mm) REVERT: D 658 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: E 211 GLU cc_start: 0.7767 (tp30) cc_final: 0.7409 (mm-30) REVERT: E 327 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7957 (ptt-90) REVERT: F 530 MET cc_start: 0.8399 (mtp) cc_final: 0.8061 (mtp) REVERT: F 660 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7186 (tp) REVERT: I 34 LEU cc_start: 0.7855 (tp) cc_final: 0.7463 (mt) REVERT: K 62 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5717 (pptt) REVERT: K 69 MET cc_start: 0.7518 (mtm) cc_final: 0.6922 (mtm) REVERT: K 100 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6962 (pt0) REVERT: L 46 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6746 (tt) outliers start: 65 outliers final: 25 residues processed: 265 average time/residue: 0.6567 time to fit residues: 194.6083 Evaluate side-chains 249 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 105 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN I 32 ASN I 105 GLN K 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.194213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137503 restraints weight = 20738.216| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.24 r_work: 0.3331 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20451 Z= 0.254 Angle : 0.702 10.082 27933 Z= 0.344 Chirality : 0.047 0.262 3354 Planarity : 0.004 0.037 3402 Dihedral : 6.715 58.393 4356 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.98 % Allowed : 16.12 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.18), residues: 2352 helix: 1.13 (0.27), residues: 414 sheet: 0.82 (0.18), residues: 777 loop : 0.33 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 579 TYR 0.023 0.002 TYR C 384 PHE 0.016 0.002 PHE E 383 TRP 0.016 0.002 TRP A 427 HIS 0.006 0.002 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00605 (20322) covalent geometry : angle 0.65714 (27588) SS BOND : bond 0.00448 ( 42) SS BOND : angle 1.34546 ( 84) hydrogen bonds : bond 0.04655 ( 732) hydrogen bonds : angle 5.00945 ( 2025) link_ALPHA1-2 : bond 0.00148 ( 3) link_ALPHA1-2 : angle 1.78617 ( 9) link_ALPHA1-3 : bond 0.00779 ( 3) link_ALPHA1-3 : angle 1.13377 ( 9) link_BETA1-4 : bond 0.00483 ( 36) link_BETA1-4 : angle 1.63759 ( 108) link_NAG-ASN : bond 0.00575 ( 45) link_NAG-ASN : angle 3.19853 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: A 271 MET cc_start: 0.8469 (mmm) cc_final: 0.8215 (mmm) REVERT: A 327 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7859 (ptt-90) REVERT: A 467 THR cc_start: 0.8558 (m) cc_final: 0.8220 (m) REVERT: A 502 LYS cc_start: 0.8271 (tttm) cc_final: 0.7901 (tttm) REVERT: B 584 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 46 LYS cc_start: 0.7938 (tttp) cc_final: 0.7633 (mmtp) REVERT: C 151 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7430 (mtt-85) REVERT: C 327 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7759 (ptt-90) REVERT: C 444 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7537 (tmm-80) REVERT: D 635 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7069 (mm) REVERT: D 658 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: E 327 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7795 (ptt-90) REVERT: F 530 MET cc_start: 0.8425 (mtp) cc_final: 0.8129 (mtp) REVERT: F 660 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7236 (tp) REVERT: G 75 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7114 (pt) REVERT: I 34 LEU cc_start: 0.7847 (tp) cc_final: 0.7534 (tp) REVERT: I 100 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6866 (pt0) REVERT: K 62 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5666 (pptt) REVERT: K 100 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: L 46 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6829 (tt) outliers start: 83 outliers final: 37 residues processed: 267 average time/residue: 0.6834 time to fit residues: 204.0725 Evaluate side-chains 250 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 99 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN C 355 ASN I 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.197653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142542 restraints weight = 20848.896| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.18 r_work: 0.3374 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20451 Z= 0.159 Angle : 0.604 9.485 27933 Z= 0.297 Chirality : 0.044 0.249 3354 Planarity : 0.004 0.036 3402 Dihedral : 6.035 56.705 4356 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 17.79 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2352 helix: 1.29 (0.27), residues: 414 sheet: 0.91 (0.18), residues: 762 loop : 0.32 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.018 0.002 TYR A 173 PHE 0.014 0.002 PHE E 383 TRP 0.019 0.002 TRP C 427 HIS 0.003 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00370 (20322) covalent geometry : angle 0.55995 (27588) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.14309 ( 84) hydrogen bonds : bond 0.04023 ( 732) hydrogen bonds : angle 4.82315 ( 2025) link_ALPHA1-2 : bond 0.00184 ( 3) link_ALPHA1-2 : angle 1.79726 ( 9) link_ALPHA1-3 : bond 0.00837 ( 3) link_ALPHA1-3 : angle 1.08206 ( 9) link_BETA1-4 : bond 0.00408 ( 36) link_BETA1-4 : angle 1.51055 ( 108) link_NAG-ASN : bond 0.00391 ( 45) link_NAG-ASN : angle 2.89976 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: A 327 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7848 (ptt-90) REVERT: A 467 THR cc_start: 0.8568 (m) cc_final: 0.8249 (m) REVERT: A 502 LYS cc_start: 0.8308 (tttm) cc_final: 0.7975 (tttm) REVERT: C 46 LYS cc_start: 0.8005 (tttp) cc_final: 0.7710 (mmtp) REVERT: C 97 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8180 (mppt) REVERT: C 151 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7551 (mtt-85) REVERT: C 327 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7888 (ptt-90) REVERT: C 444 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7562 (tmm-80) REVERT: D 635 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7138 (mm) REVERT: D 658 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: E 103 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: E 104 MET cc_start: 0.8951 (ttt) cc_final: 0.8554 (ttt) REVERT: E 327 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7886 (ptt-90) REVERT: F 530 MET cc_start: 0.8417 (mtp) cc_final: 0.8200 (mtp) REVERT: G 75 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7234 (pt) REVERT: I 34 LEU cc_start: 0.7970 (tp) cc_final: 0.7531 (mt) REVERT: K 62 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5741 (pptt) REVERT: K 76 ASN cc_start: 0.7575 (m-40) cc_final: 0.7273 (m110) REVERT: K 100 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7015 (pt0) REVERT: L 46 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6919 (tt) outliers start: 57 outliers final: 27 residues processed: 254 average time/residue: 0.6931 time to fit residues: 196.8840 Evaluate side-chains 242 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 653 GLN I 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.197173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140080 restraints weight = 20649.916| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.45 r_work: 0.3390 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20451 Z= 0.140 Angle : 0.586 9.371 27933 Z= 0.288 Chirality : 0.043 0.248 3354 Planarity : 0.003 0.036 3402 Dihedral : 5.767 59.723 4356 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.83 % Allowed : 17.70 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.18), residues: 2352 helix: 1.41 (0.28), residues: 414 sheet: 0.92 (0.18), residues: 762 loop : 0.35 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 444 TYR 0.019 0.002 TYR A 173 PHE 0.013 0.001 PHE E 383 TRP 0.017 0.001 TRP E 427 HIS 0.003 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00323 (20322) covalent geometry : angle 0.54358 (27588) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.10794 ( 84) hydrogen bonds : bond 0.03875 ( 732) hydrogen bonds : angle 4.75169 ( 2025) link_ALPHA1-2 : bond 0.00203 ( 3) link_ALPHA1-2 : angle 1.75900 ( 9) link_ALPHA1-3 : bond 0.00850 ( 3) link_ALPHA1-3 : angle 1.04594 ( 9) link_BETA1-4 : bond 0.00401 ( 36) link_BETA1-4 : angle 1.47428 ( 108) link_NAG-ASN : bond 0.00360 ( 45) link_NAG-ASN : angle 2.79674 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: A 327 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7785 (ptt-90) REVERT: A 467 THR cc_start: 0.8554 (m) cc_final: 0.8256 (m) REVERT: C 46 LYS cc_start: 0.7935 (tttp) cc_final: 0.7630 (mmtp) REVERT: C 97 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8135 (mppt) REVERT: C 151 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7467 (mtt-85) REVERT: C 327 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7831 (ptt-90) REVERT: C 444 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7416 (tmm-80) REVERT: D 635 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7062 (mm) REVERT: D 658 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: E 103 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: E 104 MET cc_start: 0.8982 (ttt) cc_final: 0.8603 (ttt) REVERT: E 327 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7849 (ptt-90) REVERT: F 530 MET cc_start: 0.8374 (mtp) cc_final: 0.8136 (mtp) REVERT: F 660 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7142 (tp) REVERT: G 75 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7189 (pt) REVERT: K 76 ASN cc_start: 0.7347 (m-40) cc_final: 0.7114 (m110) REVERT: K 100 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: L 46 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6730 (tt) outliers start: 59 outliers final: 26 residues processed: 254 average time/residue: 0.6355 time to fit residues: 180.6075 Evaluate side-chains 242 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN B 607 ASN C 462 ASN E 462 ASN F 607 ASN F 658 GLN I 32 ASN I 105 GLN K 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.194243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139971 restraints weight = 20859.930| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.91 r_work: 0.3332 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 20451 Z= 0.332 Angle : 0.787 10.847 27933 Z= 0.385 Chirality : 0.051 0.273 3354 Planarity : 0.005 0.047 3402 Dihedral : 6.666 58.220 4356 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.21 % Allowed : 17.31 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2352 helix: 0.54 (0.26), residues: 414 sheet: 0.62 (0.18), residues: 771 loop : 0.24 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 360 TYR 0.030 0.003 TYR C 384 PHE 0.017 0.003 PHE E 383 TRP 0.017 0.003 TRP C 427 HIS 0.006 0.002 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00789 (20322) covalent geometry : angle 0.73859 (27588) SS BOND : bond 0.00669 ( 42) SS BOND : angle 1.73187 ( 84) hydrogen bonds : bond 0.05180 ( 732) hydrogen bonds : angle 5.18414 ( 2025) link_ALPHA1-2 : bond 0.00145 ( 3) link_ALPHA1-2 : angle 1.95941 ( 9) link_ALPHA1-3 : bond 0.00673 ( 3) link_ALPHA1-3 : angle 1.18713 ( 9) link_BETA1-4 : bond 0.00527 ( 36) link_BETA1-4 : angle 1.79735 ( 108) link_NAG-ASN : bond 0.00714 ( 45) link_NAG-ASN : angle 3.46514 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 327 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7742 (ptt-90) REVERT: A 467 THR cc_start: 0.8565 (m) cc_final: 0.8265 (m) REVERT: B 584 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7318 (mt-10) REVERT: B 635 ILE cc_start: 0.7487 (mp) cc_final: 0.7279 (mm) REVERT: B 658 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: C 46 LYS cc_start: 0.7912 (tttp) cc_final: 0.7540 (mmtp) REVERT: C 327 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7721 (ptt-90) REVERT: C 444 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7601 (tmm-80) REVERT: D 584 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7423 (mt-10) REVERT: D 658 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: E 117 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8041 (mtmt) REVERT: E 327 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7648 (ptt-90) REVERT: F 530 MET cc_start: 0.8476 (mtp) cc_final: 0.8028 (mtp) REVERT: G 75 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7138 (pt) REVERT: K 75 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7507 (pt) REVERT: K 100 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: L 46 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6891 (tt) outliers start: 67 outliers final: 36 residues processed: 255 average time/residue: 0.6796 time to fit residues: 193.3355 Evaluate side-chains 246 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 215 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 348 GLN C 137 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.198015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142708 restraints weight = 20811.893| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.16 r_work: 0.3393 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20451 Z= 0.127 Angle : 0.589 9.425 27933 Z= 0.290 Chirality : 0.043 0.239 3354 Planarity : 0.003 0.036 3402 Dihedral : 5.783 55.769 4356 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.01 % Allowed : 18.85 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.17), residues: 2352 helix: 1.26 (0.27), residues: 414 sheet: 0.85 (0.18), residues: 762 loop : 0.31 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 444 TYR 0.021 0.001 TYR A 173 PHE 0.013 0.001 PHE A 383 TRP 0.021 0.001 TRP C 427 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00286 (20322) covalent geometry : angle 0.54606 (27588) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.16529 ( 84) hydrogen bonds : bond 0.03856 ( 732) hydrogen bonds : angle 4.79340 ( 2025) link_ALPHA1-2 : bond 0.00159 ( 3) link_ALPHA1-2 : angle 1.81677 ( 9) link_ALPHA1-3 : bond 0.00818 ( 3) link_ALPHA1-3 : angle 1.07399 ( 9) link_BETA1-4 : bond 0.00387 ( 36) link_BETA1-4 : angle 1.49333 ( 108) link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 2.82687 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: A 467 THR cc_start: 0.8486 (m) cc_final: 0.8197 (m) REVERT: B 584 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 46 LYS cc_start: 0.7871 (tttp) cc_final: 0.7565 (mmtp) REVERT: C 91 GLU cc_start: 0.7590 (tp30) cc_final: 0.7314 (tt0) REVERT: C 97 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8132 (mppt) REVERT: C 327 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7811 (ptt-90) REVERT: C 444 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7404 (tmm-80) REVERT: D 635 ILE cc_start: 0.7369 (mp) cc_final: 0.7143 (mm) REVERT: D 658 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: E 103 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: E 327 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: G 75 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7286 (pt) REVERT: I 23 ARG cc_start: 0.7198 (ttt90) cc_final: 0.6969 (tpt170) REVERT: K 100 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: L 46 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6791 (tt) outliers start: 42 outliers final: 19 residues processed: 239 average time/residue: 0.6421 time to fit residues: 172.4021 Evaluate side-chains 230 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 91 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN I 105 GLN K 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.197300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142176 restraints weight = 20992.770| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.06 r_work: 0.3379 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20451 Z= 0.163 Angle : 0.618 9.594 27933 Z= 0.304 Chirality : 0.044 0.247 3354 Planarity : 0.004 0.037 3402 Dihedral : 5.681 55.978 4356 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.68 % Allowed : 19.42 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2352 helix: 1.29 (0.27), residues: 414 sheet: 0.80 (0.18), residues: 768 loop : 0.33 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 444 TYR 0.022 0.002 TYR A 173 PHE 0.014 0.002 PHE E 383 TRP 0.017 0.002 TRP C 427 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00381 (20322) covalent geometry : angle 0.57511 (27588) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.27027 ( 84) hydrogen bonds : bond 0.04055 ( 732) hydrogen bonds : angle 4.80712 ( 2025) link_ALPHA1-2 : bond 0.00205 ( 3) link_ALPHA1-2 : angle 1.78608 ( 9) link_ALPHA1-3 : bond 0.00808 ( 3) link_ALPHA1-3 : angle 1.01755 ( 9) link_BETA1-4 : bond 0.00394 ( 36) link_BETA1-4 : angle 1.49749 ( 108) link_NAG-ASN : bond 0.00413 ( 45) link_NAG-ASN : angle 2.87091 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 467 THR cc_start: 0.8540 (m) cc_final: 0.8252 (m) REVERT: B 584 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 46 LYS cc_start: 0.7918 (tttp) cc_final: 0.7594 (mmtp) REVERT: C 91 GLU cc_start: 0.7611 (tp30) cc_final: 0.7277 (tt0) REVERT: C 327 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7819 (ptt-90) REVERT: C 444 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7423 (tmm-80) REVERT: D 658 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: E 103 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: E 327 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: G 75 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7327 (pt) REVERT: I 23 ARG cc_start: 0.7191 (ttt90) cc_final: 0.6957 (tpt170) REVERT: K 100 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6829 (pt0) REVERT: L 46 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6834 (tt) outliers start: 35 outliers final: 20 residues processed: 232 average time/residue: 0.6417 time to fit residues: 166.5581 Evaluate side-chains 230 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 183 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 198 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 229 optimal weight: 20.0000 chunk 154 optimal weight: 0.0470 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN I 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142635 restraints weight = 20975.381| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.98 r_work: 0.3378 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20451 Z= 0.173 Angle : 0.626 9.672 27933 Z= 0.308 Chirality : 0.044 0.244 3354 Planarity : 0.004 0.036 3402 Dihedral : 5.657 57.902 4356 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 19.38 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2352 helix: 1.23 (0.27), residues: 414 sheet: 0.81 (0.18), residues: 768 loop : 0.32 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.025 0.002 TYR A 173 PHE 0.015 0.002 PHE E 383 TRP 0.016 0.002 TRP C 427 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00405 (20322) covalent geometry : angle 0.58323 (27588) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.29361 ( 84) hydrogen bonds : bond 0.04115 ( 732) hydrogen bonds : angle 4.82587 ( 2025) link_ALPHA1-2 : bond 0.00200 ( 3) link_ALPHA1-2 : angle 1.78418 ( 9) link_ALPHA1-3 : bond 0.00799 ( 3) link_ALPHA1-3 : angle 1.02082 ( 9) link_BETA1-4 : bond 0.00401 ( 36) link_BETA1-4 : angle 1.49564 ( 108) link_NAG-ASN : bond 0.00415 ( 45) link_NAG-ASN : angle 2.91435 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8672.60 seconds wall clock time: 148 minutes 2.46 seconds (8882.46 seconds total)