Starting phenix.real_space_refine on Sun May 18 13:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d1w_46478/05_2025/9d1w_46478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d1w_46478/05_2025/9d1w_46478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d1w_46478/05_2025/9d1w_46478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d1w_46478/05_2025/9d1w_46478.map" model { file = "/net/cci-nas-00/data/ceres_data/9d1w_46478/05_2025/9d1w_46478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d1w_46478/05_2025/9d1w_46478.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.022 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 115 5.16 5 C 10601 2.51 5 N 2802 2.21 5 O 3518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17036 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3528 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "C" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3528 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "H" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1100 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} Chain: "a" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "c" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" 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: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.40, per 1000 atoms: 0.73 Number of scatterers: 17036 At special positions: 0 Unit cell: (129.48, 126.16, 176.79, 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 115 16.00 O 3518 8.00 N 2802 7.00 C 10601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.03 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 B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " 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=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 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=2.03 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=2.03 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 c 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 598 " - pdb=" SG CYS a 604 " distance=2.03 Simple disulfide: pdb=" SG CYS b 598 " - pdb=" SG CYS b 604 " distance=2.03 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " 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 D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " " MAN J 5 " - " MAN J 6 " " MAN J 7 " - " MAN J 8 " " MAN J 9 " - " MAN J 10 " " MAN M 4 " - " MAN M 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN T 4 " - " MAN T 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 7 " - " MAN D 8 " " BMA J 3 " - " MAN J 9 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA D 3 " - " MAN D 7 " " MAN D 7 " - " MAN D 9 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 7 " " BMA M 3 " - " MAN M 6 " " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 9 " " BMA T 3 " - " MAN T 6 " " BMA V 3 " - " MAN V 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 355 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 448 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 133 " " NAG B 603 " - " ASN B 234 " " NAG B 604 " - " ASN B 301 " " NAG B 605 " - " ASN B 332 " " NAG B 606 " - " ASN B 339 " " NAG B 607 " - " ASN B 355 " " NAG B 608 " - " ASN B 392 " " NAG B 609 " - " ASN B 137 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 339 " " NAG C 607 " - " ASN C 355 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 448 " " NAG D 1 " - " ASN A 160 " " NAG E 1 " - " ASN A 295 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 363 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN B 160 " " NAG K 1 " - " ASN B 156 " " NAG M 1 " - " ASN B 262 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 160 " " NAG P 1 " - " ASN C 386 " " NAG Q 1 " - " ASN C 363 " " NAG R 1 " - " ASN C 197 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 276 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN B 197 " " NAG Z 1 " - " ASN B 276 " " NAG a 701 " - " ASN a 611 " " NAG a 702 " - " ASN a 637 " " NAG b 701 " - " ASN b 611 " " NAG b 702 " - " ASN b 637 " " NAG c 701 " - " ASN c 611 " " NAG c 702 " - " ASN c 637 " " NAG d 1 " - " ASN B 295 " " NAG x 1 " - " ASN B 363 " " NAG y 1 " - " ASN B 386 " " NAG z 1 " - " ASN B 448 " Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.0 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 29 sheets defined 23.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.116A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.675A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.753A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.711A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 4.285A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.197A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 3.566A pdb=" N ARG B 151 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.599A pdb=" N ASN B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.735A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.260A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.536A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.522A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 64 " --> pdb=" O TYR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.927A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.794A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.642A 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 387 through 390 Processing helix chain 'C' and resid 475 through 480 removed outlier: 4.153A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 484 removed outlier: 4.918A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 484' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.865A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'a' and resid 529 through 534 removed outlier: 3.564A pdb=" N SER a 534 " --> pdb=" O MET a 530 " (cutoff:3.500A) Processing helix chain 'a' and resid 536 through 542 removed outlier: 4.492A pdb=" N GLN a 540 " --> pdb=" O THR a 536 " (cutoff:3.500A) Processing helix chain 'a' and resid 570 through 596 removed outlier: 4.215A pdb=" N LYS a 574 " --> pdb=" O VAL a 570 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLN a 575 " --> pdb=" O TRP a 571 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU a 576 " --> pdb=" O GLY a 572 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU a 581 " --> pdb=" O GLN a 577 " (cutoff:3.500A) Processing helix chain 'a' and resid 627 through 636 removed outlier: 4.072A pdb=" N LYS a 633 " --> pdb=" O LEU a 629 " (cutoff:3.500A) Processing helix chain 'a' and resid 638 through 655 removed outlier: 3.929A pdb=" N GLY a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU a 647 " --> pdb=" O TYR a 643 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU a 648 " --> pdb=" O GLY a 644 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN a 650 " --> pdb=" O LEU a 646 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN a 653 " --> pdb=" O SER a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 655 through 662 removed outlier: 3.587A pdb=" N LEU a 660 " --> pdb=" O ASN a 656 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU a 661 " --> pdb=" O GLU a 657 " (cutoff:3.500A) Processing helix chain 'b' and resid 523 through 528 removed outlier: 4.497A 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 542 removed outlier: 3.849A pdb=" N GLN b 540 " --> pdb=" O THR b 536 " (cutoff:3.500A) Processing helix chain 'b' and resid 543 through 545 No H-bonds generated for 'chain 'b' and resid 543 through 545' Processing helix chain 'b' and resid 569 through 572 Processing helix chain 'b' and resid 573 through 595 removed outlier: 4.470A pdb=" N ARG b 579 " --> pdb=" O GLN b 575 " (cutoff:3.500A) Processing helix chain 'b' and resid 618 through 624 removed outlier: 3.615A pdb=" N ASP b 624 " --> pdb=" O SER b 620 " (cutoff:3.500A) Processing helix chain 'b' and resid 627 through 663 removed outlier: 4.272A pdb=" N LYS b 633 " --> pdb=" O LEU b 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU b 634 " --> pdb=" O GLN b 630 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN b 637 " --> pdb=" O LYS b 633 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR b 638 " --> pdb=" O GLU b 634 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN b 640 " --> pdb=" O SER b 636 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE b 641 " --> pdb=" O ASN b 637 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE b 642 " --> pdb=" O TYR b 638 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR b 643 " --> pdb=" O THR b 639 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY b 644 " --> pdb=" O GLN b 640 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN b 650 " --> pdb=" O LEU b 646 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN b 651 " --> pdb=" O GLU b 647 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN b 652 " --> pdb=" O GLU b 648 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN b 653 " --> pdb=" O SER b 649 " (cutoff:3.500A) Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 536 through 543 removed outlier: 3.924A pdb=" N GLN c 540 " --> pdb=" O THR c 536 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN c 543 " --> pdb=" O VAL c 539 " (cutoff:3.500A) Processing helix chain 'c' and resid 570 through 596 removed outlier: 3.537A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN c 575 " --> pdb=" O TRP c 571 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU c 576 " --> pdb=" O GLY c 572 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN c 577 " --> pdb=" O ILE c 573 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP c 589 " --> pdb=" O ARG c 585 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP c 596 " --> pdb=" O LEU c 592 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 622 Processing helix chain 'c' and resid 627 through 635 removed outlier: 3.824A pdb=" N LYS c 633 " --> pdb=" O LEU c 629 " (cutoff:3.500A) Processing helix chain 'c' and resid 638 through 663 removed outlier: 3.684A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU c 645 " --> pdb=" O ILE c 641 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU c 646 " --> pdb=" O ILE c 642 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU c 647 " --> pdb=" O TYR c 643 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU c 648 " --> pdb=" O GLY c 644 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU c 661 " --> pdb=" O GLU c 657 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU c 663 " --> pdb=" O ASP c 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.456A pdb=" N VAL A 36 " --> pdb=" O THR a 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.085A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (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 92 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 202 through 203 removed outlier: 6.492A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 261 current: chain 'A' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 287 current: chain 'A' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 393 through 395 current: chain 'A' and resid 466 through 470 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.546A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.801A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.299A pdb=" N VAL B 36 " --> pdb=" O THR b 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.218A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.774A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.646A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 302 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 329 through 333 current: chain 'B' and resid 382 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 385 current: chain 'B' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'B' and resid 305 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.704A pdb=" N VAL c 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL C 38 " --> pdb=" O THR c 606 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR c 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR C 40 " --> pdb=" O CYS c 604 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N CYS c 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.037A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 86 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.005A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.880A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.351A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.619A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100L through 108 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.542A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AD2, first strand: chain 'L' and resid 27C through 27E removed outlier: 4.181A pdb=" N GLY L 27E" --> pdb=" O ASN L 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN L 30 " --> pdb=" O GLY L 27E" (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 430 hydrogen bonds defined for protein. 1116 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: 5.49 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5204 1.34 - 1.47: 4502 1.47 - 1.59: 7498 1.59 - 1.72: 1 1.72 - 1.85: 152 Bond restraints: 17357 Sorted by residual: bond pdb=" N GLY c 521 " pdb=" CA GLY c 521 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.57e+00 bond pdb=" N ASN C 33 " pdb=" CA ASN C 33 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N LEU a 520 " pdb=" CA LEU a 520 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N LEU b 520 " pdb=" CA LEU b 520 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 17352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 22758 1.53 - 3.05: 677 3.05 - 4.58: 111 4.58 - 6.10: 11 6.10 - 7.63: 4 Bond angle restraints: 23561 Sorted by residual: angle pdb=" N GLN c 658 " pdb=" CA GLN c 658 " pdb=" C GLN c 658 " ideal model delta sigma weight residual 113.43 107.99 5.44 1.26e+00 6.30e-01 1.86e+01 angle pdb=" N ILE B 184 " pdb=" CA ILE B 184 " pdb=" C ILE B 184 " ideal model delta sigma weight residual 113.71 109.94 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" N TRP a 623 " pdb=" CA TRP a 623 " pdb=" CB TRP a 623 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" N GLU A 268 " pdb=" CA GLU A 268 " pdb=" CB GLU A 268 " ideal model delta sigma weight residual 114.17 109.70 4.47 1.14e+00 7.69e-01 1.54e+01 angle pdb=" N GLU B 268 " pdb=" CA GLU B 268 " pdb=" CB GLU B 268 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 ... (remaining 23556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10782 18.00 - 35.99: 841 35.99 - 53.99: 238 53.99 - 71.98: 80 71.98 - 89.98: 21 Dihedral angle restraints: 11962 sinusoidal: 6290 harmonic: 5672 Sorted by residual: dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 37.82 55.18 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.72 54.72 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CA CYS C 119 " pdb=" C CYS C 119 " pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta harmonic sigma weight residual -180.00 -148.81 -31.19 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 11959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2372 0.044 - 0.088: 412 0.088 - 0.131: 196 0.131 - 0.175: 16 0.175 - 0.219: 3 Chirality restraints: 2999 Sorted by residual: chirality pdb=" C1 MAN J 7 " pdb=" O6 MAN J 4 " pdb=" C2 MAN J 7 " pdb=" O5 MAN J 7 " both_signs ideal model delta sigma weight residual False 2.40 2.38 0.02 2.00e-02 2.50e+03 1.45e+00 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 355 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG B 609 " pdb=" ND2 ASN B 137 " pdb=" C2 NAG B 609 " pdb=" O5 NAG B 609 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2996 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 239 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 240 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 211 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO C 212 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 497 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 498 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.022 5.00e-02 4.00e+02 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 80 2.52 - 3.11: 12777 3.11 - 3.71: 23326 3.71 - 4.30: 35012 4.30 - 4.90: 58446 Nonbonded interactions: 129641 Sorted by model distance: nonbonded pdb=" OG1 THR a 627 " pdb=" OE1 GLN a 630 " model vdw 1.921 3.040 nonbonded pdb=" O ASN A 363 " pdb=" OG SER A 364 " model vdw 2.084 3.040 nonbonded pdb=" OD2 ASP A 141 " pdb=" NE2 GLN A 328 " model vdw 2.091 3.120 nonbonded pdb=" O THR A 278 " pdb=" O6 NAG U 1 " model vdw 2.133 3.040 nonbonded pdb=" O HIS L 27D" pdb=" O6 MAN J 7 " model vdw 2.146 3.040 ... (remaining 129636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 397 or resid 411 through 505 or resid 601 throu \ gh 609)) selection = (chain 'B' and (resid 34 through 505 or resid 601 through 609)) selection = (chain 'C' and (resid 34 through 505 or resid 601 through 609)) } ncs_group { reference = (chain 'D' and (resid 1 or resid 4 through 9)) selection = (chain 'J' and (resid 2 or resid 5 through 10)) selection = (chain 'O' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'M' selection = chain 'T' selection = chain 'V' } ncs_group { reference = (chain 'a' and (resid 521 through 664 or resid 701 through 702)) selection = (chain 'b' and (resid 521 through 664 or resid 701 through 702)) selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.590 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.100 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.003 0.058 17511 Z= 0.159 Angle : 0.695 8.983 23987 Z= 0.353 Chirality : 0.042 0.219 2999 Planarity : 0.004 0.053 2830 Dihedral : 14.310 89.978 8186 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 1.73 % Allowed : 11.59 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.19), residues: 1928 helix: -1.81 (0.25), residues: 370 sheet: 0.05 (0.21), residues: 548 loop : -0.82 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.004 0.001 HIS B 352 PHE 0.010 0.001 PHE C 233 TYR 0.008 0.001 TYR B 484 ARG 0.003 0.000 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 58) link_NAG-ASN : angle 2.49439 ( 174) link_ALPHA1-6 : bond 0.01706 ( 9) link_ALPHA1-6 : angle 2.15998 ( 27) link_BETA1-4 : bond 0.00627 ( 32) link_BETA1-4 : angle 2.47377 ( 96) link_ALPHA1-2 : bond 0.00785 ( 10) link_ALPHA1-2 : angle 2.46359 ( 30) link_ALPHA1-3 : bond 0.01421 ( 9) link_ALPHA1-3 : angle 1.69663 ( 27) hydrogen bonds : bond 0.24780 ( 430) hydrogen bonds : angle 8.08802 ( 1116) SS BOND : bond 0.00358 ( 36) SS BOND : angle 1.33349 ( 72) covalent geometry : bond 0.00340 (17357) covalent geometry : angle 0.63169 (23561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 335 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8306 (m100) cc_final: 0.8087 (m100) REVERT: A 49 GLU cc_start: 0.8331 (pm20) cc_final: 0.7913 (pt0) REVERT: A 232 LYS cc_start: 0.7289 (mptt) cc_final: 0.6858 (tmtt) REVERT: A 327 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7051 (mtt-85) REVERT: B 35 TRP cc_start: 0.8402 (m100) cc_final: 0.7933 (m100) REVERT: B 69 TRP cc_start: 0.6066 (OUTLIER) cc_final: 0.4733 (m100) REVERT: B 103 GLN cc_start: 0.7196 (tt0) cc_final: 0.6694 (tm-30) REVERT: B 161 MET cc_start: 0.8480 (tpp) cc_final: 0.7987 (ttt) REVERT: B 232 LYS cc_start: 0.7977 (mmpt) cc_final: 0.7567 (tptp) REVERT: B 340 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7349 (tt0) REVERT: C 153 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6909 (tp30) REVERT: C 161 MET cc_start: 0.8354 (tpp) cc_final: 0.8006 (tpp) REVERT: C 213 ILE cc_start: 0.8200 (tp) cc_final: 0.7868 (pt) REVERT: C 308 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7664 (ttm110) REVERT: C 327 ARG cc_start: 0.7492 (mmm-85) cc_final: 0.6760 (mtm180) REVERT: C 347 LYS cc_start: 0.6855 (tttt) cc_final: 0.5833 (mptt) REVERT: C 477 ASP cc_start: 0.7760 (m-30) cc_final: 0.7257 (t0) REVERT: C 486 TYR cc_start: 0.8557 (m-80) cc_final: 0.8273 (m-80) REVERT: H 5 THR cc_start: 0.8654 (m) cc_final: 0.8192 (p) REVERT: H 12 ARG cc_start: 0.8066 (mpt90) cc_final: 0.7833 (mpt180) REVERT: H 30 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7929 (mtmm) REVERT: H 100 ASP cc_start: 0.8098 (t0) cc_final: 0.7720 (m-30) REVERT: a 660 LEU cc_start: 0.7054 (tp) cc_final: 0.6846 (mp) REVERT: b 542 ARG cc_start: 0.8261 (mtp85) cc_final: 0.8019 (mtp180) REVERT: c 574 LYS cc_start: 0.7782 (tptt) cc_final: 0.7449 (mttm) REVERT: c 647 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7765 (mt-10) outliers start: 30 outliers final: 15 residues processed: 360 average time/residue: 0.3125 time to fit residues: 162.5739 Evaluate side-chains 229 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain a residue 635 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.0870 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 0.0370 chunk 175 optimal weight: 0.9980 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 33 ASN B 246 GLN B 428 GLN B 432 GLN C 66 HIS L 9 HIS L 45 GLN a 543 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104627 restraints weight = 21112.372| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.73 r_work: 0.2969 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17511 Z= 0.146 Angle : 0.743 11.938 23987 Z= 0.350 Chirality : 0.049 0.463 2999 Planarity : 0.004 0.045 2830 Dihedral : 9.079 66.265 4532 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 2.82 % Allowed : 12.74 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1928 helix: -0.84 (0.27), residues: 355 sheet: 0.25 (0.22), residues: 513 loop : -0.60 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 35 HIS 0.003 0.001 HIS C 374 PHE 0.016 0.001 PHE C 53 TYR 0.025 0.001 TYR a 638 ARG 0.005 0.001 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.01075 ( 58) link_NAG-ASN : angle 2.89475 ( 174) link_ALPHA1-6 : bond 0.01238 ( 9) link_ALPHA1-6 : angle 2.04625 ( 27) link_BETA1-4 : bond 0.00663 ( 32) link_BETA1-4 : angle 2.17138 ( 96) link_ALPHA1-2 : bond 0.00647 ( 10) link_ALPHA1-2 : angle 1.95397 ( 30) link_ALPHA1-3 : bond 0.01133 ( 9) link_ALPHA1-3 : angle 1.39768 ( 27) hydrogen bonds : bond 0.05563 ( 430) hydrogen bonds : angle 5.49610 ( 1116) SS BOND : bond 0.00327 ( 36) SS BOND : angle 1.16130 ( 72) covalent geometry : bond 0.00312 (17357) covalent geometry : angle 0.68197 (23561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8018 (m100) cc_final: 0.7749 (m100) REVERT: A 49 GLU cc_start: 0.8266 (pm20) cc_final: 0.7950 (pt0) REVERT: A 111 LEU cc_start: 0.8212 (mp) cc_final: 0.7998 (mp) REVERT: A 232 LYS cc_start: 0.7309 (mptt) cc_final: 0.6888 (tmtt) REVERT: A 269 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7074 (tt0) REVERT: A 327 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7010 (mtt-85) REVERT: B 35 TRP cc_start: 0.8212 (m100) cc_final: 0.7706 (m100) REVERT: B 69 TRP cc_start: 0.6149 (OUTLIER) cc_final: 0.5349 (m100) REVERT: B 232 LYS cc_start: 0.8223 (mmpt) cc_final: 0.7636 (tptp) REVERT: B 326 ILE cc_start: 0.8245 (mm) cc_final: 0.7856 (mm) REVERT: B 340 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7317 (tt0) REVERT: C 35 TRP cc_start: 0.7565 (m100) cc_final: 0.6938 (m100) REVERT: C 213 ILE cc_start: 0.8146 (tp) cc_final: 0.7739 (pt) REVERT: C 308 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7736 (ttm110) REVERT: C 327 ARG cc_start: 0.7370 (mmm-85) cc_final: 0.6626 (mtm180) REVERT: C 347 LYS cc_start: 0.7237 (tttt) cc_final: 0.6189 (mptt) REVERT: C 477 ASP cc_start: 0.7824 (m-30) cc_final: 0.7320 (t0) REVERT: C 484 TYR cc_start: 0.8663 (p90) cc_final: 0.8082 (p90) REVERT: C 486 TYR cc_start: 0.8471 (m-80) cc_final: 0.8201 (m-80) REVERT: H 5 THR cc_start: 0.8690 (m) cc_final: 0.8173 (p) REVERT: H 12 ARG cc_start: 0.8176 (mpt90) cc_final: 0.7862 (mpt180) REVERT: H 30 LYS cc_start: 0.8390 (mtmt) cc_final: 0.7868 (mtmm) REVERT: H 100 ASP cc_start: 0.8088 (t0) cc_final: 0.7636 (m-30) REVERT: a 577 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8115 (mm-40) REVERT: c 610 TRP cc_start: 0.7496 (t-100) cc_final: 0.7014 (t-100) outliers start: 49 outliers final: 26 residues processed: 267 average time/residue: 0.3177 time to fit residues: 125.6580 Evaluate side-chains 229 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain a residue 577 GLN Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 642 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 246 GLN B 330 HIS C 105 HIS c 577 GLN c 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103982 restraints weight = 21003.904| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.72 r_work: 0.3000 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17511 Z= 0.251 Angle : 0.812 12.963 23987 Z= 0.383 Chirality : 0.051 0.259 2999 Planarity : 0.005 0.043 2830 Dihedral : 9.181 70.772 4517 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.97 % Rotamer: Outliers : 3.75 % Allowed : 14.18 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1928 helix: -0.75 (0.27), residues: 355 sheet: 0.09 (0.22), residues: 543 loop : -0.84 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 610 HIS 0.007 0.002 HIS C 374 PHE 0.018 0.003 PHE B 376 TYR 0.023 0.002 TYR L 49 ARG 0.006 0.001 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 58) link_NAG-ASN : angle 2.87978 ( 174) link_ALPHA1-6 : bond 0.01162 ( 9) link_ALPHA1-6 : angle 2.22721 ( 27) link_BETA1-4 : bond 0.00735 ( 32) link_BETA1-4 : angle 2.27803 ( 96) link_ALPHA1-2 : bond 0.00469 ( 10) link_ALPHA1-2 : angle 2.01750 ( 30) link_ALPHA1-3 : bond 0.01110 ( 9) link_ALPHA1-3 : angle 1.75086 ( 27) hydrogen bonds : bond 0.05617 ( 430) hydrogen bonds : angle 5.32728 ( 1116) SS BOND : bond 0.00460 ( 36) SS BOND : angle 1.60430 ( 72) covalent geometry : bond 0.00608 (17357) covalent geometry : angle 0.75326 (23561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8284 (pm20) cc_final: 0.7923 (pt0) REVERT: A 166 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7793 (mmm160) REVERT: A 232 LYS cc_start: 0.7353 (mptt) cc_final: 0.6825 (tmtt) REVERT: A 327 ARG cc_start: 0.7616 (mtp85) cc_final: 0.6805 (mtt-85) REVERT: B 33 ASN cc_start: 0.5404 (OUTLIER) cc_final: 0.5162 (p0) REVERT: B 69 TRP cc_start: 0.5752 (OUTLIER) cc_final: 0.4562 (m100) REVERT: B 111 LEU cc_start: 0.7774 (tp) cc_final: 0.7507 (tp) REVERT: B 168 LYS cc_start: 0.8681 (tppt) cc_final: 0.8421 (mmmm) REVERT: B 169 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.6854 (tttp) REVERT: B 232 LYS cc_start: 0.8122 (mmpt) cc_final: 0.7430 (tptp) REVERT: B 326 ILE cc_start: 0.7895 (mm) cc_final: 0.7606 (mm) REVERT: B 340 GLU cc_start: 0.7615 (tt0) cc_final: 0.7324 (tt0) REVERT: B 475 MET cc_start: 0.8144 (tpp) cc_final: 0.7846 (tpp) REVERT: C 35 TRP cc_start: 0.7407 (m100) cc_final: 0.6560 (m-90) REVERT: C 213 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7508 (pt) REVERT: C 308 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7569 (ttm110) REVERT: C 327 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.6539 (mtm180) REVERT: C 347 LYS cc_start: 0.6718 (tttt) cc_final: 0.5620 (mptt) REVERT: C 477 ASP cc_start: 0.8065 (m-30) cc_final: 0.7207 (t0) REVERT: H 30 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7638 (mtmm) REVERT: H 100 ASP cc_start: 0.7908 (t0) cc_final: 0.7555 (m-30) REVERT: b 634 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8051 (mt-10) outliers start: 65 outliers final: 43 residues processed: 257 average time/residue: 0.2945 time to fit residues: 111.3436 Evaluate side-chains 242 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain a residue 546 SER Chi-restraints excluded: chain a residue 599 SER Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain b residue 620 SER Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108888 restraints weight = 20725.959| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.71 r_work: 0.3016 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17511 Z= 0.131 Angle : 0.709 21.122 23987 Z= 0.325 Chirality : 0.048 0.720 2999 Planarity : 0.004 0.041 2830 Dihedral : 8.484 64.442 4517 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 3.11 % Allowed : 15.39 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1928 helix: -0.37 (0.28), residues: 355 sheet: 0.12 (0.22), residues: 507 loop : -0.84 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 610 HIS 0.003 0.001 HIS H 52A PHE 0.012 0.001 PHE C 53 TYR 0.034 0.001 TYR a 638 ARG 0.007 0.000 ARG B 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 58) link_NAG-ASN : angle 3.24070 ( 174) link_ALPHA1-6 : bond 0.01112 ( 9) link_ALPHA1-6 : angle 1.99992 ( 27) link_BETA1-4 : bond 0.00631 ( 32) link_BETA1-4 : angle 1.97196 ( 96) link_ALPHA1-2 : bond 0.00491 ( 10) link_ALPHA1-2 : angle 1.93887 ( 30) link_ALPHA1-3 : bond 0.01128 ( 9) link_ALPHA1-3 : angle 1.47095 ( 27) hydrogen bonds : bond 0.04380 ( 430) hydrogen bonds : angle 4.87257 ( 1116) SS BOND : bond 0.00350 ( 36) SS BOND : angle 1.40868 ( 72) covalent geometry : bond 0.00291 (17357) covalent geometry : angle 0.63227 (23561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8308 (pm20) cc_final: 0.7931 (pt0) REVERT: A 232 LYS cc_start: 0.7236 (mptt) cc_final: 0.6764 (tmtt) REVERT: A 327 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6713 (mtt-85) REVERT: A 424 ILE cc_start: 0.8943 (mm) cc_final: 0.8740 (mm) REVERT: B 69 TRP cc_start: 0.5761 (OUTLIER) cc_final: 0.4562 (m100) REVERT: B 111 LEU cc_start: 0.7733 (tp) cc_final: 0.7527 (tp) REVERT: B 168 LYS cc_start: 0.8674 (tppt) cc_final: 0.8408 (mmmm) REVERT: B 169 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.6871 (tttt) REVERT: B 232 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7379 (tptp) REVERT: B 326 ILE cc_start: 0.7955 (mm) cc_final: 0.7571 (mm) REVERT: B 340 GLU cc_start: 0.7503 (tt0) cc_final: 0.7199 (tt0) REVERT: C 35 TRP cc_start: 0.7382 (m100) cc_final: 0.6408 (m-90) REVERT: C 151 ARG cc_start: 0.7511 (tpp80) cc_final: 0.7178 (ttm110) REVERT: C 161 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7949 (mtp) REVERT: C 213 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7455 (pt) REVERT: C 308 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7503 (ttm110) REVERT: C 327 ARG cc_start: 0.7394 (mmm-85) cc_final: 0.6469 (mtm180) REVERT: C 347 LYS cc_start: 0.6638 (tttt) cc_final: 0.5586 (mptt) REVERT: C 477 ASP cc_start: 0.8034 (m-30) cc_final: 0.7159 (t0) REVERT: H 30 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7635 (mtmm) REVERT: H 86 ASP cc_start: 0.7105 (t0) cc_final: 0.6899 (t0) REVERT: H 100 ASP cc_start: 0.7851 (t0) cc_final: 0.7465 (m-30) REVERT: H 112 THR cc_start: 0.8170 (m) cc_final: 0.7905 (p) REVERT: b 634 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7981 (mt-10) outliers start: 54 outliers final: 34 residues processed: 246 average time/residue: 0.3076 time to fit residues: 110.7916 Evaluate side-chains 232 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 540 GLN Chi-restraints excluded: chain c residue 642 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 48 optimal weight: 9.9990 chunk 151 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103128 restraints weight = 21471.978| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.76 r_work: 0.2976 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17511 Z= 0.151 Angle : 0.695 15.557 23987 Z= 0.319 Chirality : 0.047 0.527 2999 Planarity : 0.004 0.041 2830 Dihedral : 8.269 64.248 4516 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 3.52 % Allowed : 16.37 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1928 helix: -0.29 (0.28), residues: 361 sheet: -0.05 (0.21), residues: 556 loop : -0.89 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 571 HIS 0.004 0.001 HIS C 374 PHE 0.013 0.002 PHE A 317 TYR 0.041 0.002 TYR a 638 ARG 0.005 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00785 ( 58) link_NAG-ASN : angle 3.00020 ( 174) link_ALPHA1-6 : bond 0.01004 ( 9) link_ALPHA1-6 : angle 1.95457 ( 27) link_BETA1-4 : bond 0.00617 ( 32) link_BETA1-4 : angle 1.91966 ( 96) link_ALPHA1-2 : bond 0.00452 ( 10) link_ALPHA1-2 : angle 1.90032 ( 30) link_ALPHA1-3 : bond 0.01048 ( 9) link_ALPHA1-3 : angle 1.60363 ( 27) hydrogen bonds : bond 0.04202 ( 430) hydrogen bonds : angle 4.71938 ( 1116) SS BOND : bond 0.00301 ( 36) SS BOND : angle 1.27392 ( 72) covalent geometry : bond 0.00355 (17357) covalent geometry : angle 0.62711 (23561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8354 (pm20) cc_final: 0.7979 (pt0) REVERT: A 199 SER cc_start: 0.8766 (p) cc_final: 0.8562 (t) REVERT: A 232 LYS cc_start: 0.7280 (mptt) cc_final: 0.6779 (tmtt) REVERT: A 327 ARG cc_start: 0.7420 (mtp85) cc_final: 0.6666 (mtt-85) REVERT: A 424 ILE cc_start: 0.8942 (mm) cc_final: 0.8735 (mm) REVERT: B 69 TRP cc_start: 0.5685 (OUTLIER) cc_final: 0.3658 (m100) REVERT: B 111 LEU cc_start: 0.7681 (tp) cc_final: 0.7428 (tp) REVERT: B 168 LYS cc_start: 0.8674 (tppt) cc_final: 0.8359 (mmmm) REVERT: B 169 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.6890 (tttt) REVERT: B 232 LYS cc_start: 0.8022 (mmpt) cc_final: 0.7323 (tptp) REVERT: B 326 ILE cc_start: 0.7864 (mm) cc_final: 0.7450 (mm) REVERT: B 340 GLU cc_start: 0.7510 (tt0) cc_final: 0.7195 (tt0) REVERT: B 490 LYS cc_start: 0.7727 (tttt) cc_final: 0.7029 (ttpp) REVERT: B 502 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7603 (ttmm) REVERT: C 35 TRP cc_start: 0.7331 (m100) cc_final: 0.6952 (m-90) REVERT: C 151 ARG cc_start: 0.7446 (tpp80) cc_final: 0.7100 (ttm110) REVERT: C 161 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: C 213 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7458 (pt) REVERT: C 308 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7382 (ttm110) REVERT: C 327 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.6564 (mtm180) REVERT: C 347 LYS cc_start: 0.6509 (tttt) cc_final: 0.5469 (mptt) REVERT: C 475 MET cc_start: 0.6852 (tpp) cc_final: 0.6577 (tpt) REVERT: C 477 ASP cc_start: 0.8034 (m-30) cc_final: 0.7285 (t0) REVERT: H 30 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7584 (mtmm) REVERT: H 43 GLN cc_start: 0.7436 (mp10) cc_final: 0.7202 (mp10) REVERT: H 86 ASP cc_start: 0.7104 (t0) cc_final: 0.6704 (t0) REVERT: H 100 ASP cc_start: 0.7880 (t0) cc_final: 0.7511 (m-30) REVERT: H 112 THR cc_start: 0.8323 (m) cc_final: 0.8077 (p) outliers start: 61 outliers final: 41 residues processed: 247 average time/residue: 0.3053 time to fit residues: 111.2133 Evaluate side-chains 237 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain a residue 546 SER Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 140 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 96 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132910 restraints weight = 19560.073| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.44 r_work: 0.3106 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17511 Z= 0.119 Angle : 0.658 14.458 23987 Z= 0.301 Chirality : 0.046 0.499 2999 Planarity : 0.003 0.041 2830 Dihedral : 8.066 63.299 4515 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 3.34 % Allowed : 16.77 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1928 helix: -0.11 (0.29), residues: 361 sheet: -0.03 (0.22), residues: 554 loop : -0.88 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 614 HIS 0.003 0.001 HIS H 52A PHE 0.011 0.001 PHE C 53 TYR 0.047 0.001 TYR a 638 ARG 0.004 0.000 ARG a 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 58) link_NAG-ASN : angle 2.88442 ( 174) link_ALPHA1-6 : bond 0.01016 ( 9) link_ALPHA1-6 : angle 1.89411 ( 27) link_BETA1-4 : bond 0.00586 ( 32) link_BETA1-4 : angle 1.82241 ( 96) link_ALPHA1-2 : bond 0.00475 ( 10) link_ALPHA1-2 : angle 1.88047 ( 30) link_ALPHA1-3 : bond 0.01081 ( 9) link_ALPHA1-3 : angle 1.50447 ( 27) hydrogen bonds : bond 0.03857 ( 430) hydrogen bonds : angle 4.58752 ( 1116) SS BOND : bond 0.00320 ( 36) SS BOND : angle 1.20333 ( 72) covalent geometry : bond 0.00266 (17357) covalent geometry : angle 0.59227 (23561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8334 (pm20) cc_final: 0.7995 (pt0) REVERT: A 199 SER cc_start: 0.9044 (p) cc_final: 0.8802 (t) REVERT: A 232 LYS cc_start: 0.7416 (mptt) cc_final: 0.7016 (tmtt) REVERT: A 323 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (mp) REVERT: A 327 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7250 (mtt-85) REVERT: B 69 TRP cc_start: 0.6121 (OUTLIER) cc_final: 0.3964 (m100) REVERT: B 111 LEU cc_start: 0.8272 (tp) cc_final: 0.8034 (tp) REVERT: B 168 LYS cc_start: 0.9077 (tppt) cc_final: 0.8852 (mmmm) REVERT: B 169 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7347 (tttt) REVERT: B 232 LYS cc_start: 0.8430 (mmpt) cc_final: 0.7805 (tptp) REVERT: B 304 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7862 (mtt180) REVERT: B 328 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: B 340 GLU cc_start: 0.7765 (tt0) cc_final: 0.7480 (tt0) REVERT: B 502 LYS cc_start: 0.8255 (mmmm) cc_final: 0.7910 (ttmm) REVERT: C 161 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: C 213 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7884 (pt) REVERT: C 308 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7806 (ttm110) REVERT: C 327 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7081 (mtm180) REVERT: C 475 MET cc_start: 0.7094 (tpp) cc_final: 0.6842 (tpt) REVERT: C 477 ASP cc_start: 0.8272 (m-30) cc_final: 0.7646 (t0) REVERT: H 30 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7896 (mtmm) REVERT: H 86 ASP cc_start: 0.7458 (t0) cc_final: 0.7214 (t0) REVERT: H 100 ASP cc_start: 0.8047 (t0) cc_final: 0.7731 (m-30) REVERT: c 610 TRP cc_start: 0.7558 (t-100) cc_final: 0.7248 (t-100) outliers start: 58 outliers final: 38 residues processed: 237 average time/residue: 0.3270 time to fit residues: 115.4296 Evaluate side-chains 237 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 642 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 43 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 121 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102279 restraints weight = 21317.090| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.55 r_work: 0.2952 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17511 Z= 0.121 Angle : 0.648 13.970 23987 Z= 0.297 Chirality : 0.046 0.467 2999 Planarity : 0.004 0.042 2830 Dihedral : 7.938 64.114 4515 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 3.05 % Allowed : 17.00 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1928 helix: -0.01 (0.29), residues: 361 sheet: -0.06 (0.21), residues: 571 loop : -0.85 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 35 HIS 0.003 0.001 HIS C 374 PHE 0.011 0.001 PHE A 159 TYR 0.042 0.001 TYR a 638 ARG 0.006 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 58) link_NAG-ASN : angle 2.80488 ( 174) link_ALPHA1-6 : bond 0.01002 ( 9) link_ALPHA1-6 : angle 1.90019 ( 27) link_BETA1-4 : bond 0.00629 ( 32) link_BETA1-4 : angle 1.80794 ( 96) link_ALPHA1-2 : bond 0.00464 ( 10) link_ALPHA1-2 : angle 1.84555 ( 30) link_ALPHA1-3 : bond 0.01051 ( 9) link_ALPHA1-3 : angle 1.53029 ( 27) hydrogen bonds : bond 0.03735 ( 430) hydrogen bonds : angle 4.52139 ( 1116) SS BOND : bond 0.00297 ( 36) SS BOND : angle 1.28734 ( 72) covalent geometry : bond 0.00274 (17357) covalent geometry : angle 0.58293 (23561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8353 (pm20) cc_final: 0.7987 (pt0) REVERT: A 199 SER cc_start: 0.9006 (p) cc_final: 0.8774 (t) REVERT: A 232 LYS cc_start: 0.7424 (mptt) cc_final: 0.7084 (tmtt) REVERT: A 323 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 327 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7251 (mtt-85) REVERT: B 69 TRP cc_start: 0.5994 (OUTLIER) cc_final: 0.3870 (m100) REVERT: B 111 LEU cc_start: 0.8104 (tp) cc_final: 0.7854 (tp) REVERT: B 169 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7223 (tttt) REVERT: B 232 LYS cc_start: 0.8379 (mmpt) cc_final: 0.7768 (tptp) REVERT: B 304 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7719 (mtt180) REVERT: B 328 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: B 340 GLU cc_start: 0.7659 (tt0) cc_final: 0.7377 (tt0) REVERT: B 502 LYS cc_start: 0.8260 (mmmm) cc_final: 0.7921 (ttmm) REVERT: C 161 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8253 (mtp) REVERT: C 213 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7770 (pt) REVERT: C 308 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7668 (ttm110) REVERT: C 327 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7002 (mtm180) REVERT: C 475 MET cc_start: 0.7032 (tpp) cc_final: 0.6769 (tpt) REVERT: C 477 ASP cc_start: 0.8225 (m-30) cc_final: 0.7561 (t0) REVERT: H 30 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7871 (mtmm) REVERT: H 86 ASP cc_start: 0.7464 (t0) cc_final: 0.7175 (t0) REVERT: L 100 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: a 607 ASN cc_start: 0.7645 (m-40) cc_final: 0.7185 (p0) REVERT: a 638 TYR cc_start: 0.7073 (m-10) cc_final: 0.6816 (m-10) REVERT: b 536 THR cc_start: 0.8723 (p) cc_final: 0.8497 (t) outliers start: 53 outliers final: 40 residues processed: 236 average time/residue: 0.3120 time to fit residues: 108.5291 Evaluate side-chains 237 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain b residue 598 CYS Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 109 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 141 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102821 restraints weight = 21335.515| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.34 r_work: 0.2957 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17511 Z= 0.114 Angle : 0.637 13.560 23987 Z= 0.292 Chirality : 0.046 0.445 2999 Planarity : 0.003 0.042 2830 Dihedral : 7.790 64.472 4515 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 3.40 % Allowed : 17.18 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1928 helix: 0.09 (0.29), residues: 359 sheet: 0.04 (0.22), residues: 566 loop : -0.84 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 35 HIS 0.003 0.001 HIS H 52A PHE 0.014 0.001 PHE A 159 TYR 0.028 0.001 TYR a 638 ARG 0.007 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00793 ( 58) link_NAG-ASN : angle 2.74342 ( 174) link_ALPHA1-6 : bond 0.00997 ( 9) link_ALPHA1-6 : angle 1.88495 ( 27) link_BETA1-4 : bond 0.00612 ( 32) link_BETA1-4 : angle 1.74831 ( 96) link_ALPHA1-2 : bond 0.00468 ( 10) link_ALPHA1-2 : angle 1.82866 ( 30) link_ALPHA1-3 : bond 0.01054 ( 9) link_ALPHA1-3 : angle 1.50696 ( 27) hydrogen bonds : bond 0.03529 ( 430) hydrogen bonds : angle 4.45200 ( 1116) SS BOND : bond 0.00292 ( 36) SS BOND : angle 1.14079 ( 72) covalent geometry : bond 0.00254 (17357) covalent geometry : angle 0.57512 (23561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8329 (pm20) cc_final: 0.7931 (pt0) REVERT: A 199 SER cc_start: 0.9038 (p) cc_final: 0.8803 (t) REVERT: A 232 LYS cc_start: 0.7397 (mptt) cc_final: 0.7127 (tmtt) REVERT: A 323 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 327 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7339 (mtt-85) REVERT: B 69 TRP cc_start: 0.6030 (OUTLIER) cc_final: 0.3844 (m100) REVERT: B 111 LEU cc_start: 0.8196 (tp) cc_final: 0.7939 (tp) REVERT: B 169 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7326 (tttt) REVERT: B 232 LYS cc_start: 0.8420 (mmpt) cc_final: 0.7830 (tptp) REVERT: B 304 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7746 (mtt180) REVERT: B 502 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7953 (ttmm) REVERT: C 161 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8277 (mtp) REVERT: C 213 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7850 (pt) REVERT: C 308 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7718 (ttm110) REVERT: C 327 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7149 (mtm180) REVERT: C 475 MET cc_start: 0.7036 (tpp) cc_final: 0.6797 (tpt) REVERT: C 477 ASP cc_start: 0.8230 (m-30) cc_final: 0.7592 (t0) REVERT: H 30 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7919 (mtmm) REVERT: H 86 ASP cc_start: 0.7518 (t0) cc_final: 0.7206 (t0) REVERT: L 100 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: a 607 ASN cc_start: 0.7599 (m-40) cc_final: 0.7181 (p0) REVERT: a 637 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (m-40) outliers start: 59 outliers final: 41 residues processed: 244 average time/residue: 0.3031 time to fit residues: 109.4042 Evaluate side-chains 240 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain a residue 637 ASN Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 540 GLN Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 642 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 142 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103690 restraints weight = 21446.302| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.09 r_work: 0.2934 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17511 Z= 0.227 Angle : 0.757 14.008 23987 Z= 0.352 Chirality : 0.050 0.477 2999 Planarity : 0.004 0.044 2830 Dihedral : 8.373 65.982 4515 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 3.29 % Allowed : 17.52 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1928 helix: -0.18 (0.28), residues: 359 sheet: -0.18 (0.22), residues: 558 loop : -0.95 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 35 HIS 0.006 0.001 HIS C 374 PHE 0.016 0.002 PHE B 376 TYR 0.046 0.002 TYR a 638 ARG 0.007 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00829 ( 58) link_NAG-ASN : angle 2.80048 ( 174) link_ALPHA1-6 : bond 0.00834 ( 9) link_ALPHA1-6 : angle 1.99147 ( 27) link_BETA1-4 : bond 0.00626 ( 32) link_BETA1-4 : angle 2.06171 ( 96) link_ALPHA1-2 : bond 0.00466 ( 10) link_ALPHA1-2 : angle 1.97145 ( 30) link_ALPHA1-3 : bond 0.01045 ( 9) link_ALPHA1-3 : angle 1.75689 ( 27) hydrogen bonds : bond 0.04576 ( 430) hydrogen bonds : angle 4.74342 ( 1116) SS BOND : bond 0.00502 ( 36) SS BOND : angle 1.49956 ( 72) covalent geometry : bond 0.00554 (17357) covalent geometry : angle 0.69898 (23561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8305 (pm20) cc_final: 0.7922 (pt0) REVERT: A 150 MET cc_start: 0.8583 (mmm) cc_final: 0.8256 (tpt) REVERT: A 199 SER cc_start: 0.8984 (p) cc_final: 0.8784 (t) REVERT: A 232 LYS cc_start: 0.7541 (mptt) cc_final: 0.7134 (tmtt) REVERT: A 323 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 327 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7469 (mtt-85) REVERT: B 69 TRP cc_start: 0.6192 (OUTLIER) cc_final: 0.3927 (m100) REVERT: B 111 LEU cc_start: 0.8298 (tp) cc_final: 0.8029 (tp) REVERT: B 169 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7351 (tttp) REVERT: B 199 SER cc_start: 0.8978 (p) cc_final: 0.8773 (p) REVERT: B 232 LYS cc_start: 0.8564 (mmpt) cc_final: 0.7953 (tptp) REVERT: B 481 SER cc_start: 0.9124 (m) cc_final: 0.8886 (t) REVERT: B 490 LYS cc_start: 0.8346 (tttt) cc_final: 0.7715 (ttpt) REVERT: B 502 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8031 (ttmm) REVERT: C 213 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7959 (pt) REVERT: C 322 ILE cc_start: 0.9059 (mm) cc_final: 0.8783 (mm) REVERT: C 327 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7199 (mtm180) REVERT: C 477 ASP cc_start: 0.8365 (m-30) cc_final: 0.7696 (t0) REVERT: H 30 LYS cc_start: 0.8448 (mtmt) cc_final: 0.7931 (mtmm) REVERT: H 86 ASP cc_start: 0.7576 (t0) cc_final: 0.7260 (t0) REVERT: L 100 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8467 (pm20) outliers start: 57 outliers final: 43 residues processed: 239 average time/residue: 0.3192 time to fit residues: 112.0249 Evaluate side-chains 238 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain a residue 546 SER Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain a residue 635 ILE Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 606 THR Chi-restraints excluded: chain c residue 642 ILE Chi-restraints excluded: chain c residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104184 restraints weight = 21119.913| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.76 r_work: 0.2980 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17511 Z= 0.132 Angle : 0.686 13.671 23987 Z= 0.314 Chirality : 0.047 0.451 2999 Planarity : 0.004 0.044 2830 Dihedral : 8.066 63.214 4515 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 18.21 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1928 helix: 0.01 (0.29), residues: 359 sheet: -0.07 (0.22), residues: 552 loop : -0.94 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 35 HIS 0.003 0.001 HIS C 374 PHE 0.013 0.001 PHE A 159 TYR 0.035 0.001 TYR a 638 ARG 0.015 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 58) link_NAG-ASN : angle 2.90364 ( 174) link_ALPHA1-6 : bond 0.01004 ( 9) link_ALPHA1-6 : angle 1.92057 ( 27) link_BETA1-4 : bond 0.00582 ( 32) link_BETA1-4 : angle 1.85615 ( 96) link_ALPHA1-2 : bond 0.00456 ( 10) link_ALPHA1-2 : angle 1.92107 ( 30) link_ALPHA1-3 : bond 0.01057 ( 9) link_ALPHA1-3 : angle 1.51903 ( 27) hydrogen bonds : bond 0.03918 ( 430) hydrogen bonds : angle 4.59292 ( 1116) SS BOND : bond 0.00322 ( 36) SS BOND : angle 1.19171 ( 72) covalent geometry : bond 0.00303 (17357) covalent geometry : angle 0.62163 (23561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8323 (pm20) cc_final: 0.7848 (pt0) REVERT: A 232 LYS cc_start: 0.7352 (mptt) cc_final: 0.6950 (tmtt) REVERT: A 323 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 327 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6755 (mtt-85) REVERT: B 69 TRP cc_start: 0.5646 (OUTLIER) cc_final: 0.3532 (m100) REVERT: B 169 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.6900 (tttt) REVERT: B 232 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7347 (tptp) REVERT: B 328 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: B 502 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7663 (ttmm) REVERT: C 69 TRP cc_start: 0.6256 (OUTLIER) cc_final: 0.4109 (p90) REVERT: C 213 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7258 (pt) REVERT: C 308 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7647 (ttm110) REVERT: C 327 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.6666 (mtm180) REVERT: C 477 ASP cc_start: 0.8118 (m-30) cc_final: 0.7292 (t0) REVERT: H 30 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7568 (mtmm) REVERT: H 86 ASP cc_start: 0.7085 (t0) cc_final: 0.6748 (t0) REVERT: L 100 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8334 (pm20) outliers start: 52 outliers final: 39 residues processed: 227 average time/residue: 0.3128 time to fit residues: 105.1751 Evaluate side-chains 233 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 69 TRP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 LYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain a residue 605 CYS Chi-restraints excluded: chain a residue 606 THR Chi-restraints excluded: chain b residue 648 GLU Chi-restraints excluded: chain c residue 529 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 606 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 10 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102936 restraints weight = 21234.519| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.65 r_work: 0.2966 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17511 Z= 0.183 Angle : 0.712 13.652 23987 Z= 0.330 Chirality : 0.048 0.459 2999 Planarity : 0.004 0.044 2830 Dihedral : 8.248 64.143 4515 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 3.29 % Allowed : 17.69 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1928 helix: -0.06 (0.29), residues: 359 sheet: -0.20 (0.22), residues: 555 loop : -1.00 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 35 HIS 0.005 0.001 HIS C 374 PHE 0.017 0.002 PHE A 159 TYR 0.019 0.002 TYR a 638 ARG 0.007 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00761 ( 58) link_NAG-ASN : angle 2.75340 ( 174) link_ALPHA1-6 : bond 0.00951 ( 9) link_ALPHA1-6 : angle 1.95944 ( 27) link_BETA1-4 : bond 0.00578 ( 32) link_BETA1-4 : angle 1.93394 ( 96) link_ALPHA1-2 : bond 0.00435 ( 10) link_ALPHA1-2 : angle 1.91989 ( 30) link_ALPHA1-3 : bond 0.00982 ( 9) link_ALPHA1-3 : angle 1.65362 ( 27) hydrogen bonds : bond 0.04181 ( 430) hydrogen bonds : angle 4.67136 ( 1116) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.32022 ( 72) covalent geometry : bond 0.00443 (17357) covalent geometry : angle 0.65401 (23561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7947.05 seconds wall clock time: 140 minutes 2.19 seconds (8402.19 seconds total)