Starting phenix.real_space_refine on Sat Jun 21 00:53:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msy_48591/06_2025/9msy_48591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msy_48591/06_2025/9msy_48591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9msy_48591/06_2025/9msy_48591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msy_48591/06_2025/9msy_48591.map" model { file = "/net/cci-nas-00/data/ceres_data/9msy_48591/06_2025/9msy_48591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msy_48591/06_2025/9msy_48591.cif" } resolution = 3.4 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= 0.019 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 153 5.16 5 C 15276 2.51 5 N 4050 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24315 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4189 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 9 Chain: "G" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4189 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 9 Chain: "J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "N" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "K" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4189 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 22, 'TRANS': 508} Chain breaks: 9 Chain: "O" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "Q" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "R" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 771 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "P" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.18, per 1000 atoms: 0.75 Number of scatterers: 24315 At special positions: 0 Unit cell: (168.526, 162.322, 138.543, 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 153 16.00 O 4836 8.00 N 4050 7.00 C 15276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " 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=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 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 C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " 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 ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 6 " " MAN U 4 " - " MAN U 5 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 6 " " MAN b 4 " - " MAN b 5 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 6 " " MAN i 4 " - " MAN i 5 " ALPHA1-6 " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 4 " " BMA h 3 " - " MAN h 5 " " BMA i 3 " - " MAN i 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 701 " - " ASN A 241 " " NAG A 702 " - " ASN A 88 " " NAG A 703 " - " ASN A 160 " " NAG A 704 " - " ASN A 130 " " NAG A 705 " - " ASN A 197 " " NAG A 706 " - " ASN A 611 " " NAG A 707 " - " ASN A 442 " " NAG B 701 " - " ASN B 241 " " NAG B 702 " - " ASN B 88 " " NAG B 703 " - " ASN B 160 " " NAG B 704 " - " ASN B 130 " " NAG B 705 " - " ASN B 197 " " NAG B 706 " - " ASN B 611 " " NAG B 707 " - " ASN B 442 " " NAG C 701 " - " ASN C 241 " " NAG C 702 " - " ASN C 88 " " NAG C 703 " - " ASN C 160 " " NAG C 704 " - " ASN C 130 " " NAG C 705 " - " ASN C 197 " " NAG C 706 " - " ASN C 611 " " NAG C 707 " - " ASN C 442 " " NAG D 1 " - " ASN A 230 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 289 " " NAG G1301 " - " ASN G 26 " " NAG J1301 " - " ASN J 26 " " NAG O1301 " - " ASN O 26 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN B 230 " " NAG X 1 " - " ASN B 234 " " NAG Y 1 " - " ASN B 289 " " NAG Z 1 " - " ASN B 448 " " NAG a 1 " - " ASN B 262 " " NAG b 1 " - " ASN B 332 " " NAG c 1 " - " ASN B 301 " " NAG d 1 " - " ASN C 230 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 289 " " NAG g 1 " - " ASN C 448 " " NAG h 1 " - " ASN C 262 " " NAG i 1 " - " ASN C 332 " " NAG j 1 " - " ASN C 301 " Time building additional restraints: 7.37 Conformation dependent library (CDL) restraints added in 3.3 seconds 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 54 sheets defined 15.0% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.861A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 3.992A pdb=" N LYS A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.871A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.039A pdb=" N VAL A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 removed outlier: 3.647A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 636 through 639 removed outlier: 3.715A pdb=" N THR A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 641 through 659 removed outlier: 3.950A pdb=" N LEU A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 100B through 100F Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.958A pdb=" N THR I 29 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.609A pdb=" N SER L 32 " --> pdb=" O SER L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.642A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.786A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.861A pdb=" N GLU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 352 removed outlier: 3.992A pdb=" N LYS B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.871A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 544 through 549 removed outlier: 4.039A pdb=" N VAL B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.646A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 636 through 639 removed outlier: 3.714A pdb=" N THR B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 641 through 659 removed outlier: 3.950A pdb=" N LEU B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 100B through 100F Processing helix chain 'M' and resid 26 through 30 removed outlier: 3.958A pdb=" N THR M 29 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 29 through 32 removed outlier: 3.610A pdb=" N SER N 32 " --> pdb=" O SER N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 32' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.642A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.786A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.860A pdb=" N GLU C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 352 removed outlier: 3.992A pdb=" N LYS C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.871A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.039A pdb=" N VAL C 549 " --> pdb=" O SER C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 removed outlier: 3.646A pdb=" N ARG C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 636 through 639 removed outlier: 3.715A pdb=" N THR C 639 " --> pdb=" O GLY C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 636 through 639' Processing helix chain 'C' and resid 641 through 659 removed outlier: 3.949A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.958A pdb=" N THR Q 29 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'R' and resid 29 through 32 removed outlier: 3.610A pdb=" N SER R 32 " --> pdb=" O SER R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 32' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.642A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.786A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 497 through 499 removed outlier: 5.851A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.700A pdb=" N ILE A 225 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.598A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) 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 271 through 273 removed outlier: 10.665A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N LEU A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323A removed outlier: 3.615A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 7 removed outlier: 5.886A pdb=" N GLU G 16 " --> pdb=" O SER G 82B" (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER G 82B" --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG G 94 " --> pdb=" O MET G 100M" (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET G 100M" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA G 96 " --> pdb=" O TYR G 100K" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY G 88 " --> pdb=" O VAL G 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL I 11 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL I 11 " --> pdb=" O THR I 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 19 through 24 removed outlier: 4.129A pdb=" N ALA I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE I 75 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.635A pdb=" N ILE L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 497 through 499 removed outlier: 5.851A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.700A pdb=" N ILE B 225 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.598A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'B' and resid 271 through 273 removed outlier: 10.665A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.350A pdb=" N PHE B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.471A pdb=" N LEU B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N GLU B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 451 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS B 359 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 316 through 323A removed outlier: 3.615A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 removed outlier: 5.886A pdb=" N GLU J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER J 82B" --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP J 35 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS J 92 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL J 102 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG J 94 " --> pdb=" O MET J 100M" (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET J 100M" --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA J 96 " --> pdb=" O TYR J 100K" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP J 50 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP J 35 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.129A pdb=" N ALA M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE M 75 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AD6, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.635A pdb=" N ILE N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.093A pdb=" N ALA K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.093A pdb=" N ALA K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.608A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 497 through 499 removed outlier: 5.851A pdb=" N VAL C 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR C 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.700A pdb=" N ILE C 225 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.598A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AE5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AE6, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.664A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.472A pdb=" N LEU C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 316 through 323A removed outlier: 3.615A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 3 through 7 removed outlier: 5.885A pdb=" N GLU O 16 " --> pdb=" O SER O 82B" (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER O 82B" --> pdb=" O GLU O 16 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP O 35 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS O 92 " --> pdb=" O VAL O 102 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL O 102 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG O 94 " --> pdb=" O MET O 100M" (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET O 100M" --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA O 96 " --> pdb=" O TYR O 100K" (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP O 35 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP Q 35 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.454A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 19 through 24 removed outlier: 4.129A pdb=" N ALA Q 19 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Q 75 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'R' and resid 53 through 54 removed outlier: 3.635A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 3 through 6 removed outlier: 4.094A pdb=" N ALA P 78 " --> pdb=" O CYS P 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.608A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2046 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: 10.60 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7280 1.34 - 1.47: 6685 1.47 - 1.59: 10653 1.59 - 1.72: 0 1.72 - 1.85: 216 Bond restraints: 24834 Sorted by residual: bond pdb=" N GLY C 367 " pdb=" CA GLY C 367 " ideal model delta sigma weight residual 1.448 1.477 -0.030 9.20e-03 1.18e+04 1.04e+01 bond pdb=" N GLY A 367 " pdb=" CA GLY A 367 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" N ARG H 71 " pdb=" CA ARG H 71 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.62e+00 bond pdb=" N ARG K 71 " pdb=" CA ARG K 71 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.61e+00 ... (remaining 24829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 32042 2.10 - 4.19: 1371 4.19 - 6.29: 226 6.29 - 8.38: 54 8.38 - 10.48: 18 Bond angle restraints: 33711 Sorted by residual: angle pdb=" N GLY K 55 " pdb=" CA GLY K 55 " pdb=" C GLY K 55 " ideal model delta sigma weight residual 115.21 107.59 7.62 1.30e+00 5.92e-01 3.43e+01 angle pdb=" N GLY H 55 " pdb=" CA GLY H 55 " pdb=" C GLY H 55 " ideal model delta sigma weight residual 115.21 107.61 7.60 1.30e+00 5.92e-01 3.42e+01 angle pdb=" N GLY P 55 " pdb=" CA GLY P 55 " pdb=" C GLY P 55 " ideal model delta sigma weight residual 115.21 107.62 7.59 1.30e+00 5.92e-01 3.41e+01 angle pdb=" C TRP B 338 " pdb=" N SER B 339 " pdb=" CA SER B 339 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C TRP C 338 " pdb=" N SER C 339 " pdb=" CA SER C 339 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 ... (remaining 33706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.72: 14412 20.72 - 41.45: 1136 41.45 - 62.17: 262 62.17 - 82.89: 62 82.89 - 103.61: 22 Dihedral angle restraints: 15894 sinusoidal: 7443 harmonic: 8451 Sorted by residual: dihedral pdb=" CD ARG H 71 " pdb=" NE ARG H 71 " pdb=" CZ ARG H 71 " pdb=" NH1 ARG H 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.90 82.90 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CD ARG P 71 " pdb=" NE ARG P 71 " pdb=" CZ ARG P 71 " pdb=" NH1 ARG P 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.87 82.87 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " pdb=" CZ ARG K 71 " pdb=" NH1 ARG K 71 " ideal model delta sinusoidal sigma weight residual 0.00 -82.85 82.85 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 15891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3313 0.079 - 0.158: 628 0.158 - 0.236: 55 0.236 - 0.315: 9 0.315 - 0.394: 15 Chirality restraints: 4020 Sorted by residual: chirality pdb=" C1 NAG C 701 " pdb=" ND2 ASN C 241 " pdb=" C2 NAG C 701 " pdb=" O5 NAG C 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 241 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 4017 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 71 " 1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG P 71 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG P 71 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG P 71 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG P 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -1.086 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG H 71 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 71 " 1.086 9.50e-02 1.11e+02 4.86e-01 1.43e+02 pdb=" NE ARG K 71 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG K 71 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG K 71 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG K 71 " 0.017 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5945 2.81 - 3.33: 20782 3.33 - 3.85: 38607 3.85 - 4.38: 43911 4.38 - 4.90: 77981 Nonbonded interactions: 187226 Sorted by model distance: nonbonded pdb=" OD1 ASP J 50 " pdb=" OG1 THR J 58 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP G 50 " pdb=" OG1 THR G 58 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP O 50 " pdb=" OG1 THR O 58 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.308 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" O ILE B 443 " model vdw 2.309 3.040 ... (remaining 187221 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'X' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'T' selection = chain 'a' selection = chain 'h' } ncs_group { reference = chain 'U' selection = chain 'b' selection = chain 'i' } 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: 3.410 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: 2.120 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 63.070 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24969 Z= 0.253 Angle : 1.057 12.628 34071 Z= 0.550 Chirality : 0.063 0.394 4020 Planarity : 0.016 0.487 4137 Dihedral : 15.846 103.613 10341 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.47 % Allowed : 13.16 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.50 (0.15), residues: 2868 helix: -1.34 (0.27), residues: 333 sheet: -1.47 (0.17), residues: 969 loop : -1.84 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 100D HIS 0.006 0.002 HIS K 35 PHE 0.034 0.002 PHE A 647 TYR 0.018 0.002 TYR G 100 ARG 0.024 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 45) link_NAG-ASN : angle 3.49599 ( 135) link_ALPHA1-6 : bond 0.00485 ( 6) link_ALPHA1-6 : angle 1.71717 ( 18) link_BETA1-4 : bond 0.01009 ( 30) link_BETA1-4 : angle 3.70084 ( 90) link_ALPHA1-3 : bond 0.01076 ( 9) link_ALPHA1-3 : angle 3.14645 ( 27) hydrogen bonds : bond 0.21141 ( 721) hydrogen bonds : angle 8.65874 ( 2046) SS BOND : bond 0.00640 ( 45) SS BOND : angle 2.92767 ( 90) covalent geometry : bond 0.00512 (24834) covalent geometry : angle 1.00614 (33711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 561 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.9206 (m-80) cc_final: 0.8929 (m-80) REVERT: A 46 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7709 (mtm-85) REVERT: A 107 ASP cc_start: 0.7887 (t0) cc_final: 0.7494 (t0) REVERT: A 111 LEU cc_start: 0.7907 (mt) cc_final: 0.7565 (mt) REVERT: A 200 VAL cc_start: 0.8975 (t) cc_final: 0.8738 (p) REVERT: A 215 ILE cc_start: 0.8686 (mm) cc_final: 0.8303 (pt) REVERT: A 354 HIS cc_start: 0.7821 (t-90) cc_final: 0.7421 (t-90) REVERT: A 474 ASN cc_start: 0.7240 (t0) cc_final: 0.6786 (p0) REVERT: A 575 GLN cc_start: 0.7449 (tm-30) cc_final: 0.6994 (tm-30) REVERT: G 13 LYS cc_start: 0.5690 (mmtp) cc_final: 0.5370 (mmmt) REVERT: G 22 CYS cc_start: 0.4457 (t) cc_final: 0.4161 (m) REVERT: G 100 TYR cc_start: 0.8690 (t80) cc_final: 0.8425 (t80) REVERT: G 100 MET cc_start: 0.8538 (mtt) cc_final: 0.8184 (mtt) REVERT: I 83 GLU cc_start: 0.7848 (tt0) cc_final: 0.7290 (tt0) REVERT: L 1 GLU cc_start: 0.7386 (pt0) cc_final: 0.7053 (tt0) REVERT: L 38 GLN cc_start: 0.5470 (tp-100) cc_final: 0.5144 (tp40) REVERT: L 90 GLN cc_start: 0.8556 (tp40) cc_final: 0.8344 (tp-100) REVERT: H 46 GLU cc_start: 0.5953 (mm-30) cc_final: 0.5688 (mm-30) REVERT: H 58 ASN cc_start: 0.8110 (t0) cc_final: 0.7900 (t0) REVERT: H 79 TYR cc_start: 0.7278 (m-80) cc_final: 0.6817 (m-10) REVERT: B 107 ASP cc_start: 0.7957 (t0) cc_final: 0.7633 (t0) REVERT: B 111 LEU cc_start: 0.7969 (mt) cc_final: 0.7555 (mt) REVERT: B 166 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8001 (mmt-90) REVERT: B 277 MET cc_start: 0.6748 (mtt) cc_final: 0.6432 (mtt) REVERT: B 354 HIS cc_start: 0.7757 (t-90) cc_final: 0.7516 (t70) REVERT: B 434 MET cc_start: 0.7853 (mtm) cc_final: 0.7588 (mtm) REVERT: B 474 ASN cc_start: 0.7269 (t0) cc_final: 0.6892 (p0) REVERT: B 575 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7074 (tm-30) REVERT: B 584 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7834 (mp0) REVERT: J 13 LYS cc_start: 0.5935 (mmtp) cc_final: 0.5638 (mmmt) REVERT: J 22 CYS cc_start: 0.4810 (t) cc_final: 0.4401 (m) REVERT: J 69 ILE cc_start: 0.7825 (mm) cc_final: 0.7591 (mm) REVERT: J 100 TYR cc_start: 0.8769 (p90) cc_final: 0.8411 (p90) REVERT: J 100 MET cc_start: 0.8563 (mtt) cc_final: 0.8123 (mtt) REVERT: M 83 GLU cc_start: 0.7685 (tt0) cc_final: 0.7352 (tt0) REVERT: N 38 GLN cc_start: 0.5641 (tp-100) cc_final: 0.5027 (tp-100) REVERT: K 46 GLU cc_start: 0.5911 (mm-30) cc_final: 0.5559 (mm-30) REVERT: K 79 TYR cc_start: 0.7418 (m-80) cc_final: 0.7196 (m-10) REVERT: K 109 VAL cc_start: 0.8180 (t) cc_final: 0.7939 (p) REVERT: C 54 CYS cc_start: 0.7501 (p) cc_final: 0.7242 (p) REVERT: C 107 ASP cc_start: 0.8008 (t0) cc_final: 0.7602 (t0) REVERT: C 111 LEU cc_start: 0.8054 (mt) cc_final: 0.7752 (mt) REVERT: C 434 MET cc_start: 0.7899 (mtm) cc_final: 0.7613 (mtm) REVERT: C 474 ASN cc_start: 0.7445 (t0) cc_final: 0.6874 (p0) REVERT: C 575 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7106 (tm-30) REVERT: C 584 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7688 (mp0) REVERT: O 13 LYS cc_start: 0.5443 (mmtp) cc_final: 0.5172 (mmmt) REVERT: O 22 CYS cc_start: 0.5072 (t) cc_final: 0.4705 (m) REVERT: O 100 MET cc_start: 0.8603 (mtt) cc_final: 0.8276 (mtt) REVERT: Q 45 VAL cc_start: 0.8694 (m) cc_final: 0.8492 (p) REVERT: Q 83 GLU cc_start: 0.7892 (tt0) cc_final: 0.7660 (tt0) REVERT: R 38 GLN cc_start: 0.5909 (tp-100) cc_final: 0.4678 (tm-30) REVERT: R 83 PHE cc_start: 0.4707 (m-80) cc_final: 0.4462 (m-80) REVERT: P 34 MET cc_start: 0.8369 (tpp) cc_final: 0.8133 (tpp) outliers start: 12 outliers final: 7 residues processed: 570 average time/residue: 0.3726 time to fit residues: 321.5308 Evaluate side-chains 456 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 449 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain L residue 97 PHE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain N residue 97 PHE Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain R residue 97 PHE Chi-restraints excluded: chain P residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN A 620 GLN G 100JHIS H 105 GLN B 195 ASN B 330 HIS B 620 GLN N 27 GLN N 38 GLN N 90 GLN K 102 HIS K 105 GLN C 92 ASN C 330 HIS C 354 HIS C 620 GLN Q 79 GLN R 27 GLN R 38 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111713 restraints weight = 42442.708| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.89 r_work: 0.3342 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24969 Z= 0.212 Angle : 0.737 9.104 34071 Z= 0.360 Chirality : 0.051 0.450 4020 Planarity : 0.006 0.111 4137 Dihedral : 9.800 65.863 5036 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.21 % Allowed : 15.71 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.18 (0.15), residues: 2868 helix: -0.91 (0.27), residues: 354 sheet: -1.28 (0.16), residues: 1014 loop : -1.65 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 100D HIS 0.008 0.001 HIS C 330 PHE 0.017 0.002 PHE O 78 TYR 0.021 0.002 TYR B 484 ARG 0.004 0.001 ARG J 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 45) link_NAG-ASN : angle 2.90903 ( 135) link_ALPHA1-6 : bond 0.00332 ( 6) link_ALPHA1-6 : angle 2.08234 ( 18) link_BETA1-4 : bond 0.00591 ( 30) link_BETA1-4 : angle 2.49713 ( 90) link_ALPHA1-3 : bond 0.00836 ( 9) link_ALPHA1-3 : angle 3.25981 ( 27) hydrogen bonds : bond 0.04303 ( 721) hydrogen bonds : angle 6.40380 ( 2046) SS BOND : bond 0.00922 ( 45) SS BOND : angle 2.23453 ( 90) covalent geometry : bond 0.00491 (24834) covalent geometry : angle 0.68887 (33711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 436 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7814 (mtm-85) REVERT: A 111 LEU cc_start: 0.8089 (mt) cc_final: 0.7878 (mt) REVERT: A 414 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 543 GLN cc_start: 0.5912 (tt0) cc_final: 0.5702 (tt0) REVERT: A 575 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 632 ASP cc_start: 0.7931 (t0) cc_final: 0.7665 (t0) REVERT: G 13 LYS cc_start: 0.5579 (mmtp) cc_final: 0.5280 (mmmt) REVERT: G 100 MET cc_start: 0.8709 (mtt) cc_final: 0.8213 (mtt) REVERT: I 83 GLU cc_start: 0.7841 (tt0) cc_final: 0.7241 (tt0) REVERT: L 1 GLU cc_start: 0.7594 (pt0) cc_final: 0.7273 (pt0) REVERT: H 46 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5628 (mm-30) REVERT: B 54 CYS cc_start: 0.7811 (p) cc_final: 0.7502 (p) REVERT: B 166 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8023 (mmt-90) REVERT: B 354 HIS cc_start: 0.7500 (t-90) cc_final: 0.7028 (t-90) REVERT: B 414 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8625 (mt) REVERT: B 434 MET cc_start: 0.8018 (mtm) cc_final: 0.7736 (mtm) REVERT: B 474 ASN cc_start: 0.7660 (t0) cc_final: 0.7273 (t0) REVERT: B 544 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6253 (tt) REVERT: B 575 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7220 (tm-30) REVERT: J 13 LYS cc_start: 0.5821 (mmtp) cc_final: 0.5588 (mmmt) REVERT: J 69 ILE cc_start: 0.7629 (mm) cc_final: 0.7289 (mm) REVERT: J 100 TYR cc_start: 0.8824 (p90) cc_final: 0.8450 (p90) REVERT: J 100 MET cc_start: 0.8646 (mtt) cc_final: 0.8183 (mtt) REVERT: M 83 GLU cc_start: 0.7747 (tt0) cc_final: 0.7450 (tt0) REVERT: N 1 GLU cc_start: 0.7513 (pt0) cc_final: 0.6961 (tt0) REVERT: N 35 TRP cc_start: 0.7553 (m100) cc_final: 0.7236 (m100) REVERT: N 36 TYR cc_start: 0.7235 (m-80) cc_final: 0.6974 (m-80) REVERT: K 46 GLU cc_start: 0.5769 (mm-30) cc_final: 0.5342 (mm-30) REVERT: K 58 ASN cc_start: 0.7632 (t0) cc_final: 0.6989 (t0) REVERT: K 100 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6419 (m100) REVERT: K 101 GLN cc_start: 0.8799 (tt0) cc_final: 0.8488 (mm-40) REVERT: C 100 MET cc_start: 0.8941 (mtm) cc_final: 0.8733 (mtp) REVERT: C 434 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7686 (mtm) REVERT: C 475 MET cc_start: 0.7915 (tpp) cc_final: 0.7465 (tpp) REVERT: C 575 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7211 (tm-30) REVERT: O 13 LYS cc_start: 0.5388 (mmtp) cc_final: 0.5186 (mmmt) REVERT: O 100 MET cc_start: 0.8608 (mtt) cc_final: 0.8289 (mtt) REVERT: R 83 PHE cc_start: 0.4699 (m-80) cc_final: 0.4412 (m-80) REVERT: P 100 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6615 (m100) outliers start: 82 outliers final: 37 residues processed: 488 average time/residue: 0.3924 time to fit residues: 291.5571 Evaluate side-chains 436 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 393 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 98 LEU Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 122 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 103 GLN A 195 ASN A 616 ASN H 96 ASN B 103 GLN B 195 ASN B 616 ASN J 39 GLN J 100JHIS N 27 GLN N 90 GLN K 96 ASN K 102 HIS K 105 GLN C 92 ASN C 103 GLN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN O 100JHIS Q 79 GLN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115823 restraints weight = 42122.484| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.07 r_work: 0.3340 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24969 Z= 0.157 Angle : 0.664 9.093 34071 Z= 0.321 Chirality : 0.048 0.435 4020 Planarity : 0.004 0.043 4137 Dihedral : 8.905 64.859 5026 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.21 % Allowed : 17.27 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.16), residues: 2868 helix: -0.50 (0.28), residues: 336 sheet: -1.10 (0.16), residues: 1002 loop : -1.45 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 100D HIS 0.003 0.001 HIS C 374 PHE 0.014 0.002 PHE A 317 TYR 0.016 0.001 TYR B 484 ARG 0.003 0.000 ARG J 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 45) link_NAG-ASN : angle 2.76341 ( 135) link_ALPHA1-6 : bond 0.00224 ( 6) link_ALPHA1-6 : angle 1.83628 ( 18) link_BETA1-4 : bond 0.00544 ( 30) link_BETA1-4 : angle 2.38975 ( 90) link_ALPHA1-3 : bond 0.01169 ( 9) link_ALPHA1-3 : angle 3.10810 ( 27) hydrogen bonds : bond 0.03967 ( 721) hydrogen bonds : angle 6.01237 ( 2046) SS BOND : bond 0.00742 ( 45) SS BOND : angle 1.80028 ( 90) covalent geometry : bond 0.00365 (24834) covalent geometry : angle 0.61773 (33711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 408 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7840 (mtm-85) REVERT: A 111 LEU cc_start: 0.8178 (mt) cc_final: 0.7937 (mt) REVERT: A 575 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7231 (tm-30) REVERT: G 13 LYS cc_start: 0.5538 (mmtp) cc_final: 0.5256 (mmmt) REVERT: G 100 MET cc_start: 0.8721 (mtt) cc_final: 0.8230 (mtt) REVERT: I 74 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8281 (p) REVERT: I 83 GLU cc_start: 0.7819 (tt0) cc_final: 0.7227 (tt0) REVERT: L 1 GLU cc_start: 0.7578 (pt0) cc_final: 0.7216 (pt0) REVERT: H 46 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5738 (mm-30) REVERT: H 66 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7939 (ttt90) REVERT: H 100 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: B 166 ARG cc_start: 0.8373 (mtp85) cc_final: 0.8041 (mmt-90) REVERT: B 434 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7617 (mtm) REVERT: B 474 ASN cc_start: 0.7568 (t0) cc_final: 0.6877 (p0) REVERT: B 575 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7281 (tm-30) REVERT: J 13 LYS cc_start: 0.5814 (mmtp) cc_final: 0.5591 (mmmt) REVERT: J 22 CYS cc_start: 0.4484 (t) cc_final: 0.4040 (m) REVERT: J 69 ILE cc_start: 0.7678 (mm) cc_final: 0.7386 (mm) REVERT: J 100 TYR cc_start: 0.8795 (p90) cc_final: 0.8446 (p90) REVERT: J 100 MET cc_start: 0.8635 (mtt) cc_final: 0.7931 (mtt) REVERT: M 74 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8208 (p) REVERT: M 83 GLU cc_start: 0.7786 (tt0) cc_final: 0.7451 (tt0) REVERT: K 46 GLU cc_start: 0.5771 (mm-30) cc_final: 0.5315 (mm-30) REVERT: K 58 ASN cc_start: 0.7684 (t0) cc_final: 0.6916 (t0) REVERT: K 100 TRP cc_start: 0.7390 (OUTLIER) cc_final: 0.6533 (m100) REVERT: K 101 GLN cc_start: 0.8758 (tt0) cc_final: 0.8409 (mm-40) REVERT: C 434 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7685 (mtm) REVERT: C 575 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7218 (tm-30) REVERT: O 100 MET cc_start: 0.8557 (mtt) cc_final: 0.8223 (mtt) REVERT: Q 83 GLU cc_start: 0.7807 (tt0) cc_final: 0.7596 (tp30) REVERT: R 83 PHE cc_start: 0.4489 (m-80) cc_final: 0.4191 (m-80) REVERT: P 100 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.6936 (m-10) outliers start: 82 outliers final: 48 residues processed: 453 average time/residue: 0.3936 time to fit residues: 271.2532 Evaluate side-chains 430 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 375 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 217 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 202 optimal weight: 0.2980 chunk 203 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 280 ASN B 354 HIS N 27 GLN N 90 GLN K 96 ASN K 102 HIS C 92 ASN C 354 HIS Q 79 GLN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112434 restraints weight = 42477.306| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.86 r_work: 0.3357 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24969 Z= 0.136 Angle : 0.638 9.501 34071 Z= 0.308 Chirality : 0.047 0.416 4020 Planarity : 0.004 0.034 4137 Dihedral : 8.342 63.551 5024 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.88 % Allowed : 17.20 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.16), residues: 2868 helix: -0.34 (0.29), residues: 336 sheet: -1.00 (0.17), residues: 1002 loop : -1.35 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 66 HIS 0.003 0.001 HIS C 374 PHE 0.013 0.001 PHE A 317 TYR 0.015 0.001 TYR C 484 ARG 0.004 0.000 ARG Q 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 45) link_NAG-ASN : angle 2.70557 ( 135) link_ALPHA1-6 : bond 0.00266 ( 6) link_ALPHA1-6 : angle 1.80048 ( 18) link_BETA1-4 : bond 0.00548 ( 30) link_BETA1-4 : angle 2.30608 ( 90) link_ALPHA1-3 : bond 0.01167 ( 9) link_ALPHA1-3 : angle 3.13579 ( 27) hydrogen bonds : bond 0.03664 ( 721) hydrogen bonds : angle 5.74964 ( 2046) SS BOND : bond 0.00696 ( 45) SS BOND : angle 2.02762 ( 90) covalent geometry : bond 0.00312 (24834) covalent geometry : angle 0.58885 (33711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 397 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7876 (mtm-85) REVERT: A 111 LEU cc_start: 0.8152 (mt) cc_final: 0.7919 (mt) REVERT: A 414 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8633 (mt) REVERT: A 542 ARG cc_start: 0.6334 (ptt180) cc_final: 0.5944 (ptm160) REVERT: A 575 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7176 (tm-30) REVERT: G 13 LYS cc_start: 0.5616 (mmtp) cc_final: 0.5363 (mmmt) REVERT: G 23 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7631 (p) REVERT: G 63 LEU cc_start: 0.8033 (tt) cc_final: 0.7820 (tt) REVERT: G 100 MET cc_start: 0.8672 (mtt) cc_final: 0.8200 (mtt) REVERT: I 74 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8207 (p) REVERT: I 83 GLU cc_start: 0.7851 (tt0) cc_final: 0.7273 (tt0) REVERT: L 1 GLU cc_start: 0.7543 (pt0) cc_final: 0.7165 (pt0) REVERT: H 46 GLU cc_start: 0.6024 (mm-30) cc_final: 0.5560 (mm-30) REVERT: H 100 TRP cc_start: 0.7505 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: B 166 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8027 (mmt-90) REVERT: B 434 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7613 (mtm) REVERT: B 474 ASN cc_start: 0.7532 (t0) cc_final: 0.6809 (p0) REVERT: B 575 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7346 (tm-30) REVERT: J 13 LYS cc_start: 0.5802 (mmtp) cc_final: 0.5595 (mmmt) REVERT: J 22 CYS cc_start: 0.4436 (t) cc_final: 0.4130 (m) REVERT: J 23 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7665 (p) REVERT: J 69 ILE cc_start: 0.7672 (mm) cc_final: 0.7396 (mm) REVERT: J 100 TYR cc_start: 0.8770 (p90) cc_final: 0.8426 (p90) REVERT: J 100 MET cc_start: 0.8581 (mtt) cc_final: 0.7974 (mtt) REVERT: M 74 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8243 (p) REVERT: M 83 GLU cc_start: 0.7817 (tt0) cc_final: 0.7497 (tt0) REVERT: K 46 GLU cc_start: 0.5791 (mm-30) cc_final: 0.5274 (mm-30) REVERT: K 100 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.6602 (m100) REVERT: K 101 GLN cc_start: 0.8784 (tt0) cc_final: 0.8457 (mm110) REVERT: C 429 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8511 (mttt) REVERT: C 434 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7640 (mtm) REVERT: C 575 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7195 (tm-30) REVERT: O 22 CYS cc_start: 0.4533 (t) cc_final: 0.4315 (m) REVERT: O 100 MET cc_start: 0.8513 (mtt) cc_final: 0.8208 (mtt) REVERT: Q 83 GLU cc_start: 0.7778 (tt0) cc_final: 0.7572 (tp30) REVERT: R 83 PHE cc_start: 0.4389 (m-80) cc_final: 0.4099 (m-80) REVERT: P 100 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.6589 (m100) outliers start: 99 outliers final: 55 residues processed: 453 average time/residue: 0.3854 time to fit residues: 267.3406 Evaluate side-chains 436 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 371 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 277 optimal weight: 0.9980 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN M 42 GLN N 27 GLN K 102 HIS C 92 ASN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN Q 79 GLN R 27 GLN ** R 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110216 restraints weight = 42548.153| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.87 r_work: 0.3313 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 24969 Z= 0.206 Angle : 0.702 13.009 34071 Z= 0.338 Chirality : 0.048 0.449 4020 Planarity : 0.004 0.035 4137 Dihedral : 8.336 65.080 5024 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.07 % Allowed : 18.17 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.67 (0.16), residues: 2868 helix: -0.41 (0.28), residues: 336 sheet: -0.87 (0.17), residues: 972 loop : -1.40 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 66 HIS 0.003 0.001 HIS C 374 PHE 0.012 0.002 PHE O 78 TYR 0.019 0.001 TYR C 484 ARG 0.005 0.000 ARG Q 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 45) link_NAG-ASN : angle 2.84547 ( 135) link_ALPHA1-6 : bond 0.00244 ( 6) link_ALPHA1-6 : angle 2.10406 ( 18) link_BETA1-4 : bond 0.00559 ( 30) link_BETA1-4 : angle 2.33667 ( 90) link_ALPHA1-3 : bond 0.01125 ( 9) link_ALPHA1-3 : angle 3.26840 ( 27) hydrogen bonds : bond 0.03793 ( 721) hydrogen bonds : angle 5.76735 ( 2046) SS BOND : bond 0.00858 ( 45) SS BOND : angle 3.01520 ( 90) covalent geometry : bond 0.00493 (24834) covalent geometry : angle 0.64475 (33711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 374 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7858 (mtm-85) REVERT: A 352 TYR cc_start: 0.7595 (m-80) cc_final: 0.7353 (m-80) REVERT: A 414 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8694 (mt) REVERT: A 542 ARG cc_start: 0.6407 (ptt180) cc_final: 0.5997 (ptm160) REVERT: A 575 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7241 (tm-30) REVERT: G 13 LYS cc_start: 0.5587 (mmtp) cc_final: 0.5340 (mmmt) REVERT: G 38 ARG cc_start: 0.8043 (tmm-80) cc_final: 0.7820 (tmm-80) REVERT: G 100 MET cc_start: 0.8744 (mtt) cc_final: 0.8297 (mtt) REVERT: I 74 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8176 (p) REVERT: I 83 GLU cc_start: 0.7824 (tt0) cc_final: 0.7218 (tt0) REVERT: L 1 GLU cc_start: 0.7473 (pt0) cc_final: 0.7084 (pt0) REVERT: L 96 GLU cc_start: 0.6665 (pt0) cc_final: 0.6327 (pt0) REVERT: H 46 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5654 (mm-30) REVERT: H 100 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: B 166 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8063 (mmt-90) REVERT: B 414 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 434 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: B 575 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 610 TRP cc_start: 0.6658 (t-100) cc_final: 0.6149 (t-100) REVERT: J 13 LYS cc_start: 0.5766 (mmtp) cc_final: 0.5561 (mmmt) REVERT: J 23 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7856 (p) REVERT: J 69 ILE cc_start: 0.7683 (mm) cc_final: 0.7422 (mm) REVERT: M 74 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8245 (p) REVERT: M 83 GLU cc_start: 0.7797 (tt0) cc_final: 0.7465 (tt0) REVERT: K 46 GLU cc_start: 0.5805 (mm-30) cc_final: 0.5368 (mm-30) REVERT: K 48 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7331 (mtp) REVERT: K 100 TRP cc_start: 0.7436 (OUTLIER) cc_final: 0.6639 (m100) REVERT: C 280 ASN cc_start: 0.7590 (m-40) cc_final: 0.7240 (p0) REVERT: C 352 TYR cc_start: 0.7719 (m-80) cc_final: 0.7372 (m-80) REVERT: C 429 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8461 (mttt) REVERT: C 434 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7671 (mtm) REVERT: C 575 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7109 (tm-30) REVERT: R 83 PHE cc_start: 0.4593 (m-80) cc_final: 0.4285 (m-80) REVERT: R 96 GLU cc_start: 0.6389 (pt0) cc_final: 0.6031 (pt0) outliers start: 104 outliers final: 69 residues processed: 434 average time/residue: 0.3900 time to fit residues: 258.9414 Evaluate side-chains 437 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 358 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 187 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 27 GLN N 90 GLN K 102 HIS C 92 ASN ** C 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 ASN R 27 GLN R 38 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 ASN P 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111055 restraints weight = 41834.531| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.83 r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24969 Z= 0.163 Angle : 0.667 14.330 34071 Z= 0.320 Chirality : 0.048 0.429 4020 Planarity : 0.004 0.035 4137 Dihedral : 8.089 63.545 5022 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.72 % Allowed : 19.04 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.16), residues: 2868 helix: -0.40 (0.28), residues: 336 sheet: -0.79 (0.17), residues: 981 loop : -1.35 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 66 HIS 0.004 0.001 HIS C 374 PHE 0.015 0.002 PHE A 651 TYR 0.016 0.001 TYR A 484 ARG 0.005 0.000 ARG K 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 45) link_NAG-ASN : angle 2.77685 ( 135) link_ALPHA1-6 : bond 0.00227 ( 6) link_ALPHA1-6 : angle 1.87697 ( 18) link_BETA1-4 : bond 0.00517 ( 30) link_BETA1-4 : angle 2.24507 ( 90) link_ALPHA1-3 : bond 0.01157 ( 9) link_ALPHA1-3 : angle 3.19044 ( 27) hydrogen bonds : bond 0.03581 ( 721) hydrogen bonds : angle 5.63264 ( 2046) SS BOND : bond 0.00662 ( 45) SS BOND : angle 2.42321 ( 90) covalent geometry : bond 0.00384 (24834) covalent geometry : angle 0.61587 (33711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 379 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7903 (mtm-85) REVERT: A 352 TYR cc_start: 0.7586 (m-80) cc_final: 0.7360 (m-80) REVERT: A 414 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8645 (mt) REVERT: A 542 ARG cc_start: 0.6390 (ptt180) cc_final: 0.5918 (ptm160) REVERT: A 575 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7183 (tm-30) REVERT: G 13 LYS cc_start: 0.5647 (mmtp) cc_final: 0.5421 (mmmt) REVERT: G 38 ARG cc_start: 0.8089 (tmm-80) cc_final: 0.7875 (tmm-80) REVERT: G 100 MET cc_start: 0.8677 (mtt) cc_final: 0.8252 (mtt) REVERT: I 61 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7787 (mtm110) REVERT: I 83 GLU cc_start: 0.7813 (tt0) cc_final: 0.7142 (tt0) REVERT: L 1 GLU cc_start: 0.7488 (pt0) cc_final: 0.7136 (pt0) REVERT: L 96 GLU cc_start: 0.6662 (pt0) cc_final: 0.6352 (pt0) REVERT: H 46 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5636 (mm-30) REVERT: H 94 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6908 (ttt-90) REVERT: H 100 TRP cc_start: 0.7441 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: B 166 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8082 (mmt-90) REVERT: B 280 ASN cc_start: 0.7435 (m-40) cc_final: 0.7118 (p0) REVERT: B 434 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: B 542 ARG cc_start: 0.6095 (ptt180) cc_final: 0.5814 (ptm160) REVERT: B 575 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7198 (tm-30) REVERT: J 5 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7106 (mmm-85) REVERT: J 13 LYS cc_start: 0.5804 (mmtp) cc_final: 0.5590 (mmmt) REVERT: J 22 CYS cc_start: 0.4375 (t) cc_final: 0.4049 (m) REVERT: J 23 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7792 (p) REVERT: J 69 ILE cc_start: 0.7677 (mm) cc_final: 0.7460 (mm) REVERT: J 100 MET cc_start: 0.8619 (mtt) cc_final: 0.8139 (mtt) REVERT: M 74 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8265 (p) REVERT: K 34 MET cc_start: 0.8404 (tpp) cc_final: 0.8118 (tpp) REVERT: K 46 GLU cc_start: 0.5787 (mm-30) cc_final: 0.5422 (mm-30) REVERT: K 100 TRP cc_start: 0.7281 (OUTLIER) cc_final: 0.6867 (m100) REVERT: C 280 ASN cc_start: 0.7490 (m-40) cc_final: 0.7276 (p0) REVERT: C 352 TYR cc_start: 0.7729 (m-80) cc_final: 0.7420 (m-80) REVERT: C 429 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8425 (mttt) REVERT: C 434 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7721 (mtm) REVERT: C 542 ARG cc_start: 0.6539 (ptt180) cc_final: 0.6017 (ptm160) REVERT: C 575 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7040 (tm-30) REVERT: O 22 CYS cc_start: 0.4674 (t) cc_final: 0.4443 (m) REVERT: Q 83 GLU cc_start: 0.7854 (tt0) cc_final: 0.7561 (tp30) REVERT: R 83 PHE cc_start: 0.4380 (m-80) cc_final: 0.4043 (m-80) REVERT: R 96 GLU cc_start: 0.6451 (pt0) cc_final: 0.6061 (pt0) REVERT: P 48 MET cc_start: 0.7250 (mtm) cc_final: 0.6993 (mtp) outliers start: 95 outliers final: 65 residues processed: 438 average time/residue: 0.4028 time to fit residues: 267.4190 Evaluate side-chains 432 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 360 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 95 ASN Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 192 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN L 38 GLN H 39 GLN B 377 ASN M 42 GLN N 27 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN K 102 HIS C 92 ASN C 354 HIS C 377 ASN O 95 ASN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.153556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112362 restraints weight = 41933.803| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.86 r_work: 0.3351 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 24969 Z= 0.126 Angle : 0.652 14.585 34071 Z= 0.312 Chirality : 0.047 0.401 4020 Planarity : 0.004 0.035 4137 Dihedral : 7.777 61.616 5022 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.13 % Allowed : 19.74 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.16), residues: 2868 helix: -0.11 (0.30), residues: 318 sheet: -0.64 (0.17), residues: 969 loop : -1.18 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 66 HIS 0.003 0.001 HIS O 33 PHE 0.012 0.001 PHE A 317 TYR 0.012 0.001 TYR C 484 ARG 0.005 0.000 ARG M 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 45) link_NAG-ASN : angle 2.67887 ( 135) link_ALPHA1-6 : bond 0.00327 ( 6) link_ALPHA1-6 : angle 1.76006 ( 18) link_BETA1-4 : bond 0.00498 ( 30) link_BETA1-4 : angle 2.15824 ( 90) link_ALPHA1-3 : bond 0.01151 ( 9) link_ALPHA1-3 : angle 3.09878 ( 27) hydrogen bonds : bond 0.03438 ( 721) hydrogen bonds : angle 5.51806 ( 2046) SS BOND : bond 0.00718 ( 45) SS BOND : angle 2.42794 ( 90) covalent geometry : bond 0.00290 (24834) covalent geometry : angle 0.60319 (33711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7874 (mtm-85) REVERT: A 414 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8589 (mt) REVERT: A 542 ARG cc_start: 0.6298 (ptt180) cc_final: 0.5876 (ptm160) REVERT: A 575 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7114 (tm-30) REVERT: G 13 LYS cc_start: 0.5648 (mmtp) cc_final: 0.5416 (mmmt) REVERT: G 100 MET cc_start: 0.8635 (mtt) cc_final: 0.8224 (mtt) REVERT: I 74 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8178 (p) REVERT: I 83 GLU cc_start: 0.7817 (tt0) cc_final: 0.7206 (tt0) REVERT: L 1 GLU cc_start: 0.7510 (pt0) cc_final: 0.7160 (pt0) REVERT: L 96 GLU cc_start: 0.6651 (pt0) cc_final: 0.6349 (pt0) REVERT: H 46 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5610 (mm-30) REVERT: H 94 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6729 (ttp80) REVERT: H 100 TRP cc_start: 0.7452 (OUTLIER) cc_final: 0.6954 (m-10) REVERT: B 100 MET cc_start: 0.8737 (mtm) cc_final: 0.8536 (mtp) REVERT: B 166 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8063 (mmt-90) REVERT: B 280 ASN cc_start: 0.7359 (m-40) cc_final: 0.7037 (p0) REVERT: B 434 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7731 (mtm) REVERT: B 542 ARG cc_start: 0.6049 (ptt180) cc_final: 0.5847 (ptm160) REVERT: B 575 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7012 (tm-30) REVERT: B 631 TRP cc_start: 0.7894 (t-100) cc_final: 0.6932 (t-100) REVERT: J 6 GLU cc_start: 0.6492 (mp0) cc_final: 0.5665 (mp0) REVERT: J 23 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7836 (p) REVERT: J 89 MET cc_start: 0.6263 (tpt) cc_final: 0.5759 (tpt) REVERT: J 100 TYR cc_start: 0.8734 (p90) cc_final: 0.8395 (p90) REVERT: J 100 MET cc_start: 0.8543 (mtt) cc_final: 0.8077 (mtt) REVERT: M 74 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8189 (p) REVERT: N 96 GLU cc_start: 0.6439 (pt0) cc_final: 0.6238 (pt0) REVERT: K 46 GLU cc_start: 0.5638 (mm-30) cc_final: 0.5167 (mm-30) REVERT: K 100 TRP cc_start: 0.7179 (OUTLIER) cc_final: 0.6859 (m100) REVERT: C 352 TYR cc_start: 0.7677 (m-80) cc_final: 0.7423 (m-80) REVERT: C 429 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8425 (mttt) REVERT: C 434 MET cc_start: 0.7978 (mtm) cc_final: 0.7685 (mtm) REVERT: C 542 ARG cc_start: 0.6479 (ptt180) cc_final: 0.5945 (ptm160) REVERT: C 575 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7030 (tm-30) REVERT: C 631 TRP cc_start: 0.7773 (t-100) cc_final: 0.6845 (t-100) REVERT: O 22 CYS cc_start: 0.4550 (t) cc_final: 0.4264 (m) REVERT: Q 83 GLU cc_start: 0.7819 (tt0) cc_final: 0.7572 (tp30) REVERT: R 42 LEU cc_start: 0.5765 (mp) cc_final: 0.5490 (mm) REVERT: R 83 PHE cc_start: 0.4221 (m-80) cc_final: 0.3890 (m-80) REVERT: R 96 GLU cc_start: 0.6418 (pt0) cc_final: 0.6047 (pt0) REVERT: P 37 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7690 (m) outliers start: 80 outliers final: 55 residues processed: 440 average time/residue: 0.4053 time to fit residues: 267.5703 Evaluate side-chains 431 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 368 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 86 ASP Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 42 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 39 GLN M 42 GLN N 6 GLN N 27 GLN N 90 GLN K 102 HIS C 92 ASN C 354 HIS Q 42 GLN R 27 GLN R 37 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109183 restraints weight = 42085.614| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.84 r_work: 0.3295 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 24969 Z= 0.224 Angle : 0.729 14.581 34071 Z= 0.347 Chirality : 0.049 0.450 4020 Planarity : 0.004 0.038 4137 Dihedral : 8.095 64.472 5022 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.72 % Allowed : 19.35 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.16), residues: 2868 helix: -0.51 (0.28), residues: 336 sheet: -0.73 (0.18), residues: 957 loop : -1.27 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 66 HIS 0.006 0.001 HIS C 374 PHE 0.013 0.002 PHE B 53 TYR 0.016 0.001 TYR A 484 ARG 0.008 0.001 ARG G 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 45) link_NAG-ASN : angle 2.84716 ( 135) link_ALPHA1-6 : bond 0.00245 ( 6) link_ALPHA1-6 : angle 2.18784 ( 18) link_BETA1-4 : bond 0.00562 ( 30) link_BETA1-4 : angle 2.29289 ( 90) link_ALPHA1-3 : bond 0.01050 ( 9) link_ALPHA1-3 : angle 3.24154 ( 27) hydrogen bonds : bond 0.03735 ( 721) hydrogen bonds : angle 5.70344 ( 2046) SS BOND : bond 0.00934 ( 45) SS BOND : angle 2.88498 ( 90) covalent geometry : bond 0.00533 (24834) covalent geometry : angle 0.67664 (33711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 369 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7899 (mtm-85) REVERT: A 200 VAL cc_start: 0.9081 (t) cc_final: 0.8820 (m) REVERT: A 414 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 542 ARG cc_start: 0.6428 (ptt180) cc_final: 0.6224 (ptm160) REVERT: A 575 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 605 CYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6957 (m) REVERT: G 13 LYS cc_start: 0.5650 (mmtp) cc_final: 0.5419 (mmmt) REVERT: G 100 MET cc_start: 0.8679 (mtt) cc_final: 0.8255 (mtt) REVERT: I 61 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7787 (mtm110) REVERT: I 74 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8185 (p) REVERT: I 83 GLU cc_start: 0.7862 (tt0) cc_final: 0.7194 (tt0) REVERT: L 1 GLU cc_start: 0.7411 (pt0) cc_final: 0.7039 (pt0) REVERT: L 27 GLN cc_start: 0.7701 (tt0) cc_final: 0.6976 (pm20) REVERT: L 96 GLU cc_start: 0.6777 (pt0) cc_final: 0.6470 (pt0) REVERT: H 46 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5602 (mm-30) REVERT: H 94 ARG cc_start: 0.7134 (ttp80) cc_final: 0.6841 (ttp80) REVERT: H 100 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: B 434 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: B 542 ARG cc_start: 0.6408 (ptt180) cc_final: 0.6129 (ptm160) REVERT: B 543 GLN cc_start: 0.5220 (tp40) cc_final: 0.4863 (tp40) REVERT: B 575 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 610 TRP cc_start: 0.6727 (t-100) cc_final: 0.6173 (t-100) REVERT: J 23 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7916 (p) REVERT: J 100 MET cc_start: 0.8655 (mtt) cc_final: 0.8190 (mtt) REVERT: K 46 GLU cc_start: 0.5674 (mm-30) cc_final: 0.5204 (mm-30) REVERT: K 100 TRP cc_start: 0.7220 (OUTLIER) cc_final: 0.6753 (m100) REVERT: C 352 TYR cc_start: 0.7746 (m-80) cc_final: 0.7462 (m-80) REVERT: C 429 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8382 (mttt) REVERT: C 434 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7737 (mtm) REVERT: C 542 ARG cc_start: 0.6605 (ptt180) cc_final: 0.6310 (ptm160) REVERT: C 575 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7114 (tm-30) REVERT: Q 83 GLU cc_start: 0.7867 (tt0) cc_final: 0.7598 (tp30) REVERT: R 83 PHE cc_start: 0.4258 (m-80) cc_final: 0.3968 (m-80) REVERT: P 94 ARG cc_start: 0.7184 (ttp-170) cc_final: 0.6873 (ttp80) REVERT: P 100 TRP cc_start: 0.7459 (OUTLIER) cc_final: 0.7157 (m-10) outliers start: 95 outliers final: 72 residues processed: 425 average time/residue: 0.4044 time to fit residues: 261.4610 Evaluate side-chains 434 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 353 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 227 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 96 ASN M 42 GLN N 27 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 HIS C 92 ASN C 354 HIS Q 42 GLN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111441 restraints weight = 42011.905| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.85 r_work: 0.3335 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24969 Z= 0.139 Angle : 0.670 14.570 34071 Z= 0.319 Chirality : 0.047 0.406 4020 Planarity : 0.004 0.035 4137 Dihedral : 7.761 61.605 5022 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.29 % Allowed : 19.74 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.16), residues: 2868 helix: -0.37 (0.28), residues: 327 sheet: -0.51 (0.18), residues: 924 loop : -1.20 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 66 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE N 83 TYR 0.011 0.001 TYR N 49 ARG 0.007 0.000 ARG G 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 45) link_NAG-ASN : angle 2.69550 ( 135) link_ALPHA1-6 : bond 0.00295 ( 6) link_ALPHA1-6 : angle 1.77279 ( 18) link_BETA1-4 : bond 0.00482 ( 30) link_BETA1-4 : angle 2.15924 ( 90) link_ALPHA1-3 : bond 0.01097 ( 9) link_ALPHA1-3 : angle 3.08807 ( 27) hydrogen bonds : bond 0.03450 ( 721) hydrogen bonds : angle 5.51082 ( 2046) SS BOND : bond 0.00827 ( 45) SS BOND : angle 2.78287 ( 90) covalent geometry : bond 0.00327 (24834) covalent geometry : angle 0.61781 (33711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 378 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8181 (mtp-110) cc_final: 0.7896 (mtm-85) REVERT: A 200 VAL cc_start: 0.9074 (t) cc_final: 0.8829 (m) REVERT: A 414 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8609 (mt) REVERT: A 542 ARG cc_start: 0.6551 (ptt180) cc_final: 0.6302 (ptm160) REVERT: A 575 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7138 (tm-30) REVERT: G 5 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.6938 (mmm-85) REVERT: G 13 LYS cc_start: 0.5609 (mmtp) cc_final: 0.5374 (mmmt) REVERT: G 23 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7865 (p) REVERT: G 100 MET cc_start: 0.8607 (mtt) cc_final: 0.8204 (mtt) REVERT: I 61 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7777 (mtm110) REVERT: I 74 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8061 (p) REVERT: I 83 GLU cc_start: 0.7857 (tt0) cc_final: 0.7193 (tt0) REVERT: L 1 GLU cc_start: 0.7359 (pt0) cc_final: 0.7002 (pt0) REVERT: L 27 GLN cc_start: 0.7555 (tt0) cc_final: 0.6964 (pm20) REVERT: L 96 GLU cc_start: 0.6766 (pt0) cc_final: 0.6385 (pt0) REVERT: H 46 GLU cc_start: 0.6010 (mm-30) cc_final: 0.5801 (mm-30) REVERT: H 94 ARG cc_start: 0.6980 (ttp80) cc_final: 0.6749 (ttp80) REVERT: H 100 TRP cc_start: 0.7428 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: B 277 MET cc_start: 0.7074 (mtt) cc_final: 0.6869 (mtt) REVERT: B 280 ASN cc_start: 0.7583 (m-40) cc_final: 0.7204 (p0) REVERT: B 434 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: B 542 ARG cc_start: 0.6382 (ptt180) cc_final: 0.6101 (ptm160) REVERT: B 543 GLN cc_start: 0.5295 (tp40) cc_final: 0.4944 (tp40) REVERT: B 575 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 610 TRP cc_start: 0.6668 (t-100) cc_final: 0.6226 (t-100) REVERT: B 631 TRP cc_start: 0.7889 (t-100) cc_final: 0.6938 (t-100) REVERT: J 6 GLU cc_start: 0.6978 (mp0) cc_final: 0.6044 (mp0) REVERT: J 23 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7811 (p) REVERT: J 100 MET cc_start: 0.8562 (mtt) cc_final: 0.8107 (mtt) REVERT: M 74 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.7955 (p) REVERT: K 46 GLU cc_start: 0.5559 (mm-30) cc_final: 0.5110 (mm-30) REVERT: K 100 TRP cc_start: 0.7073 (OUTLIER) cc_final: 0.6772 (m100) REVERT: C 352 TYR cc_start: 0.7678 (m-80) cc_final: 0.7449 (m-80) REVERT: C 429 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8336 (mttt) REVERT: C 434 MET cc_start: 0.8000 (mtm) cc_final: 0.7710 (mtm) REVERT: C 542 ARG cc_start: 0.6596 (ptt180) cc_final: 0.6261 (ptm160) REVERT: C 543 GLN cc_start: 0.5416 (tp40) cc_final: 0.5209 (tp40) REVERT: C 575 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7000 (tm-30) REVERT: Q 83 GLU cc_start: 0.7886 (tt0) cc_final: 0.7605 (tp30) REVERT: R 83 PHE cc_start: 0.3910 (m-80) cc_final: 0.3607 (m-80) REVERT: P 37 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (m) REVERT: P 94 ARG cc_start: 0.7015 (ttp-170) cc_final: 0.6384 (ttt-90) REVERT: P 100 TRP cc_start: 0.7359 (OUTLIER) cc_final: 0.7036 (m-10) outliers start: 84 outliers final: 63 residues processed: 431 average time/residue: 0.3785 time to fit residues: 250.5481 Evaluate side-chains 433 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 159 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 251 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 195 ASN M 42 GLN N 27 GLN N 90 GLN K 102 HIS C 92 ASN C 354 HIS Q 42 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111487 restraints weight = 41916.039| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.85 r_work: 0.3335 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24969 Z= 0.144 Angle : 0.675 14.889 34071 Z= 0.322 Chirality : 0.047 0.406 4020 Planarity : 0.004 0.049 4137 Dihedral : 7.679 61.015 5022 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.17 % Allowed : 19.82 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.16), residues: 2868 helix: -0.31 (0.29), residues: 327 sheet: -0.46 (0.18), residues: 918 loop : -1.15 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 66 HIS 0.007 0.001 HIS C 354 PHE 0.018 0.001 PHE A 361 TYR 0.011 0.001 TYR N 49 ARG 0.006 0.000 ARG G 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 45) link_NAG-ASN : angle 2.68411 ( 135) link_ALPHA1-6 : bond 0.00272 ( 6) link_ALPHA1-6 : angle 1.83553 ( 18) link_BETA1-4 : bond 0.00499 ( 30) link_BETA1-4 : angle 2.14810 ( 90) link_ALPHA1-3 : bond 0.01073 ( 9) link_ALPHA1-3 : angle 3.06837 ( 27) hydrogen bonds : bond 0.03443 ( 721) hydrogen bonds : angle 5.47268 ( 2046) SS BOND : bond 0.00822 ( 45) SS BOND : angle 2.85853 ( 90) covalent geometry : bond 0.00341 (24834) covalent geometry : angle 0.62284 (33711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 370 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7893 (mtm-85) REVERT: A 200 VAL cc_start: 0.9074 (t) cc_final: 0.8850 (m) REVERT: A 414 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8605 (mt) REVERT: A 542 ARG cc_start: 0.6488 (ptt180) cc_final: 0.6253 (ptm160) REVERT: A 575 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7133 (tm-30) REVERT: G 13 LYS cc_start: 0.5543 (mmtp) cc_final: 0.5319 (mmmt) REVERT: G 100 MET cc_start: 0.8592 (mtt) cc_final: 0.8196 (mtt) REVERT: I 61 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7815 (mtm110) REVERT: I 74 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8219 (p) REVERT: I 83 GLU cc_start: 0.7847 (tt0) cc_final: 0.7184 (tt0) REVERT: L 1 GLU cc_start: 0.7344 (pt0) cc_final: 0.6978 (pt0) REVERT: L 27 GLN cc_start: 0.7562 (tt0) cc_final: 0.6965 (pm20) REVERT: L 96 GLU cc_start: 0.6742 (pt0) cc_final: 0.6355 (pt0) REVERT: H 46 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5802 (mm-30) REVERT: H 94 ARG cc_start: 0.7013 (ttp80) cc_final: 0.6699 (ttp80) REVERT: H 100 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: B 277 MET cc_start: 0.7086 (mtt) cc_final: 0.6869 (mtt) REVERT: B 280 ASN cc_start: 0.7524 (m-40) cc_final: 0.7187 (p0) REVERT: B 434 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7796 (mtm) REVERT: B 542 ARG cc_start: 0.6457 (ptt180) cc_final: 0.6180 (ptm160) REVERT: B 543 GLN cc_start: 0.5294 (tp40) cc_final: 0.4939 (tp40) REVERT: B 575 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7083 (tm-30) REVERT: B 610 TRP cc_start: 0.6674 (t-100) cc_final: 0.6170 (t-100) REVERT: J 6 GLU cc_start: 0.6774 (mp0) cc_final: 0.5995 (mp0) REVERT: J 23 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7794 (p) REVERT: J 66 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.6036 (mtt180) REVERT: J 100 MET cc_start: 0.8545 (mtt) cc_final: 0.8099 (mtt) REVERT: M 74 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8369 (p) REVERT: N 27 GLN cc_start: 0.7798 (tt0) cc_final: 0.7486 (tt0) REVERT: K 34 MET cc_start: 0.8322 (tpp) cc_final: 0.7882 (tpp) REVERT: K 46 GLU cc_start: 0.5545 (mm-30) cc_final: 0.5083 (mm-30) REVERT: K 100 TRP cc_start: 0.7031 (OUTLIER) cc_final: 0.6659 (m100) REVERT: C 110 SER cc_start: 0.9012 (m) cc_final: 0.8778 (m) REVERT: C 352 TYR cc_start: 0.7733 (m-80) cc_final: 0.7489 (m-80) REVERT: C 429 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8282 (mttt) REVERT: C 434 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7717 (mtm) REVERT: C 542 ARG cc_start: 0.6562 (ptt180) cc_final: 0.6215 (ptm160) REVERT: C 543 GLN cc_start: 0.5410 (tp40) cc_final: 0.5151 (tp40) REVERT: C 575 GLN cc_start: 0.7536 (tm-30) cc_final: 0.7042 (tm-30) REVERT: Q 83 GLU cc_start: 0.7869 (tt0) cc_final: 0.7604 (tp30) REVERT: R 83 PHE cc_start: 0.3859 (m-80) cc_final: 0.3571 (m-80) REVERT: P 37 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7733 (m) REVERT: P 94 ARG cc_start: 0.7027 (ttp-170) cc_final: 0.6387 (ttt-90) REVERT: P 100 TRP cc_start: 0.7365 (OUTLIER) cc_final: 0.6965 (m-10) outliers start: 81 outliers final: 60 residues processed: 421 average time/residue: 0.3914 time to fit residues: 252.8105 Evaluate side-chains 429 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 358 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 100 TRP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 89 VAL Chi-restraints excluded: chain P residue 100 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 120 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 116 optimal weight: 0.2980 chunk 129 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 222 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN G 105 GLN H 96 ASN B 195 ASN M 42 GLN N 90 GLN K 102 HIS C 92 ASN C 354 HIS Q 42 GLN R 27 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112840 restraints weight = 41801.685| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.86 r_work: 0.3356 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24969 Z= 0.126 Angle : 0.656 14.928 34071 Z= 0.313 Chirality : 0.046 0.384 4020 Planarity : 0.004 0.041 4137 Dihedral : 7.432 59.063 5022 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.82 % Allowed : 20.09 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.16), residues: 2868 helix: -0.16 (0.29), residues: 327 sheet: -0.33 (0.18), residues: 927 loop : -1.11 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 66 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE C 361 TYR 0.009 0.001 TYR L 49 ARG 0.006 0.000 ARG G 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 45) link_NAG-ASN : angle 2.60277 ( 135) link_ALPHA1-6 : bond 0.00350 ( 6) link_ALPHA1-6 : angle 1.73491 ( 18) link_BETA1-4 : bond 0.00493 ( 30) link_BETA1-4 : angle 2.10953 ( 90) link_ALPHA1-3 : bond 0.01045 ( 9) link_ALPHA1-3 : angle 3.00406 ( 27) hydrogen bonds : bond 0.03351 ( 721) hydrogen bonds : angle 5.36758 ( 2046) SS BOND : bond 0.00783 ( 45) SS BOND : angle 2.77129 ( 90) covalent geometry : bond 0.00296 (24834) covalent geometry : angle 0.60589 (33711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12787.41 seconds wall clock time: 220 minutes 36.77 seconds (13236.77 seconds total)