Starting phenix.real_space_refine on Tue May 20 20:34:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bf6_44491/05_2025/9bf6_44491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bf6_44491/05_2025/9bf6_44491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bf6_44491/05_2025/9bf6_44491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bf6_44491/05_2025/9bf6_44491.map" model { file = "/net/cci-nas-00/data/ceres_data/9bf6_44491/05_2025/9bf6_44491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bf6_44491/05_2025/9bf6_44491.cif" } resolution = 4.5 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= 0.009 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 120 5.16 5 C 12732 2.51 5 N 3318 2.21 5 O 4159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20330 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 973 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3390 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 6 Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 973 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3390 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 6 Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "H" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 973 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "J" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3390 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 6 Chain: "K" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 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: "Q" 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: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" 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: "T" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" 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: "a" 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: "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: 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: "d" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 159 Unusual residues: {'NAG': 11, 'PO4': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.27, per 1000 atoms: 0.65 Number of scatterers: 20330 At special positions: 0 Unit cell: (155.629, 154.555, 150.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 1 15.00 O 4159 8.00 N 3318 7.00 C 12732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 432A" distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 432A" distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 432A" distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.05 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " " MAN W 4 " - " MAN W 5 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 6 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG A 701 " - " ASN A 637 " " NAG A 702 " - " ASN A 611 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 616 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 362 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 133 " " NAG C 609 " - " ASN C 413 " " NAG C 610 " - " ASN C 392 " " NAG C 611 " - " ASN C 230 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 276 " " NAG F 603 " - " ASN F 295 " " NAG F 604 " - " ASN F 301 " " NAG F 605 " - " ASN F 362 " " NAG F 606 " - " ASN F 386 " " NAG F 607 " - " ASN F 448 " " NAG F 608 " - " ASN F 133 " " NAG F 609 " - " ASN F 413 " " NAG F 610 " - " ASN F 392 " " NAG F 611 " - " ASN F 230 " " NAG I 701 " - " ASN I 637 " " NAG I 702 " - " ASN I 611 " " NAG I 703 " - " ASN I 625 " " NAG I 704 " - " ASN I 616 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 276 " " NAG J 603 " - " ASN J 295 " " NAG J 604 " - " ASN J 301 " " NAG J 605 " - " ASN J 362 " " NAG J 606 " - " ASN J 386 " " NAG J 607 " - " ASN J 448 " " NAG J 608 " - " ASN J 133 " " NAG J 609 " - " ASN J 413 " " NAG J 610 " - " ASN J 392 " " NAG J 611 " - " ASN J 230 " " NAG M 1 " - " ASN C 241 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 49 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 160 " " NAG R 1 " - " ASN C 156 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN F 241 " " NAG U 1 " - " ASN F 262 " " NAG V 1 " - " ASN F 49 " " NAG W 1 " - " ASN F 332 " " NAG X 1 " - " ASN F 160 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 197 " " NAG a 1 " - " ASN J 241 " " NAG b 1 " - " ASN J 262 " " NAG c 1 " - " ASN J 49 " " NAG d 1 " - " ASN J 332 " " NAG e 1 " - " ASN J 160 " " NAG f 1 " - " ASN J 156 " " NAG g 1 " - " ASN J 197 " Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 42 sheets defined 15.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.662A pdb=" N VAL A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.691A pdb=" N VAL A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.895A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 4.228A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 336 through 353 removed outlier: 3.524A pdb=" N GLN C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.666A pdb=" N MET C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.844A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 4.710A pdb=" N VAL B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.539A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.922A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 661 removed outlier: 4.280A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 115 Processing helix chain 'F' and resid 336 through 353 removed outlier: 4.355A pdb=" N GLU F 351 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.655A pdb=" N MET F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.818A pdb=" N GLU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 535 No H-bonds generated for 'chain 'I' and resid 533 through 535' Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.515A pdb=" N LEU I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 596 removed outlier: 3.613A pdb=" N VAL I 580 " --> pdb=" O LEU I 576 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA I 582 " --> pdb=" O ALA I 578 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 592 " --> pdb=" O LYS I 588 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU I 593 " --> pdb=" O ASP I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 661 removed outlier: 3.723A pdb=" N ILE I 635 " --> pdb=" O TRP I 631 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN I 637 " --> pdb=" O ARG I 633 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TYR I 638 " --> pdb=" O GLU I 634 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY I 640 " --> pdb=" O ASP I 636 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE I 641 " --> pdb=" O ASN I 637 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE I 642 " --> pdb=" O TYR I 638 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR I 643 " --> pdb=" O THR I 639 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR I 644 " --> pdb=" O GLY I 640 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU I 647 " --> pdb=" O TYR I 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN I 652 " --> pdb=" O GLU I 648 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN I 653 " --> pdb=" O SER I 649 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU I 658 " --> pdb=" O GLU I 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU I 659 " --> pdb=" O LYS I 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 Processing helix chain 'J' and resid 336 through 353 removed outlier: 3.672A pdb=" N GLN J 344 " --> pdb=" O ASN J 340 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU J 351 " --> pdb=" O ASP J 347 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.644A pdb=" N MET J 373 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.640A pdb=" N ASP K 86 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER K 87 " --> pdb=" O ALA K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.764A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.754A pdb=" N VAL C 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.209A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.562A pdb=" N LEU C 129 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR C 191 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 3.610A pdb=" N TYR C 435 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 272 removed outlier: 3.757A pdb=" N ILE C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 374 through 375 removed outlier: 3.570A pdb=" N ILE C 414 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 302 through 306 removed outlier: 6.478A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.290A pdb=" N ILE C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.680A pdb=" N THR D 105 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 90 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 107 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR D 33 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.706A pdb=" N VAL E 13 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N TRP E 35 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU E 46 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN E 37 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG E 39 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 18 through 22 removed outlier: 4.204A pdb=" N THR E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 40 Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 46 removed outlier: 4.241A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AB9, first strand: chain 'F' and resid 129 through 130 removed outlier: 4.133A pdb=" N TYR F 191 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AC2, first strand: chain 'F' and resid 201 through 203 removed outlier: 3.597A pdb=" N TYR F 435 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 271 through 272 removed outlier: 3.663A pdb=" N ILE F 271 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 374 through 375 Processing sheet with id=AC5, first strand: chain 'F' and resid 302 through 306 removed outlier: 6.487A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 319 " --> pdb=" O ARG F 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 360 through 361 removed outlier: 6.393A pdb=" N ILE F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.704A pdb=" N THR G 105 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR G 90 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 107 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR G 33 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TRP G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.674A pdb=" N VAL H 13 " --> pdb=" O ILE H 105 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TRP H 35 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU H 46 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN H 37 " --> pdb=" O PRO H 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG H 39 " --> pdb=" O GLN H 42 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.194A pdb=" N THR H 74 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 37 through 40 Processing sheet with id=AD3, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=AD5, first strand: chain 'J' and resid 129 through 130 removed outlier: 4.148A pdb=" N TYR J 191 " --> pdb=" O LEU J 129 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 157 through 158 Processing sheet with id=AD7, first strand: chain 'J' and resid 201 through 203 removed outlier: 3.684A pdb=" N TYR J 435 " --> pdb=" O THR J 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 271 through 272 removed outlier: 3.723A pdb=" N ILE J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 374 through 375 removed outlier: 3.573A pdb=" N ILE J 414 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE J 333 " --> pdb=" O ILE J 414 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 302 through 306 removed outlier: 6.356A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA J 319 " --> pdb=" O ARG J 305 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 360 through 361 removed outlier: 6.464A pdb=" N ILE J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.771A pdb=" N THR K 105 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR K 90 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL K 107 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA K 88 " --> pdb=" O VAL K 107 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR K 33 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR K 50 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.546A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TRP L 35 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU L 46 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN L 37 " --> pdb=" O PRO L 44 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG L 39 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.190A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1140 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: 6.79 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6142 1.34 - 1.47: 5448 1.47 - 1.59: 8988 1.59 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 20740 Sorted by residual: bond pdb=" O3 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.569 1.521 0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" O4 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.568 1.522 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" O2 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.567 1.523 0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" O1 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.565 1.522 0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 20735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 27358 1.76 - 3.51: 679 3.51 - 5.27: 132 5.27 - 7.02: 15 7.02 - 8.78: 4 Bond angle restraints: 28188 Sorted by residual: angle pdb=" N THR J 162 " pdb=" CA THR J 162 " pdb=" C THR J 162 " ideal model delta sigma weight residual 110.24 119.02 -8.78 1.41e+00 5.03e-01 3.88e+01 angle pdb=" C THR C 163 " pdb=" CA THR C 163 " pdb=" CB THR C 163 " ideal model delta sigma weight residual 110.06 102.93 7.13 1.44e+00 4.82e-01 2.46e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" C THR C 163 " ideal model delta sigma weight residual 113.28 120.94 -7.66 1.57e+00 4.06e-01 2.38e+01 angle pdb=" N ASP C 167 " pdb=" CA ASP C 167 " pdb=" C ASP C 167 " ideal model delta sigma weight residual 108.38 113.83 -5.45 1.35e+00 5.49e-01 1.63e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" CB THR C 163 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 28183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12708 17.88 - 35.75: 1015 35.75 - 53.63: 232 53.63 - 71.50: 33 71.50 - 89.38: 16 Dihedral angle restraints: 14004 sinusoidal: 7206 harmonic: 6798 Sorted by residual: dihedral pdb=" CB CYS J 228 " pdb=" SG CYS J 228 " pdb=" SG CYS J 239 " pdb=" CB CYS J 239 " ideal model delta sinusoidal sigma weight residual 93.00 4.49 88.51 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS J 113 " pdb=" SG CYS J 113 " pdb=" SG CYS J 432A" pdb=" CB CYS J 432A" ideal model delta sinusoidal sigma weight residual 93.00 179.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 432A" pdb=" CB CYS C 432A" ideal model delta sinusoidal sigma weight residual 93.00 170.79 -77.79 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3272 0.089 - 0.177: 274 0.177 - 0.266: 5 0.266 - 0.354: 0 0.354 - 0.443: 7 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CA THR C 162 " pdb=" N THR C 162 " pdb=" C THR C 162 " pdb=" CB THR C 162 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA THR J 162 " pdb=" N THR J 162 " pdb=" C THR J 162 " pdb=" CB THR J 162 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 637 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 3555 not shown) Planarity restraints: 3450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 94 " 0.321 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG E 94 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG E 94 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG E 94 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 94 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 117 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO J 118 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO J 118 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 118 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 117 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO F 118 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO F 118 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 118 " -0.034 5.00e-02 4.00e+02 ... (remaining 3447 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 223 2.60 - 3.17: 17456 3.17 - 3.75: 28706 3.75 - 4.32: 38090 4.32 - 4.90: 62688 Nonbonded interactions: 147163 Sorted by model distance: nonbonded pdb=" OG1 THR A 538 " pdb=" OE1 GLU B 647 " model vdw 2.022 3.040 nonbonded pdb=" OG SER J 334 " pdb=" OE1 GLU J 336 " model vdw 2.087 3.040 nonbonded pdb=" OG SER J 256 " pdb=" O LEU J 259 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG A 585 " pdb=" O ILE C 491 " model vdw 2.171 3.120 nonbonded pdb=" OG SER K 70 " pdb=" OG SER K 79 " model vdw 2.171 3.040 ... (remaining 147158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 32 through 505 or resid 601 through 611)) selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'U' selection = chain 'W' selection = chain 'b' selection = chain 'd' } ncs_group { reference = chain 'R' selection = chain 'Y' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 48.150 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20908 Z= 0.146 Angle : 0.714 8.779 28653 Z= 0.350 Chirality : 0.047 0.443 3558 Planarity : 0.005 0.144 3384 Dihedral : 12.768 89.376 9507 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.43 % Favored : 91.40 % Rotamer: Outliers : 0.10 % Allowed : 0.24 % Favored : 99.66 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.57 (0.17), residues: 2301 helix: -0.64 (0.29), residues: 315 sheet: 0.00 (0.23), residues: 543 loop : -1.62 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 479 HIS 0.005 0.001 HIS F 216 PHE 0.011 0.001 PHE F 159 TYR 0.020 0.001 TYR F 435 ARG 0.009 0.000 ARG J 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 66) link_NAG-ASN : angle 2.28390 ( 198) link_ALPHA1-6 : bond 0.01123 ( 6) link_ALPHA1-6 : angle 1.54284 ( 18) link_BETA1-4 : bond 0.00676 ( 42) link_BETA1-4 : angle 2.17717 ( 126) link_ALPHA1-2 : bond 0.00803 ( 6) link_ALPHA1-2 : angle 2.99816 ( 18) link_ALPHA1-3 : bond 0.01001 ( 9) link_ALPHA1-3 : angle 2.07537 ( 27) hydrogen bonds : bond 0.27506 ( 437) hydrogen bonds : angle 8.72546 ( 1140) SS BOND : bond 0.00534 ( 39) SS BOND : angle 1.43173 ( 78) covalent geometry : bond 0.00311 (20740) covalent geometry : angle 0.66563 (28188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 2.305 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 ASP cc_start: 0.9319 (m-30) cc_final: 0.8717 (p0) REVERT: A 595 ILE cc_start: 0.9638 (mm) cc_final: 0.8986 (tt) REVERT: C 215 ILE cc_start: 0.9561 (pt) cc_final: 0.9189 (mp) REVERT: C 284 ILE cc_start: 0.9254 (mm) cc_final: 0.8841 (tt) REVERT: C 373 MET cc_start: 0.9088 (mtm) cc_final: 0.8804 (ptp) REVERT: D 30 ARG cc_start: 0.9425 (tmm-80) cc_final: 0.9191 (mpt180) REVERT: D 90 TYR cc_start: 0.8868 (m-80) cc_final: 0.8648 (m-80) REVERT: B 589 ASP cc_start: 0.9510 (m-30) cc_final: 0.8778 (p0) REVERT: B 595 ILE cc_start: 0.9491 (mm) cc_final: 0.9259 (mt) REVERT: F 215 ILE cc_start: 0.9612 (pt) cc_final: 0.9302 (mp) REVERT: F 284 ILE cc_start: 0.9296 (mm) cc_final: 0.8830 (tt) REVERT: G 30 ARG cc_start: 0.9304 (tmm-80) cc_final: 0.9022 (mtm-85) REVERT: G 31 ASP cc_start: 0.9555 (t0) cc_final: 0.9319 (m-30) REVERT: I 589 ASP cc_start: 0.9513 (m-30) cc_final: 0.8953 (p0) REVERT: I 595 ILE cc_start: 0.9573 (mm) cc_final: 0.8966 (tp) REVERT: J 454 LEU cc_start: 0.9535 (mt) cc_final: 0.9317 (mt) REVERT: K 31 ASP cc_start: 0.9546 (t0) cc_final: 0.9341 (m-30) REVERT: K 90 TYR cc_start: 0.8724 (m-80) cc_final: 0.8324 (m-80) REVERT: K 100 MET cc_start: 0.9714 (mpp) cc_final: 0.9444 (mmp) REVERT: L 90 ILE cc_start: 0.9588 (pt) cc_final: 0.9302 (mp) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.3891 time to fit residues: 124.4192 Evaluate side-chains 116 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 70 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN C 389 GLN D 3 HIS D 76 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS G 68 HIS G 76 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 GLN I 577 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.035526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.028700 restraints weight = 337736.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.029405 restraints weight = 206189.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.029902 restraints weight = 144544.035| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20908 Z= 0.177 Angle : 0.746 13.204 28653 Z= 0.348 Chirality : 0.049 0.377 3558 Planarity : 0.004 0.060 3384 Dihedral : 8.508 59.225 5154 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 0.19 % Allowed : 4.76 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.65 (0.17), residues: 2301 helix: -0.69 (0.26), residues: 330 sheet: 0.11 (0.24), residues: 489 loop : -1.71 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 101 HIS 0.004 0.001 HIS J 374 PHE 0.025 0.001 PHE J 159 TYR 0.013 0.001 TYR C 217 ARG 0.008 0.001 ARG J 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 66) link_NAG-ASN : angle 2.93258 ( 198) link_ALPHA1-6 : bond 0.00762 ( 6) link_ALPHA1-6 : angle 1.62670 ( 18) link_BETA1-4 : bond 0.00704 ( 42) link_BETA1-4 : angle 2.19579 ( 126) link_ALPHA1-2 : bond 0.00952 ( 6) link_ALPHA1-2 : angle 3.23399 ( 18) link_ALPHA1-3 : bond 0.00955 ( 9) link_ALPHA1-3 : angle 2.01926 ( 27) hydrogen bonds : bond 0.05363 ( 437) hydrogen bonds : angle 6.03191 ( 1140) SS BOND : bond 0.00210 ( 39) SS BOND : angle 1.00687 ( 78) covalent geometry : bond 0.00366 (20740) covalent geometry : angle 0.68474 (28188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 2.264 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: symmetry clash revert: symmetry clash REVERT: A 626 MET cc_start: 0.7360 (tmm) cc_final: 0.7030 (tmm) REVERT: C 373 MET cc_start: 0.9139 (mtm) cc_final: 0.8894 (ptp) REVERT: B 530 MET cc_start: 0.7740 (mmp) cc_final: 0.7397 (mmm) REVERT: B 595 ILE cc_start: 0.9613 (mm) cc_final: 0.9408 (mt) REVERT: B 626 MET cc_start: 0.6766 (ppp) cc_final: 0.5527 (ppp) REVERT: B 629 MET cc_start: 0.9585 (mmt) cc_final: 0.9370 (mmt) REVERT: F 154 MET cc_start: 0.8001 (mmp) cc_final: 0.6727 (mmp) REVERT: G 90 TYR cc_start: 0.8940 (m-10) cc_final: 0.8645 (m-10) REVERT: H 85 ASP cc_start: 0.8800 (t0) cc_final: 0.8526 (t0) REVERT: I 595 ILE cc_start: 0.9719 (mm) cc_final: 0.9311 (tt) REVERT: I 626 MET cc_start: 0.7615 (ppp) cc_final: 0.6301 (ppp) REVERT: J 150 MET cc_start: 0.7208 (pmm) cc_final: 0.6488 (tpp) REVERT: J 154 MET cc_start: 0.7856 (mmp) cc_final: 0.7356 (mmp) REVERT: J 163 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9123 (m) REVERT: J 454 LEU cc_start: 0.9580 (mt) cc_final: 0.9363 (mt) REVERT: K 31 ASP cc_start: 0.9616 (t0) cc_final: 0.9353 (m-30) REVERT: K 68 HIS cc_start: 0.9417 (t70) cc_final: 0.9158 (t70) REVERT: K 90 TYR cc_start: 0.8888 (m-80) cc_final: 0.8571 (m-10) REVERT: K 100 MET cc_start: 0.9599 (mpp) cc_final: 0.8950 (mpp) REVERT: L 90 ILE cc_start: 0.9619 (pt) cc_final: 0.9322 (mp) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.3563 time to fit residues: 76.3313 Evaluate side-chains 98 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 120 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 199 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 222 optimal weight: 0.1980 chunk 114 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.035629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.028823 restraints weight = 334693.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.029566 restraints weight = 201522.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.030063 restraints weight = 140509.478| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20908 Z= 0.130 Angle : 0.693 14.216 28653 Z= 0.318 Chirality : 0.048 0.379 3558 Planarity : 0.004 0.078 3384 Dihedral : 8.296 59.243 5154 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.82 % Favored : 92.00 % Rotamer: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.44 (0.17), residues: 2301 helix: -0.26 (0.27), residues: 330 sheet: 0.40 (0.26), residues: 429 loop : -1.62 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 338 HIS 0.006 0.001 HIS F 216 PHE 0.009 0.001 PHE C 233 TYR 0.012 0.001 TYR C 217 ARG 0.004 0.000 ARG J 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 66) link_NAG-ASN : angle 3.00939 ( 198) link_ALPHA1-6 : bond 0.00836 ( 6) link_ALPHA1-6 : angle 1.41780 ( 18) link_BETA1-4 : bond 0.00679 ( 42) link_BETA1-4 : angle 1.99975 ( 126) link_ALPHA1-2 : bond 0.01087 ( 6) link_ALPHA1-2 : angle 3.33399 ( 18) link_ALPHA1-3 : bond 0.00998 ( 9) link_ALPHA1-3 : angle 1.78461 ( 27) hydrogen bonds : bond 0.04464 ( 437) hydrogen bonds : angle 5.54834 ( 1140) SS BOND : bond 0.00283 ( 39) SS BOND : angle 1.12395 ( 78) covalent geometry : bond 0.00269 (20740) covalent geometry : angle 0.62570 (28188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 2.317 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9214 (pm20) REVERT: D 90 TYR cc_start: 0.9078 (m-10) cc_final: 0.8809 (m-10) REVERT: B 589 ASP cc_start: 0.9248 (m-30) cc_final: 0.8628 (p0) REVERT: B 595 ILE cc_start: 0.9371 (mm) cc_final: 0.9052 (tp) REVERT: B 626 MET cc_start: 0.8607 (ppp) cc_final: 0.7904 (tmm) REVERT: F 154 MET cc_start: 0.8055 (mmp) cc_final: 0.7536 (mmp) REVERT: I 530 MET cc_start: 0.8447 (mmm) cc_final: 0.8074 (mmp) REVERT: I 595 ILE cc_start: 0.9587 (mm) cc_final: 0.9194 (tt) REVERT: I 626 MET cc_start: 0.8862 (ppp) cc_final: 0.7472 (ppp) REVERT: J 150 MET cc_start: 0.6925 (pmm) cc_final: 0.6193 (tpp) REVERT: J 454 LEU cc_start: 0.9538 (mt) cc_final: 0.9275 (mt) REVERT: L 90 ILE cc_start: 0.9546 (pt) cc_final: 0.9262 (mp) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.3956 time to fit residues: 72.7589 Evaluate side-chains 103 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 10 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN B 577 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN K 1 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.033296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026619 restraints weight = 350289.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.027306 restraints weight = 210879.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.027762 restraints weight = 148454.641| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20908 Z= 0.188 Angle : 0.743 12.271 28653 Z= 0.343 Chirality : 0.048 0.404 3558 Planarity : 0.004 0.046 3384 Dihedral : 8.238 57.372 5154 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.35 % Rotamer: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.48 (0.17), residues: 2301 helix: -0.02 (0.27), residues: 342 sheet: -0.07 (0.24), residues: 489 loop : -1.63 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 479 HIS 0.006 0.001 HIS C 374 PHE 0.012 0.001 PHE C 233 TYR 0.014 0.002 TYR C 435 ARG 0.004 0.000 ARG F 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 66) link_NAG-ASN : angle 2.99358 ( 198) link_ALPHA1-6 : bond 0.00753 ( 6) link_ALPHA1-6 : angle 1.43357 ( 18) link_BETA1-4 : bond 0.00659 ( 42) link_BETA1-4 : angle 2.02652 ( 126) link_ALPHA1-2 : bond 0.00817 ( 6) link_ALPHA1-2 : angle 3.21810 ( 18) link_ALPHA1-3 : bond 0.00820 ( 9) link_ALPHA1-3 : angle 2.03177 ( 27) hydrogen bonds : bond 0.03985 ( 437) hydrogen bonds : angle 5.43154 ( 1140) SS BOND : bond 0.00300 ( 39) SS BOND : angle 1.13055 ( 78) covalent geometry : bond 0.00388 (20740) covalent geometry : angle 0.68148 (28188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 2.275 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 530 MET cc_start: 0.8257 (mmm) cc_final: 0.7919 (mmm) REVERT: A 626 MET cc_start: 0.7567 (tmm) cc_final: 0.6121 (ppp) REVERT: A 629 MET cc_start: 0.9457 (mmp) cc_final: 0.9196 (mmp) REVERT: C 131 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8632 (p) REVERT: D 90 TYR cc_start: 0.9314 (m-10) cc_final: 0.9005 (m-10) REVERT: B 577 GLN cc_start: 0.9513 (mm110) cc_final: 0.9308 (mm110) REVERT: B 589 ASP cc_start: 0.9594 (m-30) cc_final: 0.9025 (p0) REVERT: B 595 ILE cc_start: 0.9667 (mm) cc_final: 0.9295 (tt) REVERT: B 626 MET cc_start: 0.6064 (ppp) cc_final: 0.4365 (ppp) REVERT: F 104 MET cc_start: 0.9518 (ppp) cc_final: 0.9239 (ppp) REVERT: F 154 MET cc_start: 0.8704 (mmp) cc_final: 0.8032 (mmm) REVERT: I 589 ASP cc_start: 0.9385 (m-30) cc_final: 0.9110 (m-30) REVERT: I 595 ILE cc_start: 0.9727 (mm) cc_final: 0.9403 (tt) REVERT: I 626 MET cc_start: 0.8078 (ppp) cc_final: 0.6059 (ppp) REVERT: J 100 MET cc_start: 0.9319 (mtm) cc_final: 0.9031 (mtt) REVERT: J 150 MET cc_start: 0.7152 (pmm) cc_final: 0.6596 (tpp) REVERT: J 154 MET cc_start: 0.7929 (mmp) cc_final: 0.7378 (mmp) REVERT: J 454 LEU cc_start: 0.9593 (mt) cc_final: 0.9388 (mt) REVERT: K 90 TYR cc_start: 0.8892 (m-80) cc_final: 0.8393 (m-10) outliers start: 4 outliers final: 2 residues processed: 117 average time/residue: 0.3694 time to fit residues: 65.3692 Evaluate side-chains 97 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 9.9990 chunk 213 optimal weight: 40.0000 chunk 34 optimal weight: 0.0470 chunk 107 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 233 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 1 GLN D 3 HIS ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 GLN K 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.033184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.026609 restraints weight = 346825.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.027288 restraints weight = 205048.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027749 restraints weight = 143660.744| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20908 Z= 0.144 Angle : 0.692 16.377 28653 Z= 0.319 Chirality : 0.048 0.443 3558 Planarity : 0.003 0.039 3384 Dihedral : 8.293 59.753 5154 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.78 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.48 (0.17), residues: 2301 helix: -0.04 (0.27), residues: 333 sheet: -0.04 (0.25), residues: 477 loop : -1.62 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 479 HIS 0.003 0.001 HIS C 130 PHE 0.011 0.001 PHE C 233 TYR 0.014 0.001 TYR C 217 ARG 0.004 0.000 ARG I 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 66) link_NAG-ASN : angle 2.93921 ( 198) link_ALPHA1-6 : bond 0.00828 ( 6) link_ALPHA1-6 : angle 1.34581 ( 18) link_BETA1-4 : bond 0.00597 ( 42) link_BETA1-4 : angle 1.79791 ( 126) link_ALPHA1-2 : bond 0.00788 ( 6) link_ALPHA1-2 : angle 3.33480 ( 18) link_ALPHA1-3 : bond 0.00885 ( 9) link_ALPHA1-3 : angle 1.75518 ( 27) hydrogen bonds : bond 0.03601 ( 437) hydrogen bonds : angle 5.17651 ( 1140) SS BOND : bond 0.00257 ( 39) SS BOND : angle 1.25403 ( 78) covalent geometry : bond 0.00300 (20740) covalent geometry : angle 0.62903 (28188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.156 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 530 MET cc_start: 0.8723 (mmm) cc_final: 0.8404 (mmm) REVERT: A 626 MET cc_start: 0.7452 (tmm) cc_final: 0.5888 (ppp) REVERT: D 90 TYR cc_start: 0.9302 (m-10) cc_final: 0.8962 (m-10) REVERT: E 60 ASP cc_start: 0.9709 (t0) cc_final: 0.9507 (p0) REVERT: B 530 MET cc_start: 0.8179 (mmm) cc_final: 0.7550 (mmm) REVERT: B 589 ASP cc_start: 0.9606 (m-30) cc_final: 0.9050 (p0) REVERT: B 595 ILE cc_start: 0.9656 (mm) cc_final: 0.9282 (tt) REVERT: B 626 MET cc_start: 0.6464 (ppp) cc_final: 0.5220 (ppp) REVERT: F 154 MET cc_start: 0.8721 (mmp) cc_final: 0.8036 (mmm) REVERT: I 589 ASP cc_start: 0.9385 (m-30) cc_final: 0.9125 (m-30) REVERT: I 595 ILE cc_start: 0.9732 (mm) cc_final: 0.9398 (tt) REVERT: I 626 MET cc_start: 0.7496 (ppp) cc_final: 0.7180 (tmm) REVERT: J 100 MET cc_start: 0.9323 (mtm) cc_final: 0.9042 (mtt) REVERT: J 150 MET cc_start: 0.7132 (pmm) cc_final: 0.6598 (tpp) REVERT: K 90 TYR cc_start: 0.9035 (m-80) cc_final: 0.8563 (m-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3762 time to fit residues: 61.3879 Evaluate side-chains 87 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 54 optimal weight: 0.0270 chunk 162 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 229 optimal weight: 50.0000 overall best weight: 1.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 1 GLN G 3 HIS ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.033160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026581 restraints weight = 347559.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.027248 restraints weight = 206082.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.027721 restraints weight = 144226.037| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20908 Z= 0.125 Angle : 0.668 14.505 28653 Z= 0.306 Chirality : 0.048 0.403 3558 Planarity : 0.004 0.112 3384 Dihedral : 8.142 59.215 5154 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.04 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.41 (0.17), residues: 2301 helix: 0.22 (0.28), residues: 345 sheet: -0.00 (0.25), residues: 477 loop : -1.63 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 479 HIS 0.003 0.001 HIS J 374 PHE 0.009 0.001 PHE C 233 TYR 0.011 0.001 TYR C 217 ARG 0.006 0.000 ARG K 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 66) link_NAG-ASN : angle 2.84443 ( 198) link_ALPHA1-6 : bond 0.00836 ( 6) link_ALPHA1-6 : angle 1.30734 ( 18) link_BETA1-4 : bond 0.00595 ( 42) link_BETA1-4 : angle 1.78224 ( 126) link_ALPHA1-2 : bond 0.00865 ( 6) link_ALPHA1-2 : angle 3.32613 ( 18) link_ALPHA1-3 : bond 0.00885 ( 9) link_ALPHA1-3 : angle 1.71630 ( 27) hydrogen bonds : bond 0.03336 ( 437) hydrogen bonds : angle 5.09528 ( 1140) SS BOND : bond 0.00201 ( 39) SS BOND : angle 1.09405 ( 78) covalent geometry : bond 0.00263 (20740) covalent geometry : angle 0.60647 (28188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 2.324 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 530 MET cc_start: 0.8782 (mmm) cc_final: 0.8354 (mmm) REVERT: A 577 GLN cc_start: 0.9348 (mm110) cc_final: 0.9115 (mm-40) REVERT: A 595 ILE cc_start: 0.9753 (mm) cc_final: 0.9524 (tt) REVERT: A 626 MET cc_start: 0.7386 (tmm) cc_final: 0.5816 (ppp) REVERT: D 13 LYS cc_start: 0.9281 (mtmm) cc_final: 0.9043 (mmmt) REVERT: D 90 TYR cc_start: 0.9291 (m-10) cc_final: 0.8953 (m-10) REVERT: B 530 MET cc_start: 0.8353 (mmm) cc_final: 0.7563 (mmm) REVERT: B 577 GLN cc_start: 0.9532 (mm110) cc_final: 0.9002 (tp40) REVERT: B 589 ASP cc_start: 0.9599 (m-30) cc_final: 0.9055 (p0) REVERT: B 595 ILE cc_start: 0.9669 (mm) cc_final: 0.9319 (tt) REVERT: B 626 MET cc_start: 0.6583 (ppp) cc_final: 0.5352 (ppp) REVERT: F 104 MET cc_start: 0.9517 (ppp) cc_final: 0.9220 (ppp) REVERT: F 154 MET cc_start: 0.8597 (mmp) cc_final: 0.8289 (mmm) REVERT: I 589 ASP cc_start: 0.9369 (m-30) cc_final: 0.9113 (m-30) REVERT: I 595 ILE cc_start: 0.9724 (mm) cc_final: 0.9406 (tt) REVERT: I 626 MET cc_start: 0.7705 (ppp) cc_final: 0.6574 (ppp) REVERT: J 100 MET cc_start: 0.9335 (mtm) cc_final: 0.9063 (mtt) REVERT: J 150 MET cc_start: 0.7102 (pmm) cc_final: 0.6553 (tpp) REVERT: J 154 MET cc_start: 0.7842 (mmp) cc_final: 0.7383 (mmp) REVERT: J 454 LEU cc_start: 0.9635 (mt) cc_final: 0.9420 (mt) REVERT: K 90 TYR cc_start: 0.9017 (m-80) cc_final: 0.8545 (m-10) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3629 time to fit residues: 62.0928 Evaluate side-chains 91 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 146 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 133 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 GLN J 474 ASN ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.030768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.024385 restraints weight = 364334.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.025002 restraints weight = 221921.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.025397 restraints weight = 157064.777| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20908 Z= 0.256 Angle : 0.843 15.447 28653 Z= 0.394 Chirality : 0.049 0.416 3558 Planarity : 0.005 0.075 3384 Dihedral : 8.616 57.769 5154 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.60 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.78 (0.17), residues: 2301 helix: -0.38 (0.26), residues: 363 sheet: -0.31 (0.24), residues: 495 loop : -1.81 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 479 HIS 0.008 0.002 HIS J 374 PHE 0.016 0.002 PHE J 159 TYR 0.027 0.002 TYR J 191 ARG 0.008 0.001 ARG I 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 66) link_NAG-ASN : angle 3.64918 ( 198) link_ALPHA1-6 : bond 0.00715 ( 6) link_ALPHA1-6 : angle 1.42360 ( 18) link_BETA1-4 : bond 0.00567 ( 42) link_BETA1-4 : angle 1.95994 ( 126) link_ALPHA1-2 : bond 0.00539 ( 6) link_ALPHA1-2 : angle 3.14869 ( 18) link_ALPHA1-3 : bond 0.00721 ( 9) link_ALPHA1-3 : angle 2.12042 ( 27) hydrogen bonds : bond 0.04006 ( 437) hydrogen bonds : angle 5.76730 ( 1140) SS BOND : bond 0.00332 ( 39) SS BOND : angle 1.53063 ( 78) covalent geometry : bond 0.00527 (20740) covalent geometry : angle 0.77058 (28188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 2.285 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 530 MET cc_start: 0.9012 (mmm) cc_final: 0.8638 (mmm) REVERT: A 589 ASP cc_start: 0.9353 (m-30) cc_final: 0.9130 (m-30) REVERT: A 626 MET cc_start: 0.7953 (tmm) cc_final: 0.6805 (ppp) REVERT: C 154 MET cc_start: 0.7388 (mmp) cc_final: 0.6963 (mmp) REVERT: B 595 ILE cc_start: 0.9703 (mm) cc_final: 0.9307 (tt) REVERT: B 626 MET cc_start: 0.6329 (ppp) cc_final: 0.4826 (ppp) REVERT: F 104 MET cc_start: 0.9537 (ppp) cc_final: 0.9323 (ppp) REVERT: F 154 MET cc_start: 0.8899 (mmp) cc_final: 0.8348 (mmp) REVERT: I 589 ASP cc_start: 0.9461 (m-30) cc_final: 0.9243 (m-30) REVERT: I 626 MET cc_start: 0.7764 (ppp) cc_final: 0.6515 (ppp) REVERT: J 100 MET cc_start: 0.9367 (mtm) cc_final: 0.9093 (mtt) REVERT: J 150 MET cc_start: 0.7471 (pmm) cc_final: 0.7103 (tpp) REVERT: K 90 TYR cc_start: 0.9120 (m-80) cc_final: 0.8699 (m-10) REVERT: K 100 MET cc_start: 0.9484 (mpp) cc_final: 0.8825 (mpp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3182 time to fit residues: 50.8540 Evaluate side-chains 81 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 140 optimal weight: 0.9980 chunk 31 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 198 optimal weight: 0.2980 chunk 199 optimal weight: 0.2980 chunk 160 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 192 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN F 33 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.032195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.025848 restraints weight = 353664.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026507 restraints weight = 208822.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.026971 restraints weight = 144364.919| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20908 Z= 0.119 Angle : 0.695 14.306 28653 Z= 0.320 Chirality : 0.049 0.420 3558 Planarity : 0.003 0.048 3384 Dihedral : 8.309 58.834 5154 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.30 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.54 (0.17), residues: 2301 helix: 0.18 (0.27), residues: 345 sheet: -0.16 (0.23), residues: 528 loop : -1.76 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 338 HIS 0.002 0.001 HIS J 105 PHE 0.009 0.001 PHE J 233 TYR 0.017 0.001 TYR J 191 ARG 0.013 0.000 ARG K 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 66) link_NAG-ASN : angle 2.96709 ( 198) link_ALPHA1-6 : bond 0.00886 ( 6) link_ALPHA1-6 : angle 1.24212 ( 18) link_BETA1-4 : bond 0.00622 ( 42) link_BETA1-4 : angle 1.72573 ( 126) link_ALPHA1-2 : bond 0.00836 ( 6) link_ALPHA1-2 : angle 3.33710 ( 18) link_ALPHA1-3 : bond 0.00913 ( 9) link_ALPHA1-3 : angle 1.58071 ( 27) hydrogen bonds : bond 0.03278 ( 437) hydrogen bonds : angle 5.16664 ( 1140) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.27769 ( 78) covalent geometry : bond 0.00257 (20740) covalent geometry : angle 0.63256 (28188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 3.053 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9129 (mmm) cc_final: 0.8881 (mmm) REVERT: A 589 ASP cc_start: 0.9316 (m-30) cc_final: 0.9028 (m-30) REVERT: A 626 MET cc_start: 0.7104 (tmm) cc_final: 0.6788 (tmm) REVERT: C 154 MET cc_start: 0.7766 (mmp) cc_final: 0.7545 (mmp) REVERT: B 589 ASP cc_start: 0.9605 (m-30) cc_final: 0.9105 (p0) REVERT: B 595 ILE cc_start: 0.9670 (mm) cc_final: 0.9310 (tt) REVERT: B 626 MET cc_start: 0.6378 (ppp) cc_final: 0.4896 (ppp) REVERT: F 104 MET cc_start: 0.9574 (ppp) cc_final: 0.9263 (ppp) REVERT: F 154 MET cc_start: 0.8602 (mmp) cc_final: 0.8020 (mmp) REVERT: H 60 ASP cc_start: 0.9772 (t0) cc_final: 0.9516 (p0) REVERT: I 589 ASP cc_start: 0.9437 (m-30) cc_final: 0.9184 (m-30) REVERT: I 626 MET cc_start: 0.7601 (ppp) cc_final: 0.6575 (ppp) REVERT: J 150 MET cc_start: 0.7242 (pmm) cc_final: 0.6703 (tpp) REVERT: K 90 TYR cc_start: 0.9012 (m-80) cc_final: 0.8576 (m-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3586 time to fit residues: 57.5753 Evaluate side-chains 86 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 172 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.030468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.024199 restraints weight = 367457.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.024806 restraints weight = 222164.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025228 restraints weight = 156333.417| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20908 Z= 0.247 Angle : 0.773 13.457 28653 Z= 0.366 Chirality : 0.048 0.427 3558 Planarity : 0.004 0.066 3384 Dihedral : 8.509 57.463 5154 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.87 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.80 (0.17), residues: 2301 helix: 0.10 (0.27), residues: 345 sheet: -0.45 (0.22), residues: 564 loop : -1.95 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 571 HIS 0.006 0.001 HIS C 374 PHE 0.012 0.002 PHE J 468 TYR 0.020 0.002 TYR J 191 ARG 0.007 0.001 ARG K 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 66) link_NAG-ASN : angle 3.00243 ( 198) link_ALPHA1-6 : bond 0.00702 ( 6) link_ALPHA1-6 : angle 1.39827 ( 18) link_BETA1-4 : bond 0.00477 ( 42) link_BETA1-4 : angle 1.73066 ( 126) link_ALPHA1-2 : bond 0.00530 ( 6) link_ALPHA1-2 : angle 3.11106 ( 18) link_ALPHA1-3 : bond 0.00698 ( 9) link_ALPHA1-3 : angle 1.98986 ( 27) hydrogen bonds : bond 0.03725 ( 437) hydrogen bonds : angle 5.60351 ( 1140) SS BOND : bond 0.00687 ( 39) SS BOND : angle 1.56139 ( 78) covalent geometry : bond 0.00509 (20740) covalent geometry : angle 0.71574 (28188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 2.171 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 589 ASP cc_start: 0.9387 (m-30) cc_final: 0.9149 (m-30) REVERT: A 626 MET cc_start: 0.7514 (tmm) cc_final: 0.7147 (tmm) REVERT: C 154 MET cc_start: 0.8019 (mmp) cc_final: 0.7772 (mmp) REVERT: B 530 MET cc_start: 0.8743 (mmm) cc_final: 0.8006 (mpp) REVERT: B 595 ILE cc_start: 0.9702 (mm) cc_final: 0.9334 (tt) REVERT: B 626 MET cc_start: 0.6548 (ppp) cc_final: 0.4707 (ppp) REVERT: F 104 MET cc_start: 0.9596 (ppp) cc_final: 0.9375 (ppp) REVERT: F 154 MET cc_start: 0.8829 (mmp) cc_final: 0.8201 (mmp) REVERT: I 589 ASP cc_start: 0.9503 (m-30) cc_final: 0.9282 (m-30) REVERT: I 626 MET cc_start: 0.7652 (ppp) cc_final: 0.6805 (ppp) REVERT: J 100 MET cc_start: 0.9389 (mtm) cc_final: 0.9143 (mtt) REVERT: J 150 MET cc_start: 0.7453 (pmm) cc_final: 0.6886 (tpp) REVERT: J 373 MET cc_start: 0.9291 (mpp) cc_final: 0.8766 (mmm) REVERT: K 31 ASP cc_start: 0.9218 (m-30) cc_final: 0.9007 (m-30) REVERT: K 90 TYR cc_start: 0.9156 (m-80) cc_final: 0.8697 (m-10) REVERT: K 100 MET cc_start: 0.9488 (mpp) cc_final: 0.8916 (mpp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.3344 time to fit residues: 50.6300 Evaluate side-chains 80 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 116 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 113 optimal weight: 0.0970 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 229 optimal weight: 50.0000 chunk 228 optimal weight: 7.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.030841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.024659 restraints weight = 362142.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.025294 restraints weight = 214170.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.025730 restraints weight = 149168.468| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20908 Z= 0.155 Angle : 0.698 13.519 28653 Z= 0.326 Chirality : 0.048 0.426 3558 Planarity : 0.003 0.046 3384 Dihedral : 8.449 57.889 5154 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.26 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.73 (0.17), residues: 2301 helix: 0.24 (0.27), residues: 345 sheet: -0.47 (0.22), residues: 564 loop : -1.89 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 571 HIS 0.005 0.001 HIS F 130 PHE 0.013 0.001 PHE J 233 TYR 0.015 0.001 TYR J 191 ARG 0.004 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 66) link_NAG-ASN : angle 2.86879 ( 198) link_ALPHA1-6 : bond 0.00811 ( 6) link_ALPHA1-6 : angle 1.29298 ( 18) link_BETA1-4 : bond 0.00534 ( 42) link_BETA1-4 : angle 1.67663 ( 126) link_ALPHA1-2 : bond 0.00625 ( 6) link_ALPHA1-2 : angle 3.18003 ( 18) link_ALPHA1-3 : bond 0.00804 ( 9) link_ALPHA1-3 : angle 1.66788 ( 27) hydrogen bonds : bond 0.03292 ( 437) hydrogen bonds : angle 5.34556 ( 1140) SS BOND : bond 0.00271 ( 39) SS BOND : angle 1.42708 ( 78) covalent geometry : bond 0.00326 (20740) covalent geometry : angle 0.63918 (28188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 2.365 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 589 ASP cc_start: 0.9395 (m-30) cc_final: 0.9133 (m-30) REVERT: A 626 MET cc_start: 0.7685 (tmm) cc_final: 0.7445 (tmm) REVERT: B 595 ILE cc_start: 0.9696 (mm) cc_final: 0.9334 (tt) REVERT: B 626 MET cc_start: 0.6699 (ppp) cc_final: 0.6187 (ppp) REVERT: F 154 MET cc_start: 0.8710 (mmp) cc_final: 0.8200 (mmp) REVERT: H 60 ASP cc_start: 0.9768 (t0) cc_final: 0.9542 (p0) REVERT: I 589 ASP cc_start: 0.9503 (m-30) cc_final: 0.9269 (m-30) REVERT: I 626 MET cc_start: 0.7407 (ppp) cc_final: 0.6383 (ppp) REVERT: J 100 MET cc_start: 0.9409 (mtm) cc_final: 0.9146 (mtt) REVERT: J 150 MET cc_start: 0.7400 (pmm) cc_final: 0.6897 (tpp) REVERT: J 454 LEU cc_start: 0.9586 (mt) cc_final: 0.9380 (mt) REVERT: K 31 ASP cc_start: 0.9289 (m-30) cc_final: 0.9080 (m-30) REVERT: K 90 TYR cc_start: 0.9185 (m-80) cc_final: 0.8648 (m-10) REVERT: K 100 MET cc_start: 0.9474 (mpp) cc_final: 0.8912 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3340 time to fit residues: 48.7709 Evaluate side-chains 80 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 179 optimal weight: 0.3980 chunk 191 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.030459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.024316 restraints weight = 367549.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.024943 restraints weight = 216389.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.025372 restraints weight = 150557.297| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20908 Z= 0.161 Angle : 0.699 13.100 28653 Z= 0.327 Chirality : 0.047 0.426 3558 Planarity : 0.004 0.051 3384 Dihedral : 8.377 57.394 5154 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.87 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.66 (0.17), residues: 2301 helix: 0.26 (0.28), residues: 345 sheet: -0.38 (0.23), residues: 540 loop : -1.84 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 571 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE J 233 TYR 0.017 0.002 TYR J 191 ARG 0.008 0.000 ARG I 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 66) link_NAG-ASN : angle 2.76951 ( 198) link_ALPHA1-6 : bond 0.00801 ( 6) link_ALPHA1-6 : angle 1.26722 ( 18) link_BETA1-4 : bond 0.00505 ( 42) link_BETA1-4 : angle 1.68738 ( 126) link_ALPHA1-2 : bond 0.00584 ( 6) link_ALPHA1-2 : angle 3.09947 ( 18) link_ALPHA1-3 : bond 0.00722 ( 9) link_ALPHA1-3 : angle 1.68411 ( 27) hydrogen bonds : bond 0.03265 ( 437) hydrogen bonds : angle 5.41186 ( 1140) SS BOND : bond 0.00240 ( 39) SS BOND : angle 1.32637 ( 78) covalent geometry : bond 0.00343 (20740) covalent geometry : angle 0.64437 (28188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.22 seconds wall clock time: 100 minutes 34.67 seconds (6034.67 seconds total)