Starting phenix.real_space_refine on Fri Aug 7 08:10:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yii_72991/08_2026/9yii_72991.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yii_72991/08_2026/9yii_72991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yii_72991/08_2026/9yii_72991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yii_72991/08_2026/9yii_72991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yii_72991/08_2026/9yii_72991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yii_72991/08_2026/9yii_72991.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12450 2.51 5 N 3276 2.21 5 O 4011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19863 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3388 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 5 Chain: "F" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3388 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 5 Chain: "G" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3388 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 5 Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "J" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 958 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "N" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'GLC': 2, 'MAN': 1, '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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'GLC': 2, 'MAN': 1, '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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'GLC': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.87, per 1000 atoms: 0.25 Number of scatterers: 19863 At special positions: 0 Unit cell: (156.6, 162.69, 138.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4011 8.00 N 3276 7.00 C 12450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " 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=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 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=2.03 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 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " 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 P 4 " - " GLC P 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " GLC X 5 " " MAN a 4 " - " MAN a 5 " " MAN f 4 " - " GLC f 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " GLC S 6 " - " MAN S 7 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " GLC a 6 " - " MAN a 7 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " GLC i 6 " - " MAN i 7 " ALPHA1-6 " BMA P 3 " - " GLC P 6 " " BMA R 3 " - " GLC R 5 " " BMA S 3 " - " GLC S 6 " " BMA X 3 " - " GLC X 6 " " BMA Z 3 " - " GLC Z 5 " " BMA a 3 " - " GLC a 6 " " BMA f 3 " - " GLC f 6 " " BMA h 3 " - " GLC h 5 " " BMA i 3 " - " GLC i 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN E 156 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 392 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 276 " " NAG F 604 " - " ASN F 339 " " NAG F 605 " - " ASN F 392 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 197 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 392 " " NAG I 1 " - " ASN E 160 " " NAG O 1 " - " ASN E 234 " " NAG P 1 " - " ASN E 262 " " NAG Q 1 " - " ASN E 295 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 160 " " NAG W 1 " - " ASN F 234 " " NAG X 1 " - " ASN F 262 " " NAG Y 1 " - " ASN F 295 " " NAG Z 1 " - " ASN F 301 " " NAG a 1 " - " ASN F 332 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN G 160 " " NAG e 1 " - " ASN G 234 " " NAG f 1 " - " ASN G 262 " " NAG g 1 " - " ASN G 295 " " NAG h 1 " - " ASN G 301 " " NAG i 1 " - " ASN G 332 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 905.6 milliseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4350 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 42 sheets defined 19.3% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.560A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.812A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 removed outlier: 3.529A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 4.019A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.561A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.812A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.530A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 4.019A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.561A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.812A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 651 removed outlier: 3.529A pdb=" N LEU C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 4.020A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.621A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.779A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.562A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.186A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.620A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.778A pdb=" N THR F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.562A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.185A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.620A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.778A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.562A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.186A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.560A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.559A pdb=" N THR B 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL F 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.561A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.581A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AA8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.350A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.782A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.581A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'F' and resid 169 through 174 Processing sheet with id=AB7, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.350A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.782A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.582A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 174 Processing sheet with id=AC6, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.350A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.781A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.572A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.679A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.679A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.572A pdb=" N SER J 70 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.680A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.680A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.896A pdb=" N LEU K 38 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU K 47 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.896A pdb=" N LEU L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU L 47 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AE2, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.572A pdb=" N SER M 70 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 57 through 59 removed outlier: 3.680A pdb=" N SER M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 57 through 59 removed outlier: 3.680A pdb=" N SER M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.896A pdb=" N LEU N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU N 47 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 19 through 23 684 hydrogen bonds defined for protein. 1800 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: 3.84 Time building geometry restraints manager: 2.60 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: 6170 1.34 - 1.46: 4597 1.46 - 1.58: 9339 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 20271 Sorted by residual: bond pdb=" C1 MAN P 4 " pdb=" O5 MAN P 4 " ideal model delta sigma weight residual 1.399 1.435 -0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C1 MAN i 5 " pdb=" O5 MAN i 5 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 MAN f 4 " pdb=" O5 MAN f 4 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.434 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 20266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 26520 1.66 - 3.31: 839 3.31 - 4.97: 127 4.97 - 6.63: 33 6.63 - 8.28: 12 Bond angle restraints: 27531 Sorted by residual: angle pdb=" C THR E 257 " pdb=" N GLN E 258 " pdb=" CA GLN E 258 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.80e+00 angle pdb=" C THR F 257 " pdb=" N GLN F 258 " pdb=" CA GLN F 258 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" C THR G 257 " pdb=" N GLN G 258 " pdb=" CA GLN G 258 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.72e+00 angle pdb=" C1 BMA f 3 " pdb=" O5 BMA f 3 " pdb=" C5 BMA f 3 " ideal model delta sigma weight residual 118.82 110.54 8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" C1 BMA P 3 " pdb=" O5 BMA P 3 " pdb=" C5 BMA P 3 " ideal model delta sigma weight residual 118.82 110.55 8.27 3.00e+00 1.11e-01 7.61e+00 ... (remaining 27526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 12422 24.31 - 48.63: 727 48.63 - 72.94: 108 72.94 - 97.26: 60 97.26 - 121.57: 96 Dihedral angle restraints: 13413 sinusoidal: 6639 harmonic: 6774 Sorted by residual: dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -20.55 -65.45 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -20.59 -65.41 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 -20.61 -65.39 1 1.00e+01 1.00e-02 5.60e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 3351 1.016 - 2.031: 0 2.031 - 3.047: 0 3.047 - 4.063: 0 4.063 - 5.079: 15 Chirality restraints: 3366 Sorted by residual: chirality pdb=" C4 NAG j 2 " pdb=" C3 NAG j 2 " pdb=" C5 NAG j 2 " pdb=" O4 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C4 NAG b 2 " pdb=" C3 NAG b 2 " pdb=" C5 NAG b 2 " pdb=" O4 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.53 2.54 -5.08 2.00e-01 2.50e+01 6.44e+02 chirality pdb=" C4 NAG T 2 " pdb=" C3 NAG T 2 " pdb=" C5 NAG T 2 " pdb=" O4 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.53 2.54 -5.07 2.00e-01 2.50e+01 6.44e+02 ... (remaining 3363 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 80 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C LEU H 80 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU H 80 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN H 81 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 80 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C LEU J 80 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU J 80 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN J 81 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 80 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.48e+00 pdb=" C LEU M 80 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU M 80 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN M 81 " 0.016 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 9099 2.95 - 3.44: 18295 3.44 - 3.93: 31095 3.93 - 4.41: 33478 4.41 - 4.90: 56951 Nonbonded interactions: 148918 Sorted by model distance: nonbonded pdb=" C4 NAG b 1 " pdb=" O5 NAG b 2 " model vdw 2.466 2.776 nonbonded pdb=" C4 NAG j 1 " pdb=" O5 NAG j 2 " model vdw 2.466 2.776 nonbonded pdb=" C4 NAG T 1 " pdb=" O5 NAG T 2 " model vdw 2.467 2.776 nonbonded pdb=" N LYS M 31 " pdb=" O LYS M 31 " model vdw 2.611 2.496 nonbonded pdb=" N LYS H 31 " pdb=" O LYS H 31 " model vdw 2.611 2.496 ... (remaining 148913 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'P' and (resid 1 or resid 4 through 5)) selection = (chain 'S' and (resid 2 or resid 5 through 6)) selection = (chain 'X' and (resid 1 or resid 4 through 5)) selection = (chain 'a' and (resid 2 or resid 5 through 6)) selection = (chain 'f' and (resid 1 or resid 4 through 5)) selection = (chain 'i' and (resid 2 or resid 5 through 6)) } ncs_group { reference = chain 'R' selection = chain 'Z' selection = chain 'h' } 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: 3.940 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.370 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20412 Z= 0.228 Angle : 0.688 10.137 27912 Z= 0.295 Chirality : 0.340 5.079 3366 Planarity : 0.003 0.045 3357 Dihedral : 19.389 121.570 8937 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.15 % Allowed : 7.61 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 2298 helix: 1.57 (0.27), residues: 384 sheet: -0.39 (0.21), residues: 609 loop : -1.39 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 500 TYR 0.017 0.001 TYR N 95 PHE 0.009 0.001 PHE F 159 TRP 0.008 0.001 TRP C 610 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 (20271) covalent geometry : angle 0.66342 / 0.29 (27531) SS BOND : bond 0.00298 / 0.17 ( 42) SS BOND : angle 0.46722 / 0.34 ( 84) hydrogen bonds : bond 0.11250 / 7.59 ( 636) hydrogen bonds : angle 5.44173 / 3.83 ( 1800) link_ALPHA1-2 : bond 0.00639 / 0.31 ( 6) link_ALPHA1-2 : angle 0.55196 / 0.33 ( 18) link_ALPHA1-3 : bond 0.00395 / 0.23 ( 12) link_ALPHA1-3 : angle 1.26415 / 0.83 ( 36) link_ALPHA1-6 : bond 0.00153 / 0.09 ( 9) link_ALPHA1-6 : angle 0.50019 / 0.31 ( 27) link_BETA1-4 : bond 0.00401 / 0.25 ( 33) link_BETA1-4 : angle 1.33507 / 0.92 ( 99) link_NAG-ASN : bond 0.00480 / 0.27 ( 39) link_NAG-ASN : angle 2.68722 / 1.98 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 646 time to evaluate : 0.778 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: A 539 VAL cc_start: 0.9555 (t) cc_final: 0.9090 (p) REVERT: A 540 GLN cc_start: 0.8014 (mp10) cc_final: 0.7665 (mp10) REVERT: A 543 ASN cc_start: 0.8743 (m-40) cc_final: 0.8051 (t0) REVERT: A 584 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 596 TRP cc_start: 0.9090 (m-10) cc_final: 0.8578 (m-10) REVERT: A 603 ILE cc_start: 0.8795 (mm) cc_final: 0.8492 (mm) REVERT: A 624 ASP cc_start: 0.8362 (m-30) cc_final: 0.8155 (m-30) REVERT: A 649 SER cc_start: 0.8646 (p) cc_final: 0.8379 (p) REVERT: B 535 MET cc_start: 0.7248 (mmp) cc_final: 0.6801 (tpp) REVERT: B 543 ASN cc_start: 0.8710 (m-40) cc_final: 0.8137 (t0) REVERT: B 584 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7682 (tm-30) REVERT: B 596 TRP cc_start: 0.9078 (m-10) cc_final: 0.8582 (m-10) REVERT: B 641 ILE cc_start: 0.8981 (mp) cc_final: 0.8740 (tt) REVERT: B 649 SER cc_start: 0.8631 (p) cc_final: 0.8363 (p) REVERT: C 536 THR cc_start: 0.8652 (p) cc_final: 0.7419 (p) REVERT: C 539 VAL cc_start: 0.9515 (t) cc_final: 0.9017 (p) REVERT: C 540 GLN cc_start: 0.7920 (mp10) cc_final: 0.7525 (mp10) REVERT: C 543 ASN cc_start: 0.8722 (m-40) cc_final: 0.8037 (t0) REVERT: C 596 TRP cc_start: 0.9132 (m-10) cc_final: 0.8667 (m-10) REVERT: C 649 SER cc_start: 0.8629 (p) cc_final: 0.8386 (p) REVERT: E 35 TRP cc_start: 0.8489 (m100) cc_final: 0.8169 (m100) REVERT: E 95 MET cc_start: 0.8751 (ppp) cc_final: 0.8198 (ppp) REVERT: E 128 THR cc_start: 0.9530 (m) cc_final: 0.8911 (t) REVERT: E 155 LYS cc_start: 0.8594 (mmmt) cc_final: 0.7111 (mmmt) REVERT: E 161 MET cc_start: 0.8965 (tpp) cc_final: 0.8558 (tpt) REVERT: E 377 ASN cc_start: 0.8544 (p0) cc_final: 0.8224 (p0) REVERT: E 475 MET cc_start: 0.8917 (mmm) cc_final: 0.8429 (mmm) REVERT: F 35 TRP cc_start: 0.8509 (m100) cc_final: 0.8212 (m100) REVERT: F 95 MET cc_start: 0.8816 (ppp) cc_final: 0.8319 (ppp) REVERT: F 102 GLU cc_start: 0.7417 (mp0) cc_final: 0.7200 (mp0) REVERT: F 161 MET cc_start: 0.9041 (tpp) cc_final: 0.8400 (tpt) REVERT: F 377 ASN cc_start: 0.8512 (p0) cc_final: 0.8201 (p0) REVERT: F 475 MET cc_start: 0.8902 (mmm) cc_final: 0.8280 (mmm) REVERT: G 95 MET cc_start: 0.8814 (ppp) cc_final: 0.8306 (ppp) REVERT: G 128 THR cc_start: 0.9579 (m) cc_final: 0.9142 (t) REVERT: G 155 LYS cc_start: 0.8602 (mmmt) cc_final: 0.7196 (mmmt) REVERT: G 161 MET cc_start: 0.9018 (tpp) cc_final: 0.7970 (tpt) REVERT: G 280 ASN cc_start: 0.7977 (p0) cc_final: 0.7497 (p0) REVERT: G 377 ASN cc_start: 0.8418 (p0) cc_final: 0.8179 (p0) REVERT: G 475 MET cc_start: 0.8774 (mmm) cc_final: 0.8257 (mmm) REVERT: H 50 VAL cc_start: 0.9085 (t) cc_final: 0.8722 (p) REVERT: H 72 GLU cc_start: 0.7487 (pm20) cc_final: 0.7049 (pm20) REVERT: H 91 TYR cc_start: 0.7949 (m-80) cc_final: 0.7744 (m-80) REVERT: H 100 TYR cc_start: 0.8582 (t80) cc_final: 0.8264 (t80) REVERT: H 101 ASP cc_start: 0.8076 (p0) cc_final: 0.7615 (p0) REVERT: H 103 TRP cc_start: 0.8917 (m100) cc_final: 0.8709 (m-10) REVERT: J 50 VAL cc_start: 0.8930 (t) cc_final: 0.8458 (p) REVERT: J 72 GLU cc_start: 0.7453 (pm20) cc_final: 0.6956 (pm20) REVERT: J 79 TYR cc_start: 0.7825 (m-10) cc_final: 0.7597 (m-80) REVERT: J 101 ASP cc_start: 0.7830 (p0) cc_final: 0.7123 (p0) REVERT: J 103 TRP cc_start: 0.8947 (m100) cc_final: 0.8734 (m-10) REVERT: K 24 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7110 (ttp80) REVERT: K 32 THR cc_start: 0.7814 (p) cc_final: 0.7199 (p) REVERT: K 39 GLN cc_start: 0.8249 (tp40) cc_final: 0.7744 (tp40) REVERT: L 32 THR cc_start: 0.7760 (p) cc_final: 0.7264 (p) REVERT: L 39 GLN cc_start: 0.8152 (tp40) cc_final: 0.7758 (tp40) REVERT: L 78 ARG cc_start: 0.7330 (mmt-90) cc_final: 0.6972 (mpt180) REVERT: M 50 VAL cc_start: 0.8974 (t) cc_final: 0.8575 (p) REVERT: M 82 MET cc_start: 0.7622 (mmm) cc_final: 0.7389 (tpt) REVERT: M 91 TYR cc_start: 0.7887 (m-80) cc_final: 0.7357 (m-80) REVERT: M 100 TYR cc_start: 0.8516 (t80) cc_final: 0.8098 (t80) REVERT: M 101 ASP cc_start: 0.8006 (p0) cc_final: 0.7535 (p0) REVERT: N 32 THR cc_start: 0.7902 (p) cc_final: 0.7440 (p) REVERT: N 34 LEU cc_start: 0.8885 (tt) cc_final: 0.7982 (tt) REVERT: N 39 GLN cc_start: 0.8146 (tp40) cc_final: 0.7594 (tp40) outliers start: 3 outliers final: 0 residues processed: 646 average time/residue: 0.1488 time to fit residues: 149.0483 Evaluate side-chains 432 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN B 630 GLN C 630 GLN C 650 GLN E 330 HIS E 478 ASN F 279 ASN F 330 HIS ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 330 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27DHIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105123 restraints weight = 36859.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105033 restraints weight = 31511.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106086 restraints weight = 27503.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106516 restraints weight = 24620.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106743 restraints weight = 22523.520| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20412 Z= 0.226 Angle : 0.753 11.556 27912 Z= 0.359 Chirality : 0.051 0.427 3366 Planarity : 0.004 0.045 3357 Dihedral : 11.487 86.203 4602 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.48 % Allowed : 6.30 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.18), residues: 2298 helix: 1.20 (0.26), residues: 390 sheet: -0.44 (0.20), residues: 645 loop : -1.50 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 327 TYR 0.026 0.002 TYR A 586 PHE 0.016 0.002 PHE F 223 TRP 0.019 0.002 TRP C 571 HIS 0.012 0.002 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (20271) covalent geometry : angle 0.69735 / 0.34 (27531) SS BOND : bond 0.00372 / 0.27 ( 42) SS BOND : angle 2.62016 / 1.85 ( 84) hydrogen bonds : bond 0.04093 / 2.89 ( 636) hydrogen bonds : angle 5.16069 / 3.68 ( 1800) link_ALPHA1-2 : bond 0.01355 / 0.67 ( 6) link_ALPHA1-2 : angle 1.07815 / 0.52 ( 18) link_ALPHA1-3 : bond 0.01065 / 0.65 ( 12) link_ALPHA1-3 : angle 1.94977 / 1.22 ( 36) link_ALPHA1-6 : bond 0.00293 / 0.18 ( 9) link_ALPHA1-6 : angle 1.32320 / 0.84 ( 27) link_BETA1-4 : bond 0.00348 / 0.23 ( 33) link_BETA1-4 : angle 1.89920 / 1.33 ( 99) link_NAG-ASN : bond 0.00588 / 0.37 ( 39) link_NAG-ASN : angle 3.33686 / 2.38 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 519 time to evaluate : 0.602 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: A 535 MET cc_start: 0.7241 (mmp) cc_final: 0.6658 (tpp) REVERT: A 536 THR cc_start: 0.8638 (p) cc_final: 0.7708 (p) REVERT: A 539 VAL cc_start: 0.9549 (t) cc_final: 0.9182 (p) REVERT: A 540 GLN cc_start: 0.8180 (mp10) cc_final: 0.7684 (mp10) REVERT: A 543 ASN cc_start: 0.8749 (m-40) cc_final: 0.8141 (t0) REVERT: A 584 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 596 TRP cc_start: 0.9132 (m-10) cc_final: 0.8877 (m-10) REVERT: A 649 SER cc_start: 0.8509 (p) cc_final: 0.8253 (p) REVERT: B 543 ASN cc_start: 0.8823 (m-40) cc_final: 0.8219 (t0) REVERT: B 584 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 647 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7309 (mt-10) REVERT: B 649 SER cc_start: 0.8477 (p) cc_final: 0.8254 (p) REVERT: C 536 THR cc_start: 0.8654 (p) cc_final: 0.7539 (p) REVERT: C 539 VAL cc_start: 0.9545 (t) cc_final: 0.9164 (p) REVERT: C 540 GLN cc_start: 0.8128 (mp10) cc_final: 0.7564 (mp10) REVERT: C 543 ASN cc_start: 0.8680 (m-40) cc_final: 0.8325 (t0) REVERT: E 161 MET cc_start: 0.8887 (tpp) cc_final: 0.8526 (tpt) REVERT: E 232 THR cc_start: 0.8832 (p) cc_final: 0.8559 (p) REVERT: E 294 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8198 (pt) REVERT: E 428 GLN cc_start: 0.8239 (mp10) cc_final: 0.7912 (mp10) REVERT: E 475 MET cc_start: 0.8832 (mmm) cc_final: 0.8574 (mmm) REVERT: F 161 MET cc_start: 0.8930 (tpp) cc_final: 0.8383 (tpt) REVERT: F 180 ASP cc_start: 0.8891 (m-30) cc_final: 0.8582 (m-30) REVERT: F 428 GLN cc_start: 0.8270 (mp10) cc_final: 0.7925 (mp10) REVERT: F 475 MET cc_start: 0.8788 (mmm) cc_final: 0.8448 (mmm) REVERT: G 161 MET cc_start: 0.8977 (tpp) cc_final: 0.8016 (tpt) REVERT: G 180 ASP cc_start: 0.8812 (m-30) cc_final: 0.8328 (m-30) REVERT: G 280 ASN cc_start: 0.8011 (p0) cc_final: 0.7688 (p0) REVERT: G 289 ASN cc_start: 0.9207 (p0) cc_final: 0.8893 (p0) REVERT: G 428 GLN cc_start: 0.8220 (mp10) cc_final: 0.7898 (mp10) REVERT: G 475 MET cc_start: 0.8658 (mmm) cc_final: 0.8205 (mmm) REVERT: H 27 LEU cc_start: 0.7565 (mt) cc_final: 0.7325 (mp) REVERT: H 50 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8891 (p) REVERT: H 77 THR cc_start: 0.6387 (p) cc_final: 0.5135 (p) REVERT: H 100 TYR cc_start: 0.8615 (t80) cc_final: 0.8303 (t80) REVERT: H 101 ASP cc_start: 0.8051 (p0) cc_final: 0.7649 (p0) REVERT: J 36 TRP cc_start: 0.8792 (m100) cc_final: 0.8316 (m100) REVERT: J 50 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8608 (p) REVERT: J 72 GLU cc_start: 0.7592 (pm20) cc_final: 0.7223 (pm20) REVERT: J 77 THR cc_start: 0.7172 (t) cc_final: 0.6702 (p) REVERT: J 79 TYR cc_start: 0.8074 (m-10) cc_final: 0.7854 (m-10) REVERT: J 100 TYR cc_start: 0.8401 (t80) cc_final: 0.8164 (t80) REVERT: K 24 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7462 (ttp80) REVERT: K 32 THR cc_start: 0.7821 (p) cc_final: 0.7348 (p) REVERT: K 43 GLN cc_start: 0.7109 (tp-100) cc_final: 0.6869 (mm-40) REVERT: K 48 LEU cc_start: 0.9267 (tp) cc_final: 0.9018 (tp) REVERT: K 104 LYS cc_start: 0.8367 (mtpp) cc_final: 0.7969 (tttt) REVERT: L 32 THR cc_start: 0.7700 (p) cc_final: 0.7209 (p) REVERT: L 43 GLN cc_start: 0.7131 (tp-100) cc_final: 0.6864 (mm-40) REVERT: M 27 LEU cc_start: 0.7584 (mt) cc_final: 0.7231 (mp) REVERT: M 50 VAL cc_start: 0.9222 (t) cc_final: 0.8879 (p) REVERT: M 100 TYR cc_start: 0.8615 (t80) cc_final: 0.8371 (t80) REVERT: M 101 ASP cc_start: 0.7908 (p0) cc_final: 0.7703 (p0) REVERT: N 32 THR cc_start: 0.8025 (p) cc_final: 0.7676 (p) outliers start: 10 outliers final: 2 residues processed: 526 average time/residue: 0.1201 time to fit residues: 101.5999 Evaluate side-chains 379 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 374 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 91 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 GLN A 650 GLN B 630 GLN B 650 GLN B 652 GLN C 590 GLN C 630 GLN C 652 GLN E 352 HIS E 386 ASN F 352 HIS F 386 ASN G 352 HIS G 386 ASN L 27DHIS N 27DHIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105396 restraints weight = 37152.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105960 restraints weight = 27297.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106870 restraints weight = 24139.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107277 restraints weight = 21664.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108190 restraints weight = 19942.478| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20412 Z= 0.164 Angle : 0.699 19.481 27912 Z= 0.332 Chirality : 0.050 0.528 3366 Planarity : 0.004 0.047 3357 Dihedral : 10.612 78.613 4602 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 2298 helix: 1.53 (0.27), residues: 375 sheet: -0.44 (0.20), residues: 672 loop : -1.46 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 327 TYR 0.036 0.002 TYR F 134 PHE 0.010 0.002 PHE G 159 TRP 0.022 0.001 TRP A 610 HIS 0.010 0.002 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (20271) covalent geometry : angle 0.63599 / 0.32 (27531) SS BOND : bond 0.00423 / 0.26 ( 42) SS BOND : angle 1.88463 / 1.26 ( 84) hydrogen bonds : bond 0.03863 / 2.75 ( 636) hydrogen bonds : angle 5.06684 / 3.64 ( 1800) link_ALPHA1-2 : bond 0.01135 / 0.56 ( 6) link_ALPHA1-2 : angle 0.85499 / 0.44 ( 18) link_ALPHA1-3 : bond 0.00910 / 0.54 ( 12) link_ALPHA1-3 : angle 1.53538 / 1.05 ( 36) link_ALPHA1-6 : bond 0.00327 / 0.20 ( 9) link_ALPHA1-6 : angle 1.17755 / 0.74 ( 27) link_BETA1-4 : bond 0.00375 / 0.25 ( 33) link_BETA1-4 : angle 1.65392 / 1.13 ( 99) link_NAG-ASN : bond 0.00634 / 0.37 ( 39) link_NAG-ASN : angle 3.90052 / 2.80 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 515 time to evaluate : 0.781 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 534 SER cc_start: 0.8178 (m) cc_final: 0.7950 (m) REVERT: A 536 THR cc_start: 0.8500 (p) cc_final: 0.7985 (p) REVERT: A 539 VAL cc_start: 0.9565 (t) cc_final: 0.9345 (p) REVERT: A 543 ASN cc_start: 0.8710 (m-40) cc_final: 0.7806 (t0) REVERT: A 584 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 603 ILE cc_start: 0.8950 (mm) cc_final: 0.8727 (mm) REVERT: A 649 SER cc_start: 0.8541 (p) cc_final: 0.8264 (p) REVERT: B 539 VAL cc_start: 0.9656 (t) cc_final: 0.9372 (p) REVERT: B 540 GLN cc_start: 0.8224 (mp-120) cc_final: 0.7908 (mp10) REVERT: B 543 ASN cc_start: 0.8848 (m-40) cc_final: 0.8209 (t0) REVERT: B 584 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 633 LYS cc_start: 0.9054 (mptt) cc_final: 0.8847 (mmtm) REVERT: C 536 THR cc_start: 0.8552 (p) cc_final: 0.7967 (p) REVERT: C 540 GLN cc_start: 0.8095 (mp10) cc_final: 0.7858 (mp10) REVERT: C 543 ASN cc_start: 0.8704 (m-40) cc_final: 0.8161 (t0) REVERT: C 633 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8603 (mmtm) REVERT: C 649 SER cc_start: 0.8638 (p) cc_final: 0.8372 (p) REVERT: E 95 MET cc_start: 0.8965 (ppp) cc_final: 0.8612 (ppp) REVERT: E 161 MET cc_start: 0.8901 (tpp) cc_final: 0.8528 (tpt) REVERT: E 294 ILE cc_start: 0.8350 (pt) cc_final: 0.8125 (pt) REVERT: E 428 GLN cc_start: 0.8304 (mp10) cc_final: 0.7958 (mp10) REVERT: F 95 MET cc_start: 0.8992 (ppp) cc_final: 0.8742 (ppp) REVERT: F 104 MET cc_start: 0.8849 (ttt) cc_final: 0.8521 (tpp) REVERT: F 161 MET cc_start: 0.8887 (tpp) cc_final: 0.8417 (tpt) REVERT: F 180 ASP cc_start: 0.8907 (m-30) cc_final: 0.8629 (m-30) REVERT: F 289 ASN cc_start: 0.9281 (p0) cc_final: 0.9010 (p0) REVERT: F 294 ILE cc_start: 0.8406 (pt) cc_final: 0.8131 (pt) REVERT: F 428 GLN cc_start: 0.8269 (mp10) cc_final: 0.7971 (mp10) REVERT: F 475 MET cc_start: 0.8827 (mmm) cc_final: 0.8417 (mmm) REVERT: G 161 MET cc_start: 0.8926 (tpp) cc_final: 0.8112 (tpt) REVERT: G 180 ASP cc_start: 0.8826 (m-30) cc_final: 0.8389 (m-30) REVERT: G 280 ASN cc_start: 0.7909 (p0) cc_final: 0.7652 (p0) REVERT: G 294 ILE cc_start: 0.8386 (pt) cc_final: 0.8118 (pt) REVERT: G 428 GLN cc_start: 0.8202 (mp10) cc_final: 0.7939 (mp10) REVERT: G 475 MET cc_start: 0.8606 (mmm) cc_final: 0.8038 (mmm) REVERT: H 27 LEU cc_start: 0.7660 (mt) cc_final: 0.7307 (mp) REVERT: H 50 VAL cc_start: 0.9261 (t) cc_final: 0.9005 (p) REVERT: H 100 TYR cc_start: 0.8646 (t80) cc_final: 0.8442 (t80) REVERT: H 101 ASP cc_start: 0.7878 (p0) cc_final: 0.7541 (p0) REVERT: J 50 VAL cc_start: 0.9137 (t) cc_final: 0.8807 (p) REVERT: J 72 GLU cc_start: 0.7588 (pm20) cc_final: 0.7287 (pm20) REVERT: J 100 TYR cc_start: 0.8548 (t80) cc_final: 0.8307 (t80) REVERT: J 101 ASP cc_start: 0.7995 (p0) cc_final: 0.7623 (p0) REVERT: K 24 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7301 (ttp80) REVERT: K 32 THR cc_start: 0.7997 (p) cc_final: 0.7624 (p) REVERT: K 43 GLN cc_start: 0.7208 (tp-100) cc_final: 0.6953 (mm-40) REVERT: K 69 ASP cc_start: 0.7822 (m-30) cc_final: 0.7512 (t0) REVERT: K 104 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8009 (tttt) REVERT: L 32 THR cc_start: 0.7839 (p) cc_final: 0.7557 (p) REVERT: L 43 GLN cc_start: 0.7175 (tp-100) cc_final: 0.6883 (mm-40) REVERT: L 69 ASP cc_start: 0.7887 (m-30) cc_final: 0.7528 (t0) REVERT: M 47 TRP cc_start: 0.8732 (t60) cc_final: 0.8289 (t60) REVERT: M 50 VAL cc_start: 0.9270 (t) cc_final: 0.8840 (p) REVERT: M 77 THR cc_start: 0.6337 (p) cc_final: 0.5085 (p) REVERT: M 79 TYR cc_start: 0.8367 (m-10) cc_final: 0.7548 (m-80) REVERT: M 82 MET cc_start: 0.7911 (mmm) cc_final: 0.7597 (tpt) REVERT: M 99 SER cc_start: 0.8524 (m) cc_final: 0.8206 (p) REVERT: M 100 TYR cc_start: 0.8662 (t80) cc_final: 0.8420 (t80) REVERT: M 101 ASP cc_start: 0.7859 (p0) cc_final: 0.7575 (p0) REVERT: N 5 THR cc_start: 0.6382 (p) cc_final: 0.6144 (p) REVERT: N 32 THR cc_start: 0.8159 (p) cc_final: 0.7788 (p) REVERT: N 43 GLN cc_start: 0.7402 (tp-100) cc_final: 0.7195 (mm-40) REVERT: N 104 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7949 (tttt) outliers start: 5 outliers final: 0 residues processed: 520 average time/residue: 0.1364 time to fit residues: 113.5172 Evaluate side-chains 395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN B 590 GLN B 630 GLN C 630 GLN E 352 HIS F 352 HIS G 352 HIS H 81 GLN L 27DHIS N 27DHIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100575 restraints weight = 37265.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.101415 restraints weight = 26997.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102284 restraints weight = 23410.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103126 restraints weight = 20203.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103258 restraints weight = 18463.962| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20412 Z= 0.177 Angle : 0.730 19.625 27912 Z= 0.342 Chirality : 0.051 0.613 3366 Planarity : 0.004 0.046 3357 Dihedral : 9.772 69.442 4602 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2298 helix: 1.47 (0.27), residues: 375 sheet: -0.37 (0.20), residues: 639 loop : -1.58 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.025 0.002 TYR L 95 PHE 0.013 0.002 PHE F 159 TRP 0.021 0.002 TRP B 610 HIS 0.005 0.002 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (20271) covalent geometry : angle 0.66374 / 0.33 (27531) SS BOND : bond 0.00306 / 0.21 ( 42) SS BOND : angle 1.67979 / 1.16 ( 84) hydrogen bonds : bond 0.03802 / 2.68 ( 636) hydrogen bonds : angle 5.06282 / 3.62 ( 1800) link_ALPHA1-2 : bond 0.01180 / 0.58 ( 6) link_ALPHA1-2 : angle 0.89735 / 0.45 ( 18) link_ALPHA1-3 : bond 0.00993 / 0.59 ( 12) link_ALPHA1-3 : angle 1.59694 / 1.04 ( 36) link_ALPHA1-6 : bond 0.00458 / 0.27 ( 9) link_ALPHA1-6 : angle 1.23134 / 0.79 ( 27) link_BETA1-4 : bond 0.00358 / 0.24 ( 33) link_BETA1-4 : angle 1.70298 / 1.17 ( 99) link_NAG-ASN : bond 0.00640 / 0.36 ( 39) link_NAG-ASN : angle 4.20589 / 2.90 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 523 time to evaluate : 0.956 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 534 SER cc_start: 0.8209 (m) cc_final: 0.8005 (m) REVERT: A 543 ASN cc_start: 0.8798 (m-40) cc_final: 0.7805 (t0) REVERT: A 584 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 647 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6287 (mt-10) REVERT: B 535 MET cc_start: 0.6736 (mmm) cc_final: 0.6382 (tpp) REVERT: B 536 THR cc_start: 0.8784 (p) cc_final: 0.8059 (p) REVERT: B 539 VAL cc_start: 0.9668 (t) cc_final: 0.9357 (p) REVERT: B 540 GLN cc_start: 0.8137 (mp10) cc_final: 0.7613 (mp10) REVERT: B 542 ARG cc_start: 0.8319 (tpt-90) cc_final: 0.8093 (ttp-170) REVERT: B 543 ASN cc_start: 0.8916 (m-40) cc_final: 0.8226 (t0) REVERT: B 584 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 633 LYS cc_start: 0.9134 (mptt) cc_final: 0.8874 (mmtm) REVERT: B 647 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6937 (mt-10) REVERT: C 536 THR cc_start: 0.8671 (p) cc_final: 0.8065 (p) REVERT: C 540 GLN cc_start: 0.8082 (mp10) cc_final: 0.7833 (mp10) REVERT: C 543 ASN cc_start: 0.8847 (m-40) cc_final: 0.8331 (t0) REVERT: C 633 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8643 (mmtm) REVERT: E 35 TRP cc_start: 0.8473 (m100) cc_final: 0.8050 (m100) REVERT: E 161 MET cc_start: 0.8876 (tpp) cc_final: 0.8542 (tpt) REVERT: E 294 ILE cc_start: 0.8364 (pt) cc_final: 0.8028 (pt) REVERT: E 426 MET cc_start: 0.6945 (ptp) cc_final: 0.6461 (mtm) REVERT: E 428 GLN cc_start: 0.8411 (mp10) cc_final: 0.8053 (mp10) REVERT: F 104 MET cc_start: 0.8917 (ttt) cc_final: 0.8517 (tpp) REVERT: F 161 MET cc_start: 0.8847 (tpp) cc_final: 0.8473 (tpt) REVERT: F 180 ASP cc_start: 0.8960 (m-30) cc_final: 0.8618 (m-30) REVERT: F 289 ASN cc_start: 0.9301 (p0) cc_final: 0.9060 (p0) REVERT: F 294 ILE cc_start: 0.8390 (pt) cc_final: 0.7981 (pt) REVERT: F 428 GLN cc_start: 0.8280 (mp10) cc_final: 0.8021 (mp10) REVERT: G 104 MET cc_start: 0.8967 (ttt) cc_final: 0.8555 (tpp) REVERT: G 161 MET cc_start: 0.8895 (tpp) cc_final: 0.8160 (tpt) REVERT: G 180 ASP cc_start: 0.8841 (m-30) cc_final: 0.8328 (m-30) REVERT: G 280 ASN cc_start: 0.7971 (p0) cc_final: 0.7767 (p0) REVERT: G 294 ILE cc_start: 0.8425 (pt) cc_final: 0.8020 (pt) REVERT: G 428 GLN cc_start: 0.8200 (mp10) cc_final: 0.7971 (mp10) REVERT: G 475 MET cc_start: 0.8499 (mmm) cc_final: 0.7894 (mmm) REVERT: H 27 LEU cc_start: 0.7862 (mt) cc_final: 0.7372 (mp) REVERT: H 50 VAL cc_start: 0.9228 (t) cc_final: 0.8932 (p) REVERT: H 101 ASP cc_start: 0.7942 (p0) cc_final: 0.7583 (p0) REVERT: J 50 VAL cc_start: 0.9225 (t) cc_final: 0.8879 (p) REVERT: J 72 GLU cc_start: 0.7801 (pm20) cc_final: 0.7385 (pm20) REVERT: J 79 TYR cc_start: 0.8187 (m-80) cc_final: 0.7946 (m-10) REVERT: J 82 MET cc_start: 0.7790 (tpt) cc_final: 0.7558 (tpt) REVERT: J 101 ASP cc_start: 0.8179 (p0) cc_final: 0.7894 (p0) REVERT: K 23 CYS cc_start: 0.4242 (t) cc_final: 0.3516 (t) REVERT: K 24 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7321 (ttp80) REVERT: K 32 THR cc_start: 0.8091 (p) cc_final: 0.7769 (p) REVERT: K 43 GLN cc_start: 0.7412 (tp-100) cc_final: 0.7151 (mm-40) REVERT: K 66 SER cc_start: 0.7218 (t) cc_final: 0.6840 (m) REVERT: K 69 ASP cc_start: 0.7919 (m-30) cc_final: 0.7455 (t0) REVERT: K 104 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8009 (tttt) REVERT: L 32 THR cc_start: 0.8088 (p) cc_final: 0.7697 (p) REVERT: L 43 GLN cc_start: 0.7504 (tp-100) cc_final: 0.7163 (mm-40) REVERT: L 48 LEU cc_start: 0.9222 (tp) cc_final: 0.8971 (tp) REVERT: L 69 ASP cc_start: 0.7995 (m-30) cc_final: 0.7627 (t0) REVERT: M 27 LEU cc_start: 0.8049 (mt) cc_final: 0.7652 (mp) REVERT: M 50 VAL cc_start: 0.9277 (t) cc_final: 0.8910 (p) REVERT: M 72 GLU cc_start: 0.7955 (pm20) cc_final: 0.7730 (pm20) REVERT: M 82 MET cc_start: 0.8031 (mmm) cc_final: 0.7631 (tpt) REVERT: M 99 SER cc_start: 0.8657 (m) cc_final: 0.8156 (p) REVERT: M 100 TYR cc_start: 0.8676 (t80) cc_final: 0.8454 (t80) REVERT: M 100 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8337 (mm-30) REVERT: N 32 THR cc_start: 0.8265 (p) cc_final: 0.7898 (p) REVERT: N 43 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7348 (mm-40) REVERT: N 48 LEU cc_start: 0.9326 (tp) cc_final: 0.9114 (tp) outliers start: 3 outliers final: 0 residues processed: 526 average time/residue: 0.1416 time to fit residues: 118.0320 Evaluate side-chains 413 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 83 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 chunk 172 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN C 630 GLN ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS L 27DHIS N 27DHIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103696 restraints weight = 37026.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105529 restraints weight = 26536.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106190 restraints weight = 22163.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107183 restraints weight = 19673.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107275 restraints weight = 18242.100| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20412 Z= 0.153 Angle : 0.708 15.226 27912 Z= 0.335 Chirality : 0.050 0.449 3366 Planarity : 0.004 0.047 3357 Dihedral : 9.214 63.800 4602 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 2298 helix: 1.59 (0.27), residues: 375 sheet: -0.36 (0.20), residues: 669 loop : -1.61 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 55 TYR 0.030 0.002 TYR E 134 PHE 0.011 0.001 PHE F 159 TRP 0.019 0.001 TRP A 610 HIS 0.005 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (20271) covalent geometry : angle 0.64613 / 0.32 (27531) SS BOND : bond 0.00364 / 0.23 ( 42) SS BOND : angle 2.11805 / 1.45 ( 84) hydrogen bonds : bond 0.03676 / 2.59 ( 636) hydrogen bonds : angle 5.00524 / 3.59 ( 1800) link_ALPHA1-2 : bond 0.01089 / 0.54 ( 6) link_ALPHA1-2 : angle 0.91558 / 0.48 ( 18) link_ALPHA1-3 : bond 0.01036 / 0.62 ( 12) link_ALPHA1-3 : angle 1.51491 / 1.02 ( 36) link_ALPHA1-6 : bond 0.00531 / 0.31 ( 9) link_ALPHA1-6 : angle 1.24501 / 0.80 ( 27) link_BETA1-4 : bond 0.00376 / 0.26 ( 33) link_BETA1-4 : angle 1.68519 / 1.16 ( 99) link_NAG-ASN : bond 0.00495 / 0.28 ( 39) link_NAG-ASN : angle 3.81313 / 2.66 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 515 time to evaluate : 0.764 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.6664 (mmp) cc_final: 0.6353 (tpp) REVERT: A 539 VAL cc_start: 0.9624 (t) cc_final: 0.9334 (p) REVERT: A 543 ASN cc_start: 0.8774 (m-40) cc_final: 0.7885 (t0) REVERT: A 584 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 596 TRP cc_start: 0.8912 (m-10) cc_final: 0.8704 (m-10) REVERT: A 649 SER cc_start: 0.8604 (p) cc_final: 0.8362 (p) REVERT: B 535 MET cc_start: 0.6718 (mmm) cc_final: 0.6334 (tpp) REVERT: B 536 THR cc_start: 0.8792 (p) cc_final: 0.7926 (p) REVERT: B 539 VAL cc_start: 0.9664 (t) cc_final: 0.9360 (p) REVERT: B 540 GLN cc_start: 0.8173 (mp10) cc_final: 0.7600 (mp10) REVERT: B 543 ASN cc_start: 0.8912 (m-40) cc_final: 0.8230 (t0) REVERT: B 584 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 647 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6854 (mt-10) REVERT: C 536 THR cc_start: 0.8637 (p) cc_final: 0.8114 (p) REVERT: C 540 GLN cc_start: 0.8081 (mp10) cc_final: 0.7775 (mp10) REVERT: C 543 ASN cc_start: 0.8798 (m-40) cc_final: 0.8258 (t0) REVERT: C 633 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8658 (mmtm) REVERT: C 649 SER cc_start: 0.8681 (p) cc_final: 0.8481 (p) REVERT: E 35 TRP cc_start: 0.8471 (m100) cc_final: 0.8232 (m100) REVERT: E 114 GLN cc_start: 0.8567 (tt0) cc_final: 0.8349 (tt0) REVERT: E 161 MET cc_start: 0.8831 (tpp) cc_final: 0.8531 (tpt) REVERT: E 428 GLN cc_start: 0.8359 (mp10) cc_final: 0.8033 (mp10) REVERT: F 104 MET cc_start: 0.8894 (ttt) cc_final: 0.8544 (tpp) REVERT: F 161 MET cc_start: 0.8798 (tpp) cc_final: 0.8474 (tpt) REVERT: F 180 ASP cc_start: 0.8943 (m-30) cc_final: 0.8547 (m-30) REVERT: F 294 ILE cc_start: 0.8272 (pt) cc_final: 0.7892 (pt) REVERT: F 428 GLN cc_start: 0.8295 (mp10) cc_final: 0.7987 (mp10) REVERT: G 104 MET cc_start: 0.8922 (ttt) cc_final: 0.8645 (tmm) REVERT: G 161 MET cc_start: 0.8875 (tpp) cc_final: 0.8170 (tpt) REVERT: G 180 ASP cc_start: 0.8821 (m-30) cc_final: 0.8268 (m-30) REVERT: G 280 ASN cc_start: 0.8004 (p0) cc_final: 0.7789 (p0) REVERT: G 428 GLN cc_start: 0.8218 (mp10) cc_final: 0.7959 (mp10) REVERT: H 50 VAL cc_start: 0.9217 (t) cc_final: 0.8951 (p) REVERT: H 82 MET cc_start: 0.7327 (tpp) cc_final: 0.7106 (mmt) REVERT: H 101 ASP cc_start: 0.8020 (p0) cc_final: 0.7791 (p0) REVERT: J 45 LEU cc_start: 0.8121 (pt) cc_final: 0.7710 (pt) REVERT: J 47 TRP cc_start: 0.8664 (t60) cc_final: 0.8153 (t60) REVERT: J 50 VAL cc_start: 0.9263 (t) cc_final: 0.8870 (p) REVERT: J 72 GLU cc_start: 0.7763 (pm20) cc_final: 0.7323 (pm20) REVERT: J 79 TYR cc_start: 0.8135 (m-80) cc_final: 0.7912 (m-10) REVERT: J 100 TYR cc_start: 0.8677 (t80) cc_final: 0.8465 (t80) REVERT: K 23 CYS cc_start: 0.4231 (t) cc_final: 0.3534 (t) REVERT: K 24 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7372 (ttp80) REVERT: K 32 THR cc_start: 0.8088 (p) cc_final: 0.7746 (p) REVERT: K 39 GLN cc_start: 0.7987 (tp40) cc_final: 0.7437 (tp40) REVERT: K 43 GLN cc_start: 0.7454 (tp-100) cc_final: 0.7142 (mm-40) REVERT: K 66 SER cc_start: 0.7268 (t) cc_final: 0.6920 (m) REVERT: K 69 ASP cc_start: 0.7996 (m-30) cc_final: 0.7463 (t0) REVERT: K 89 CYS cc_start: 0.6308 (p) cc_final: 0.6101 (p) REVERT: K 104 LYS cc_start: 0.8461 (mtpp) cc_final: 0.7986 (tttt) REVERT: L 32 THR cc_start: 0.8192 (p) cc_final: 0.7709 (p) REVERT: L 43 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7187 (mm-40) REVERT: L 48 LEU cc_start: 0.9245 (tp) cc_final: 0.8986 (tp) REVERT: L 55 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7238 (mpp80) REVERT: L 69 ASP cc_start: 0.7946 (m-30) cc_final: 0.7436 (t0) REVERT: M 50 VAL cc_start: 0.9260 (t) cc_final: 0.8902 (p) REVERT: M 72 GLU cc_start: 0.7891 (pm20) cc_final: 0.7566 (pm20) REVERT: M 82 MET cc_start: 0.8014 (mmm) cc_final: 0.7613 (tpt) REVERT: M 99 SER cc_start: 0.8843 (m) cc_final: 0.8371 (p) REVERT: M 100 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8369 (mm-30) REVERT: M 101 ASP cc_start: 0.8020 (p0) cc_final: 0.7772 (p0) REVERT: N 32 THR cc_start: 0.8384 (p) cc_final: 0.7992 (p) REVERT: N 43 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7301 (mm-40) outliers start: 2 outliers final: 0 residues processed: 517 average time/residue: 0.1336 time to fit residues: 110.0119 Evaluate side-chains 407 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 118 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN B 630 GLN C 630 GLN E 258 GLN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27DHIS N 27DHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102857 restraints weight = 36877.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104063 restraints weight = 27451.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104706 restraints weight = 22380.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.105235 restraints weight = 20489.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105707 restraints weight = 19062.897| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20412 Z= 0.153 Angle : 0.698 14.360 27912 Z= 0.330 Chirality : 0.049 0.435 3366 Planarity : 0.004 0.047 3357 Dihedral : 8.792 57.738 4602 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2298 helix: 1.65 (0.28), residues: 375 sheet: -0.35 (0.20), residues: 663 loop : -1.62 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 55 TYR 0.026 0.002 TYR J 32 PHE 0.015 0.001 PHE E 53 TRP 0.019 0.001 TRP E 45 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (20271) covalent geometry : angle 0.64143 / 0.32 (27531) SS BOND : bond 0.00386 / 0.24 ( 42) SS BOND : angle 1.75985 / 1.22 ( 84) hydrogen bonds : bond 0.03733 / 2.65 ( 636) hydrogen bonds : angle 4.99540 / 3.58 ( 1800) link_ALPHA1-2 : bond 0.01102 / 0.54 ( 6) link_ALPHA1-2 : angle 0.88659 / 0.46 ( 18) link_ALPHA1-3 : bond 0.01035 / 0.62 ( 12) link_ALPHA1-3 : angle 1.51553 / 1.01 ( 36) link_ALPHA1-6 : bond 0.00565 / 0.33 ( 9) link_ALPHA1-6 : angle 1.23006 / 0.79 ( 27) link_BETA1-4 : bond 0.00375 / 0.26 ( 33) link_BETA1-4 : angle 1.67743 / 1.16 ( 99) link_NAG-ASN : bond 0.00518 / 0.29 ( 39) link_NAG-ASN : angle 3.71354 / 2.58 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 0.739 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.6523 (mmp) cc_final: 0.6303 (tpp) REVERT: A 536 THR cc_start: 0.8548 (p) cc_final: 0.8345 (p) REVERT: A 543 ASN cc_start: 0.8767 (m-40) cc_final: 0.7895 (t0) REVERT: A 596 TRP cc_start: 0.8915 (m-10) cc_final: 0.8683 (m-10) REVERT: A 647 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6465 (mt-10) REVERT: B 535 MET cc_start: 0.6725 (mmm) cc_final: 0.6356 (tpp) REVERT: B 536 THR cc_start: 0.8742 (p) cc_final: 0.7959 (p) REVERT: B 539 VAL cc_start: 0.9664 (t) cc_final: 0.9277 (p) REVERT: B 540 GLN cc_start: 0.8144 (mp10) cc_final: 0.7375 (mp10) REVERT: B 542 ARG cc_start: 0.8327 (tpt-90) cc_final: 0.7790 (ttp-170) REVERT: B 543 ASN cc_start: 0.8924 (m-40) cc_final: 0.8222 (t0) REVERT: B 584 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 536 THR cc_start: 0.8606 (p) cc_final: 0.8072 (p) REVERT: C 540 GLN cc_start: 0.7985 (mp10) cc_final: 0.7681 (mp10) REVERT: C 543 ASN cc_start: 0.8766 (m-40) cc_final: 0.8252 (t0) REVERT: C 633 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8680 (mmtm) REVERT: E 35 TRP cc_start: 0.8484 (m100) cc_final: 0.8280 (m100) REVERT: E 114 GLN cc_start: 0.8562 (tt0) cc_final: 0.8334 (tt0) REVERT: E 161 MET cc_start: 0.8878 (tpp) cc_final: 0.8574 (tpt) REVERT: E 426 MET cc_start: 0.6992 (ptp) cc_final: 0.6476 (mtm) REVERT: E 428 GLN cc_start: 0.8383 (mp10) cc_final: 0.8062 (mp10) REVERT: F 104 MET cc_start: 0.8949 (ttt) cc_final: 0.8524 (tpp) REVERT: F 161 MET cc_start: 0.8772 (tpp) cc_final: 0.8479 (tpt) REVERT: F 180 ASP cc_start: 0.8931 (m-30) cc_final: 0.8535 (m-30) REVERT: F 294 ILE cc_start: 0.8306 (pt) cc_final: 0.8021 (pt) REVERT: F 428 GLN cc_start: 0.8292 (mp10) cc_final: 0.7953 (mp10) REVERT: G 104 MET cc_start: 0.8957 (ttt) cc_final: 0.8639 (tmm) REVERT: G 161 MET cc_start: 0.8891 (tpp) cc_final: 0.8357 (tpt) REVERT: G 180 ASP cc_start: 0.8821 (m-30) cc_final: 0.8404 (m-30) REVERT: G 280 ASN cc_start: 0.7980 (p0) cc_final: 0.7763 (p0) REVERT: G 428 GLN cc_start: 0.8190 (mp10) cc_final: 0.7976 (mp10) REVERT: H 47 TRP cc_start: 0.8802 (t60) cc_final: 0.8517 (t60) REVERT: H 50 VAL cc_start: 0.9263 (t) cc_final: 0.8950 (p) REVERT: H 100 TYR cc_start: 0.8653 (t80) cc_final: 0.8436 (t80) REVERT: J 45 LEU cc_start: 0.8107 (pt) cc_final: 0.7671 (pt) REVERT: J 50 VAL cc_start: 0.9235 (t) cc_final: 0.8837 (p) REVERT: J 72 GLU cc_start: 0.7783 (pm20) cc_final: 0.7364 (pm20) REVERT: J 79 TYR cc_start: 0.8153 (m-80) cc_final: 0.7904 (m-10) REVERT: J 100 TYR cc_start: 0.8673 (t80) cc_final: 0.8455 (t80) REVERT: J 101 ASP cc_start: 0.8035 (p0) cc_final: 0.7770 (p0) REVERT: K 23 CYS cc_start: 0.4313 (t) cc_final: 0.3548 (t) REVERT: K 24 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7336 (ttp80) REVERT: K 32 THR cc_start: 0.8124 (p) cc_final: 0.7814 (p) REVERT: K 39 GLN cc_start: 0.7925 (tp40) cc_final: 0.7439 (tp-100) REVERT: K 43 GLN cc_start: 0.7538 (tp-100) cc_final: 0.7194 (mm-40) REVERT: K 48 LEU cc_start: 0.9373 (tp) cc_final: 0.9165 (tp) REVERT: K 104 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8006 (tttt) REVERT: L 32 THR cc_start: 0.8112 (p) cc_final: 0.7839 (p) REVERT: L 43 GLN cc_start: 0.7582 (tp-100) cc_final: 0.7237 (mm-40) REVERT: L 55 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7279 (mpp80) REVERT: L 66 SER cc_start: 0.7282 (t) cc_final: 0.6938 (m) REVERT: L 69 ASP cc_start: 0.7938 (m-30) cc_final: 0.7594 (t0) REVERT: M 30 SER cc_start: 0.6501 (p) cc_final: 0.6030 (p) REVERT: M 50 VAL cc_start: 0.9260 (t) cc_final: 0.8918 (p) REVERT: M 72 GLU cc_start: 0.7806 (pm20) cc_final: 0.7285 (pm20) REVERT: M 77 THR cc_start: 0.6438 (p) cc_final: 0.6037 (p) REVERT: M 99 SER cc_start: 0.8710 (m) cc_final: 0.8360 (p) REVERT: M 100 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8382 (mm-30) REVERT: M 101 ASP cc_start: 0.8120 (p0) cc_final: 0.7680 (p0) REVERT: N 32 THR cc_start: 0.8381 (p) cc_final: 0.8012 (p) REVERT: N 43 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7326 (mm-40) REVERT: N 48 LEU cc_start: 0.9299 (tp) cc_final: 0.9099 (tp) REVERT: N 66 SER cc_start: 0.7301 (t) cc_final: 0.6929 (m) outliers start: 2 outliers final: 0 residues processed: 503 average time/residue: 0.1309 time to fit residues: 104.4341 Evaluate side-chains 411 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 224 optimal weight: 0.4980 chunk 29 optimal weight: 0.0870 chunk 181 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 155 optimal weight: 0.0370 chunk 76 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN B 652 GLN C 630 GLN E 352 HIS G 258 GLN L 27DHIS N 27DHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106299 restraints weight = 36948.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108018 restraints weight = 26331.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108878 restraints weight = 21697.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110058 restraints weight = 18897.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110205 restraints weight = 17435.104| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20412 Z= 0.119 Angle : 0.687 15.783 27912 Z= 0.324 Chirality : 0.049 0.416 3366 Planarity : 0.004 0.048 3357 Dihedral : 8.163 59.626 4602 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2298 helix: 1.87 (0.28), residues: 375 sheet: -0.44 (0.20), residues: 672 loop : -1.55 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 71 TYR 0.031 0.001 TYR M 32 PHE 0.017 0.001 PHE E 53 TRP 0.033 0.001 TRP B 610 HIS 0.007 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20271) covalent geometry : angle 0.63374 / 0.31 (27531) SS BOND : bond 0.00376 / 0.22 ( 42) SS BOND : angle 1.69018 / 1.12 ( 84) hydrogen bonds : bond 0.03521 / 2.48 ( 636) hydrogen bonds : angle 4.92910 / 3.54 ( 1800) link_ALPHA1-2 : bond 0.00998 / 0.49 ( 6) link_ALPHA1-2 : angle 0.98971 / 0.53 ( 18) link_ALPHA1-3 : bond 0.01108 / 0.66 ( 12) link_ALPHA1-3 : angle 1.39780 / 0.97 ( 36) link_ALPHA1-6 : bond 0.00611 / 0.36 ( 9) link_ALPHA1-6 : angle 1.12521 / 0.74 ( 27) link_BETA1-4 : bond 0.00449 / 0.30 ( 33) link_BETA1-4 : angle 1.66334 / 1.16 ( 99) link_NAG-ASN : bond 0.00563 / 0.33 ( 39) link_NAG-ASN : angle 3.55864 / 2.48 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 0.671 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 539 VAL cc_start: 0.9584 (t) cc_final: 0.9300 (p) REVERT: A 543 ASN cc_start: 0.8731 (m-40) cc_final: 0.7914 (t0) REVERT: A 647 GLU cc_start: 0.7709 (mt-10) cc_final: 0.6320 (mt-10) REVERT: B 535 MET cc_start: 0.6705 (mmm) cc_final: 0.6310 (tpp) REVERT: B 536 THR cc_start: 0.8701 (p) cc_final: 0.8211 (p) REVERT: B 540 GLN cc_start: 0.8139 (mp10) cc_final: 0.7768 (mp10) REVERT: B 542 ARG cc_start: 0.8287 (tpt-90) cc_final: 0.7772 (ttp-170) REVERT: B 543 ASN cc_start: 0.8920 (m-40) cc_final: 0.8220 (t0) REVERT: B 596 TRP cc_start: 0.8919 (m-10) cc_final: 0.8639 (m-10) REVERT: C 535 MET cc_start: 0.6546 (tpp) cc_final: 0.5730 (tpp) REVERT: C 536 THR cc_start: 0.8567 (p) cc_final: 0.8130 (p) REVERT: C 540 GLN cc_start: 0.7925 (mp10) cc_final: 0.7688 (mp10) REVERT: C 633 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8792 (mptt) REVERT: E 35 TRP cc_start: 0.8448 (m100) cc_final: 0.8201 (m100) REVERT: E 161 MET cc_start: 0.8805 (tpp) cc_final: 0.8559 (tpt) REVERT: E 428 GLN cc_start: 0.8306 (mp10) cc_final: 0.8029 (mp10) REVERT: F 35 TRP cc_start: 0.8252 (m100) cc_final: 0.7926 (m100) REVERT: F 104 MET cc_start: 0.8842 (ttt) cc_final: 0.8230 (tpp) REVERT: F 161 MET cc_start: 0.8722 (tpp) cc_final: 0.8463 (tpt) REVERT: F 173 TYR cc_start: 0.7527 (m-80) cc_final: 0.7311 (m-80) REVERT: F 180 ASP cc_start: 0.8900 (m-30) cc_final: 0.8504 (m-30) REVERT: F 217 TYR cc_start: 0.8966 (m-10) cc_final: 0.7740 (m-10) REVERT: F 428 GLN cc_start: 0.8250 (mp10) cc_final: 0.7966 (mp10) REVERT: F 486 TYR cc_start: 0.9335 (m-80) cc_final: 0.8980 (m-10) REVERT: G 104 MET cc_start: 0.8891 (ttt) cc_final: 0.8448 (tmm) REVERT: G 161 MET cc_start: 0.8821 (tpp) cc_final: 0.8511 (tpt) REVERT: G 180 ASP cc_start: 0.8782 (m-30) cc_final: 0.8224 (m-30) REVERT: G 217 TYR cc_start: 0.8960 (m-10) cc_final: 0.8396 (m-10) REVERT: G 238 PRO cc_start: 0.8851 (Cg_endo) cc_final: 0.8573 (Cg_exo) REVERT: G 280 ASN cc_start: 0.7959 (p0) cc_final: 0.7642 (p0) REVERT: G 428 GLN cc_start: 0.8132 (mp10) cc_final: 0.7925 (mp10) REVERT: G 475 MET cc_start: 0.8434 (mmm) cc_final: 0.8152 (mmm) REVERT: H 50 VAL cc_start: 0.9268 (t) cc_final: 0.9057 (p) REVERT: H 72 GLU cc_start: 0.7912 (pm20) cc_final: 0.7296 (pm20) REVERT: H 79 TYR cc_start: 0.8038 (m-10) cc_final: 0.7706 (m-80) REVERT: H 100 TYR cc_start: 0.8630 (t80) cc_final: 0.8391 (t80) REVERT: H 101 ASP cc_start: 0.8025 (p0) cc_final: 0.7602 (p0) REVERT: J 45 LEU cc_start: 0.8064 (pt) cc_final: 0.7621 (pt) REVERT: J 50 VAL cc_start: 0.9209 (t) cc_final: 0.8856 (p) REVERT: J 72 GLU cc_start: 0.7819 (pm20) cc_final: 0.7386 (pm20) REVERT: J 79 TYR cc_start: 0.8152 (m-80) cc_final: 0.7909 (m-10) REVERT: K 23 CYS cc_start: 0.4259 (t) cc_final: 0.3620 (t) REVERT: K 24 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7280 (ttp80) REVERT: K 32 THR cc_start: 0.8159 (p) cc_final: 0.7741 (p) REVERT: K 39 GLN cc_start: 0.7914 (tp40) cc_final: 0.7458 (tp-100) REVERT: K 43 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7097 (mm-40) REVERT: K 69 ASP cc_start: 0.7688 (m-30) cc_final: 0.7467 (t0) REVERT: K 104 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7982 (tttt) REVERT: L 32 THR cc_start: 0.8031 (p) cc_final: 0.7643 (p) REVERT: L 55 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7232 (mpp80) REVERT: L 69 ASP cc_start: 0.7839 (m-30) cc_final: 0.7496 (t0) REVERT: M 50 VAL cc_start: 0.9258 (t) cc_final: 0.8901 (p) REVERT: M 101 ASP cc_start: 0.8123 (p0) cc_final: 0.7696 (p0) REVERT: N 5 THR cc_start: 0.6904 (p) cc_final: 0.6470 (p) REVERT: N 32 THR cc_start: 0.8207 (p) cc_final: 0.7816 (p) REVERT: N 43 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7352 (mm-40) REVERT: N 48 LEU cc_start: 0.9268 (tp) cc_final: 0.9048 (tp) REVERT: N 91 GLN cc_start: 0.9193 (pp30) cc_final: 0.8863 (pp30) outliers start: 2 outliers final: 0 residues processed: 504 average time/residue: 0.1277 time to fit residues: 102.4457 Evaluate side-chains 405 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 133 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 GLN B 575 GLN B 590 GLN B 630 GLN C 575 GLN C 630 GLN C 652 GLN E 352 HIS E 377 ASN F 352 HIS G 352 HIS L 27DHIS N 27DHIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102412 restraints weight = 37126.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104258 restraints weight = 28123.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105012 restraints weight = 22012.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105979 restraints weight = 20363.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106002 restraints weight = 18345.672| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 20412 Z= 0.174 Angle : 0.724 14.174 27912 Z= 0.346 Chirality : 0.049 0.432 3366 Planarity : 0.004 0.048 3357 Dihedral : 7.539 56.534 4602 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.24 % Allowed : 1.36 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2298 helix: 1.67 (0.28), residues: 372 sheet: -0.24 (0.21), residues: 633 loop : -1.61 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 55 TYR 0.020 0.002 TYR L 95 PHE 0.013 0.002 PHE F 353 TRP 0.028 0.002 TRP F 45 HIS 0.011 0.002 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (20271) covalent geometry : angle 0.66418 / 0.33 (27531) SS BOND : bond 0.00493 / 0.31 ( 42) SS BOND : angle 2.25924 / 1.50 ( 84) hydrogen bonds : bond 0.03775 / 2.65 ( 636) hydrogen bonds : angle 5.00187 / 3.59 ( 1800) link_ALPHA1-2 : bond 0.01069 / 0.53 ( 6) link_ALPHA1-2 : angle 0.91499 / 0.48 ( 18) link_ALPHA1-3 : bond 0.00912 / 0.55 ( 12) link_ALPHA1-3 : angle 1.66777 / 1.08 ( 36) link_ALPHA1-6 : bond 0.00493 / 0.29 ( 9) link_ALPHA1-6 : angle 1.06814 / 0.65 ( 27) link_BETA1-4 : bond 0.00409 / 0.28 ( 33) link_BETA1-4 : angle 1.84132 / 1.27 ( 99) link_NAG-ASN : bond 0.00526 / 0.29 ( 39) link_NAG-ASN : angle 3.65950 / 2.54 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 481 time to evaluate : 0.744 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 543 ASN cc_start: 0.8823 (m-40) cc_final: 0.7967 (t0) REVERT: A 584 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 647 GLU cc_start: 0.7848 (mt-10) cc_final: 0.6328 (mt-10) REVERT: B 535 MET cc_start: 0.6783 (mmm) cc_final: 0.6348 (tpp) REVERT: B 542 ARG cc_start: 0.8358 (tpt-90) cc_final: 0.7828 (ttp-170) REVERT: B 543 ASN cc_start: 0.8953 (m-40) cc_final: 0.8214 (t0) REVERT: B 584 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7600 (tm-30) REVERT: C 536 THR cc_start: 0.8624 (p) cc_final: 0.8197 (p) REVERT: C 540 GLN cc_start: 0.8031 (mp10) cc_final: 0.7766 (mp10) REVERT: C 633 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8745 (mptt) REVERT: E 35 TRP cc_start: 0.8502 (m100) cc_final: 0.8256 (m100) REVERT: E 161 MET cc_start: 0.8845 (tpp) cc_final: 0.8581 (tpt) REVERT: E 428 GLN cc_start: 0.8390 (mp10) cc_final: 0.8080 (mp10) REVERT: F 66 HIS cc_start: 0.6389 (p-80) cc_final: 0.6090 (p90) REVERT: F 67 ASN cc_start: 0.8595 (p0) cc_final: 0.8330 (p0) REVERT: F 161 MET cc_start: 0.8787 (tpp) cc_final: 0.8507 (tpt) REVERT: F 180 ASP cc_start: 0.8885 (m-30) cc_final: 0.8471 (m-30) REVERT: F 428 GLN cc_start: 0.8300 (mp10) cc_final: 0.8045 (mp10) REVERT: G 35 TRP cc_start: 0.8497 (m100) cc_final: 0.8242 (m100) REVERT: G 66 HIS cc_start: 0.6351 (p-80) cc_final: 0.6102 (p90) REVERT: G 114 GLN cc_start: 0.8460 (tt0) cc_final: 0.8240 (tt0) REVERT: G 161 MET cc_start: 0.8791 (tpp) cc_final: 0.8200 (tpt) REVERT: G 180 ASP cc_start: 0.8839 (m-30) cc_final: 0.8303 (m-30) REVERT: G 280 ASN cc_start: 0.7965 (p0) cc_final: 0.7729 (p0) REVERT: G 428 GLN cc_start: 0.8213 (mp10) cc_final: 0.8012 (mp10) REVERT: H 50 VAL cc_start: 0.9301 (t) cc_final: 0.9033 (p) REVERT: H 100 TYR cc_start: 0.8708 (t80) cc_final: 0.8490 (t80) REVERT: H 101 ASP cc_start: 0.8027 (p0) cc_final: 0.7621 (p0) REVERT: J 45 LEU cc_start: 0.8056 (pt) cc_final: 0.7610 (pt) REVERT: J 50 VAL cc_start: 0.9248 (t) cc_final: 0.8866 (p) REVERT: J 72 GLU cc_start: 0.7863 (pm20) cc_final: 0.7426 (pm20) REVERT: J 77 THR cc_start: 0.6620 (p) cc_final: 0.6403 (p) REVERT: J 79 TYR cc_start: 0.8207 (m-80) cc_final: 0.7897 (m-10) REVERT: J 100 TYR cc_start: 0.8755 (t80) cc_final: 0.8554 (t80) REVERT: J 101 ASP cc_start: 0.7934 (p0) cc_final: 0.7646 (p0) REVERT: K 23 CYS cc_start: 0.4297 (t) cc_final: 0.3692 (t) REVERT: K 24 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7268 (ttp80) REVERT: K 29 GLU cc_start: 0.8285 (tt0) cc_final: 0.8060 (mt-10) REVERT: K 32 THR cc_start: 0.8166 (p) cc_final: 0.7862 (p) REVERT: K 39 GLN cc_start: 0.7960 (tp40) cc_final: 0.7499 (tp-100) REVERT: K 43 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7339 (mm-40) REVERT: K 55 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7538 (mtm-85) REVERT: K 69 ASP cc_start: 0.7944 (m-30) cc_final: 0.7478 (t0) REVERT: K 89 CYS cc_start: 0.6555 (p) cc_final: 0.6245 (p) REVERT: K 104 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8019 (tttt) REVERT: L 27 PHE cc_start: 0.8432 (t80) cc_final: 0.8018 (t80) REVERT: L 32 THR cc_start: 0.8011 (p) cc_final: 0.7675 (p) REVERT: L 43 GLN cc_start: 0.7377 (tp-100) cc_final: 0.7018 (mm-40) REVERT: L 50 TYR cc_start: 0.5761 (m-10) cc_final: 0.5481 (m-10) REVERT: L 55 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7321 (mpp80) REVERT: L 69 ASP cc_start: 0.7905 (m-30) cc_final: 0.7394 (t0) REVERT: M 50 VAL cc_start: 0.9304 (t) cc_final: 0.8940 (p) REVERT: M 72 GLU cc_start: 0.7812 (pm20) cc_final: 0.7509 (pm20) REVERT: M 82 MET cc_start: 0.8034 (mmm) cc_final: 0.7781 (tpt) REVERT: M 99 SER cc_start: 0.8870 (m) cc_final: 0.8406 (p) REVERT: M 100 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8500 (mm-30) REVERT: M 101 ASP cc_start: 0.8327 (p0) cc_final: 0.7896 (p0) REVERT: N 5 THR cc_start: 0.6819 (p) cc_final: 0.6612 (p) REVERT: N 32 THR cc_start: 0.8264 (p) cc_final: 0.7921 (p) REVERT: N 43 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7457 (mm-40) REVERT: N 48 LEU cc_start: 0.9276 (tp) cc_final: 0.9056 (tp) REVERT: N 69 ASP cc_start: 0.6999 (t0) cc_final: 0.6689 (t0) REVERT: N 91 GLN cc_start: 0.9331 (pp30) cc_final: 0.9100 (pp30) outliers start: 5 outliers final: 0 residues processed: 486 average time/residue: 0.1333 time to fit residues: 102.9369 Evaluate side-chains 395 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 203 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN C 630 GLN E 352 HIS F 352 HIS G 352 HIS K 27DHIS N 27DHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103642 restraints weight = 36777.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105099 restraints weight = 27364.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105943 restraints weight = 22837.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106531 restraints weight = 19794.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106828 restraints weight = 18818.474| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20412 Z= 0.144 Angle : 0.705 14.230 27912 Z= 0.336 Chirality : 0.048 0.435 3366 Planarity : 0.004 0.049 3357 Dihedral : 7.250 56.459 4602 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.10 % Allowed : 0.82 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 2298 helix: 1.84 (0.28), residues: 372 sheet: -0.48 (0.20), residues: 705 loop : -1.56 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.025 0.002 TYR A 586 PHE 0.012 0.001 PHE L 99 TRP 0.023 0.001 TRP B 610 HIS 0.011 0.001 HIS F 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (20271) covalent geometry : angle 0.64825 / 0.32 (27531) SS BOND : bond 0.00411 / 0.25 ( 42) SS BOND : angle 2.19346 / 1.49 ( 84) hydrogen bonds : bond 0.03714 / 2.60 ( 636) hydrogen bonds : angle 4.99261 / 3.58 ( 1800) link_ALPHA1-2 : bond 0.01044 / 0.51 ( 6) link_ALPHA1-2 : angle 0.91422 / 0.49 ( 18) link_ALPHA1-3 : bond 0.00996 / 0.60 ( 12) link_ALPHA1-3 : angle 1.52295 / 1.02 ( 36) link_ALPHA1-6 : bond 0.00447 / 0.25 ( 9) link_ALPHA1-6 : angle 0.79063 / 0.52 ( 27) link_BETA1-4 : bond 0.00386 / 0.26 ( 33) link_BETA1-4 : angle 1.69350 / 1.18 ( 99) link_NAG-ASN : bond 0.00511 / 0.29 ( 39) link_NAG-ASN : angle 3.58544 / 2.50 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 476 time to evaluate : 0.766 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 536 THR cc_start: 0.8557 (p) cc_final: 0.8028 (p) REVERT: A 539 VAL cc_start: 0.9593 (t) cc_final: 0.9327 (p) REVERT: A 543 ASN cc_start: 0.8778 (m-40) cc_final: 0.7952 (t0) REVERT: A 647 GLU cc_start: 0.7800 (mt-10) cc_final: 0.6301 (mt-10) REVERT: B 535 MET cc_start: 0.6762 (mmm) cc_final: 0.6358 (tpp) REVERT: B 542 ARG cc_start: 0.8299 (tpt-90) cc_final: 0.7805 (ttp-170) REVERT: B 543 ASN cc_start: 0.8962 (m-40) cc_final: 0.8218 (t0) REVERT: B 596 TRP cc_start: 0.8981 (m-10) cc_final: 0.8702 (m-10) REVERT: C 535 MET cc_start: 0.6631 (tpp) cc_final: 0.5843 (tpp) REVERT: C 536 THR cc_start: 0.8597 (p) cc_final: 0.8181 (p) REVERT: C 540 GLN cc_start: 0.7941 (mp10) cc_final: 0.7697 (mp10) REVERT: C 633 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8649 (mmtm) REVERT: E 35 TRP cc_start: 0.8496 (m100) cc_final: 0.8229 (m100) REVERT: E 104 MET cc_start: 0.8864 (ttp) cc_final: 0.8379 (tmm) REVERT: E 161 MET cc_start: 0.8778 (tpp) cc_final: 0.8541 (tpt) REVERT: E 428 GLN cc_start: 0.8403 (mp10) cc_final: 0.8021 (mp10) REVERT: F 35 TRP cc_start: 0.8300 (m100) cc_final: 0.8053 (m100) REVERT: F 66 HIS cc_start: 0.6347 (p-80) cc_final: 0.6069 (p90) REVERT: F 67 ASN cc_start: 0.8574 (p0) cc_final: 0.8313 (p0) REVERT: F 161 MET cc_start: 0.8780 (tpp) cc_final: 0.8532 (tpt) REVERT: F 180 ASP cc_start: 0.8894 (m-30) cc_final: 0.8482 (m-30) REVERT: F 428 GLN cc_start: 0.8320 (mp10) cc_final: 0.8052 (mp10) REVERT: G 66 HIS cc_start: 0.6308 (p-80) cc_final: 0.6082 (p90) REVERT: G 102 GLU cc_start: 0.7369 (mp0) cc_final: 0.7014 (mp0) REVERT: G 104 MET cc_start: 0.9017 (ttt) cc_final: 0.8597 (tpp) REVERT: G 161 MET cc_start: 0.8859 (tpp) cc_final: 0.8227 (tpt) REVERT: G 180 ASP cc_start: 0.8784 (m-30) cc_final: 0.8253 (m-30) REVERT: G 230 ASN cc_start: 0.7755 (t0) cc_final: 0.7434 (t0) REVERT: G 280 ASN cc_start: 0.7947 (p0) cc_final: 0.7674 (p0) REVERT: G 475 MET cc_start: 0.8460 (mmm) cc_final: 0.7850 (mmm) REVERT: H 50 VAL cc_start: 0.9286 (t) cc_final: 0.9049 (p) REVERT: H 72 GLU cc_start: 0.7883 (pm20) cc_final: 0.7192 (pm20) REVERT: H 79 TYR cc_start: 0.8204 (m-10) cc_final: 0.7560 (m-80) REVERT: H 100 TYR cc_start: 0.8682 (t80) cc_final: 0.8478 (t80) REVERT: H 101 ASP cc_start: 0.8032 (p0) cc_final: 0.7570 (p0) REVERT: J 45 LEU cc_start: 0.8101 (pt) cc_final: 0.7624 (pt) REVERT: J 50 VAL cc_start: 0.9236 (t) cc_final: 0.8844 (p) REVERT: J 72 GLU cc_start: 0.7860 (pm20) cc_final: 0.7413 (pm20) REVERT: J 77 THR cc_start: 0.6456 (p) cc_final: 0.6231 (p) REVERT: J 79 TYR cc_start: 0.8211 (m-80) cc_final: 0.7926 (m-10) REVERT: J 100 TYR cc_start: 0.8750 (t80) cc_final: 0.8547 (t80) REVERT: J 101 ASP cc_start: 0.7898 (p0) cc_final: 0.7562 (p0) REVERT: K 23 CYS cc_start: 0.4216 (t) cc_final: 0.3591 (t) REVERT: K 24 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7361 (ttp80) REVERT: K 32 THR cc_start: 0.8109 (p) cc_final: 0.7814 (p) REVERT: K 43 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7530 (mm-40) REVERT: K 69 ASP cc_start: 0.7976 (m-30) cc_final: 0.7455 (t0) REVERT: K 89 CYS cc_start: 0.6405 (p) cc_final: 0.6146 (p) REVERT: K 104 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7986 (tttt) REVERT: L 27 PHE cc_start: 0.8452 (t80) cc_final: 0.8082 (t80) REVERT: L 32 THR cc_start: 0.8053 (p) cc_final: 0.7710 (p) REVERT: L 43 GLN cc_start: 0.7399 (tp-100) cc_final: 0.7018 (mm-40) REVERT: L 55 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7296 (mpp80) REVERT: L 69 ASP cc_start: 0.7934 (m-30) cc_final: 0.7389 (t0) REVERT: M 50 VAL cc_start: 0.9294 (t) cc_final: 0.8933 (p) REVERT: M 72 GLU cc_start: 0.7843 (pm20) cc_final: 0.7556 (pm20) REVERT: M 99 SER cc_start: 0.8767 (m) cc_final: 0.8462 (p) REVERT: M 100 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8544 (mm-30) REVERT: M 101 ASP cc_start: 0.8216 (p0) cc_final: 0.7799 (p0) REVERT: N 32 THR cc_start: 0.8361 (p) cc_final: 0.7921 (p) REVERT: N 43 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7530 (mm-40) REVERT: N 48 LEU cc_start: 0.9249 (tp) cc_final: 0.9024 (tp) REVERT: N 69 ASP cc_start: 0.6999 (t0) cc_final: 0.6719 (t0) REVERT: N 91 GLN cc_start: 0.9305 (pp30) cc_final: 0.9094 (pp30) outliers start: 2 outliers final: 0 residues processed: 478 average time/residue: 0.1370 time to fit residues: 103.0017 Evaluate side-chains 401 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 139 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 590 GLN B 630 GLN C 630 GLN E 352 HIS F 352 HIS G 352 HIS K 27DHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098937 restraints weight = 37390.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101689 restraints weight = 26782.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101826 restraints weight = 20064.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102424 restraints weight = 19498.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.102572 restraints weight = 18207.750| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20412 Z= 0.195 Angle : 0.751 14.228 27912 Z= 0.361 Chirality : 0.050 0.453 3366 Planarity : 0.004 0.067 3357 Dihedral : 7.479 57.426 4602 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.05 % Allowed : 0.68 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2298 helix: 1.62 (0.28), residues: 375 sheet: -0.43 (0.20), residues: 699 loop : -1.64 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.036 0.002 TYR F 134 PHE 0.016 0.002 PHE E 353 TRP 0.020 0.002 TRP B 610 HIS 0.008 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (20271) covalent geometry : angle 0.69241 / 0.35 (27531) SS BOND : bond 0.00492 / 0.33 ( 42) SS BOND : angle 2.24990 / 1.53 ( 84) hydrogen bonds : bond 0.03935 / 2.76 ( 636) hydrogen bonds : angle 5.07086 / 3.64 ( 1800) link_ALPHA1-2 : bond 0.01174 / 0.58 ( 6) link_ALPHA1-2 : angle 0.85887 / 0.44 ( 18) link_ALPHA1-3 : bond 0.00868 / 0.52 ( 12) link_ALPHA1-3 : angle 1.73873 / 1.14 ( 36) link_ALPHA1-6 : bond 0.00444 / 0.25 ( 9) link_ALPHA1-6 : angle 0.83944 / 0.56 ( 27) link_BETA1-4 : bond 0.00361 / 0.25 ( 33) link_BETA1-4 : angle 1.78574 / 1.23 ( 99) link_NAG-ASN : bond 0.00550 / 0.30 ( 39) link_NAG-ASN : angle 3.77320 / 2.62 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 0.550 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 543 ASN cc_start: 0.8862 (m-40) cc_final: 0.7973 (t0) REVERT: A 584 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 647 GLU cc_start: 0.7875 (mt-10) cc_final: 0.6331 (mt-10) REVERT: B 535 MET cc_start: 0.6817 (mmm) cc_final: 0.6479 (tpp) REVERT: B 542 ARG cc_start: 0.8321 (tpt-90) cc_final: 0.7831 (ttp-170) REVERT: B 543 ASN cc_start: 0.9014 (m-40) cc_final: 0.8637 (m-40) REVERT: B 584 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 536 THR cc_start: 0.8599 (p) cc_final: 0.8250 (p) REVERT: C 540 GLN cc_start: 0.7988 (mp10) cc_final: 0.7775 (mp10) REVERT: C 633 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8755 (mmtm) REVERT: E 35 TRP cc_start: 0.8525 (m100) cc_final: 0.8283 (m100) REVERT: E 104 MET cc_start: 0.8939 (ttp) cc_final: 0.8429 (tmm) REVERT: E 161 MET cc_start: 0.8844 (tpp) cc_final: 0.8594 (tpt) REVERT: E 428 GLN cc_start: 0.8421 (mp10) cc_final: 0.8194 (mp10) REVERT: F 35 TRP cc_start: 0.8422 (m100) cc_final: 0.8174 (m100) REVERT: F 104 MET cc_start: 0.9039 (ttt) cc_final: 0.8723 (tpp) REVERT: F 161 MET cc_start: 0.8821 (tpp) cc_final: 0.8562 (tpt) REVERT: F 180 ASP cc_start: 0.8863 (m-30) cc_final: 0.8482 (m-30) REVERT: F 428 GLN cc_start: 0.8400 (mp10) cc_final: 0.8130 (mp10) REVERT: G 66 HIS cc_start: 0.6378 (p-80) cc_final: 0.6147 (p90) REVERT: G 104 MET cc_start: 0.9063 (ttt) cc_final: 0.8634 (tpp) REVERT: G 114 GLN cc_start: 0.8490 (tt0) cc_final: 0.8275 (tt0) REVERT: G 161 MET cc_start: 0.8896 (tpp) cc_final: 0.8210 (tpt) REVERT: G 180 ASP cc_start: 0.8788 (m-30) cc_final: 0.8280 (m-30) REVERT: G 230 ASN cc_start: 0.7864 (t0) cc_final: 0.7591 (t0) REVERT: G 280 ASN cc_start: 0.7963 (p0) cc_final: 0.7743 (p0) REVERT: H 30 SER cc_start: 0.6452 (p) cc_final: 0.5791 (p) REVERT: H 45 LEU cc_start: 0.7843 (pp) cc_final: 0.7622 (pp) REVERT: H 50 VAL cc_start: 0.9321 (t) cc_final: 0.9087 (p) REVERT: H 72 GLU cc_start: 0.7850 (pm20) cc_final: 0.6713 (pm20) REVERT: H 79 TYR cc_start: 0.8129 (m-10) cc_final: 0.7387 (m-80) REVERT: H 100 TYR cc_start: 0.8763 (t80) cc_final: 0.8547 (t80) REVERT: H 101 ASP cc_start: 0.8006 (p0) cc_final: 0.7557 (p0) REVERT: J 45 LEU cc_start: 0.8126 (pt) cc_final: 0.7698 (pt) REVERT: J 50 VAL cc_start: 0.9260 (t) cc_final: 0.8873 (p) REVERT: J 72 GLU cc_start: 0.7870 (pm20) cc_final: 0.7394 (pm20) REVERT: J 77 THR cc_start: 0.6579 (p) cc_final: 0.6304 (p) REVERT: J 79 TYR cc_start: 0.8227 (m-80) cc_final: 0.7890 (m-10) REVERT: J 100 TYR cc_start: 0.8807 (t80) cc_final: 0.8604 (t80) REVERT: J 101 ASP cc_start: 0.7901 (p0) cc_final: 0.7596 (p0) REVERT: K 23 CYS cc_start: 0.4201 (t) cc_final: 0.3539 (t) REVERT: K 24 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7330 (ttp80) REVERT: K 32 THR cc_start: 0.8220 (p) cc_final: 0.7899 (p) REVERT: K 69 ASP cc_start: 0.8092 (m-30) cc_final: 0.7491 (t0) REVERT: K 89 CYS cc_start: 0.6489 (p) cc_final: 0.6162 (p) REVERT: K 104 LYS cc_start: 0.8393 (mtpp) cc_final: 0.7992 (tttt) REVERT: L 27 PHE cc_start: 0.8472 (t80) cc_final: 0.8125 (t80) REVERT: L 32 THR cc_start: 0.8114 (p) cc_final: 0.7830 (p) REVERT: L 43 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7132 (mm-40) REVERT: L 55 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7384 (mpp80) REVERT: L 69 ASP cc_start: 0.8055 (m-30) cc_final: 0.7532 (t70) REVERT: M 38 ARG cc_start: 0.7908 (mtm180) cc_final: 0.7057 (mtp180) REVERT: M 50 VAL cc_start: 0.9321 (t) cc_final: 0.8979 (p) REVERT: M 72 GLU cc_start: 0.7765 (pm20) cc_final: 0.7490 (pm20) REVERT: M 99 SER cc_start: 0.8707 (m) cc_final: 0.8407 (p) REVERT: M 100 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8577 (mm-30) REVERT: M 101 ASP cc_start: 0.8184 (p0) cc_final: 0.7840 (p0) REVERT: N 32 THR cc_start: 0.8400 (p) cc_final: 0.8025 (p) REVERT: N 43 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7538 (mm-40) REVERT: N 48 LEU cc_start: 0.9250 (tp) cc_final: 0.9022 (tp) REVERT: N 55 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7139 (mpp80) REVERT: N 69 ASP cc_start: 0.7198 (t0) cc_final: 0.6765 (t0) outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.1244 time to fit residues: 94.5779 Evaluate side-chains 404 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 652 GLN C 630 GLN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS G 352 HIS K 27DHIS K 39 GLN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100654 restraints weight = 37105.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103042 restraints weight = 25836.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104437 restraints weight = 20421.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105636 restraints weight = 17573.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106247 restraints weight = 15784.627| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20412 Z= 0.156 Angle : 0.723 14.262 27912 Z= 0.346 Chirality : 0.049 0.448 3366 Planarity : 0.004 0.054 3357 Dihedral : 7.304 57.110 4602 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2298 helix: 1.71 (0.28), residues: 375 sheet: -0.48 (0.20), residues: 711 loop : -1.63 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 38 TYR 0.031 0.002 TYR G 134 PHE 0.011 0.001 PHE E 353 TRP 0.023 0.001 TRP B 610 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (20271) covalent geometry : angle 0.66739 / 0.33 (27531) SS BOND : bond 0.00434 / 0.29 ( 42) SS BOND : angle 2.01080 / 1.37 ( 84) hydrogen bonds : bond 0.03781 / 2.63 ( 636) hydrogen bonds : angle 5.04056 / 3.61 ( 1800) link_ALPHA1-2 : bond 0.01140 / 0.56 ( 6) link_ALPHA1-2 : angle 0.93780 / 0.50 ( 18) link_ALPHA1-3 : bond 0.00926 / 0.55 ( 12) link_ALPHA1-3 : angle 1.61971 / 1.09 ( 36) link_ALPHA1-6 : bond 0.00471 / 0.27 ( 9) link_ALPHA1-6 : angle 0.77156 / 0.52 ( 27) link_BETA1-4 : bond 0.00358 / 0.24 ( 33) link_BETA1-4 : angle 1.72641 / 1.20 ( 99) link_NAG-ASN : bond 0.00517 / 0.28 ( 39) link_NAG-ASN : angle 3.66143 / 2.55 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3367.88 seconds wall clock time: 59 minutes 11.35 seconds (3551.35 seconds total)