Starting phenix.real_space_refine on Sun May 18 05:58:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ay6_43981/05_2025/9ay6_43981.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ay6_43981/05_2025/9ay6_43981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ay6_43981/05_2025/9ay6_43981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ay6_43981/05_2025/9ay6_43981.map" model { file = "/net/cci-nas-00/data/ceres_data/9ay6_43981/05_2025/9ay6_43981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ay6_43981/05_2025/9ay6_43981.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 105 5.16 5 C 10331 2.51 5 N 2812 2.21 5 O 3393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16641 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3568 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "C" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3541 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "E" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3603 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 20, 'TRANS': 436} Chain breaks: 2 Chain: "F" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "L" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.24, per 1000 atoms: 0.68 Number of scatterers: 16641 At special positions: 0 Unit cell: (132.715, 152.57, 122.265, 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 105 16.00 O 3393 8.00 N 2812 7.00 C 10331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.27 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 444 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " 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 377 " - pdb=" SG CYS E 444 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA V 3 " - " MAN V 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 289 " " NAG A 604 " - " ASN A 354 " " NAG A 605 " - " ASN A 397 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 391 " " NAG A 608 " - " ASN A 88 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 152 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 241 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 338 " " NAG C 608 " - " ASN C 385 " " NAG C 609 " - " ASN C 276 " " NAG C 610 " - " ASN C 354 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 137 " " NAG E 603 " - " ASN E 152 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 289 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 354 " " NAG E 609 " - " ASN E 338 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 152 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 331 " " NAG Q 1 " - " ASN A 362 " " NAG R 1 " - " ASN A 385 " " NAG S 1 " - " ASN A 447 " " NAG T 1 " - " ASN C 148 " " NAG U 1 " - " ASN C 197 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 289 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 331 " " NAG Z 1 " - " ASN C 362 " " NAG a 1 " - " ASN C 447 " " NAG b 1 " - " ASN C 391 " " NAG c 1 " - " ASN E 148 " " NAG d 1 " - " ASN E 241 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 276 " " NAG g 1 " - " ASN E 362 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 331 " " NAG j 1 " - " ASN E 447 " " NAG k 1 " - " ASN E 391 " " NAG l 1 " - " ASN E 461 " " NAG m 1 " - " ASN E 385 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.0 seconds 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3788 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 30 sheets defined 31.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.166A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.766A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.670A pdb=" N THR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.511A pdb=" N GLN A 427 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 428 " --> pdb=" O MET A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 428' Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.771A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.552A pdb=" N ALA B 533 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 546 removed outlier: 3.533A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.934A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.614A pdb=" N ARG C 428 " --> pdb=" O MET C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 462 Processing helix chain 'C' and resid 473 through 483 removed outlier: 4.285A pdb=" N ASN C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 535 removed outlier: 3.951A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 532 through 535' Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 548 through 557 Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.648A pdb=" N ILE D 622 " --> pdb=" O LEU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.584A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.153A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.735A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 removed outlier: 3.972A pdb=" N ASN E 280 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 352 removed outlier: 3.981A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.692A pdb=" N THR E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.788A pdb=" N GLN E 427 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 483 removed outlier: 3.575A pdb=" N ASN E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.965A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 558 removed outlier: 4.036A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 558 " --> pdb=" O ASN F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 568 Processing helix chain 'F' and resid 568 through 596 removed outlier: 3.554A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'H' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 3.665A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.526A pdb=" N ALA A 200 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR A 434 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 202 " --> pdb=" O TYR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 removed outlier: 6.136A pdb=" N GLN A 293 " --> pdb=" O SER A 333 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 333 current: chain 'A' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 380 through 384 current: chain 'A' and resid 464 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.549A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 169 Processing sheet with id=AB5, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.747A pdb=" N THR C 202 " --> pdb=" O TYR C 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 304 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 318 through 321 current: chain 'C' and resid 380 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 380 through 384 current: chain 'C' and resid 464 through 468 Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.645A pdb=" N GLN C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.879A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 169 Processing sheet with id=AC3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.708A pdb=" N THR E 202 " --> pdb=" O TYR E 434 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 270 through 271 Processing sheet with id=AC5, first strand: chain 'E' and resid 373 through 377 removed outlier: 7.017A pdb=" N CYS E 296 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER E 446 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ARG E 298 " --> pdb=" O CYS E 444 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS E 444 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN E 300 " --> pdb=" O ILE E 442 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE E 442 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 304 through 310 removed outlier: 6.818A pdb=" N GLN E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 392 through 394 removed outlier: 6.281A pdb=" N ARG E 359 " --> pdb=" O PHE E 467 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 51 through 52 removed outlier: 6.870A pdb=" N UNK H 34 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N UNK H 48 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N UNK H 32 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.563A pdb=" N UNK L 11 " --> pdb=" O UNK L 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 31 through 37 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 45 current: chain 'L' and resid 102 through 106 538 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 6.35 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: 5230 1.34 - 1.46: 3216 1.46 - 1.58: 8334 1.58 - 1.70: 0 1.70 - 1.81: 138 Bond restraints: 16918 Sorted by residual: bond pdb=" C1 NAG l 1 " pdb=" O5 NAG l 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" N ILE C 395 " pdb=" CA ILE C 395 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.22e+00 bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C1 NAG h 2 " pdb=" O5 NAG h 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 16913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 21181 1.33 - 2.66: 1527 2.66 - 3.99: 191 3.99 - 5.33: 85 5.33 - 6.66: 23 Bond angle restraints: 23007 Sorted by residual: angle pdb=" N GLN B 630 " pdb=" CA GLN B 630 " pdb=" C GLN B 630 " ideal model delta sigma weight residual 112.72 108.23 4.49 1.28e+00 6.10e-01 1.23e+01 angle pdb=" N SER D 615 " pdb=" CA SER D 615 " pdb=" CB SER D 615 " ideal model delta sigma weight residual 114.17 110.34 3.83 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N ALA A 58 " pdb=" CA ALA A 58 " pdb=" CB ALA A 58 " ideal model delta sigma weight residual 114.17 110.41 3.76 1.14e+00 7.69e-01 1.09e+01 angle pdb=" C UNK H 49 " pdb=" CA UNK H 49 " pdb=" CB UNK H 49 " ideal model delta sigma weight residual 110.08 116.01 -5.93 1.90e+00 2.77e-01 9.73e+00 angle pdb=" C UNK L 99 " pdb=" CA UNK L 99 " pdb=" CB UNK L 99 " ideal model delta sigma weight residual 110.08 115.97 -5.89 1.90e+00 2.77e-01 9.62e+00 ... (remaining 23002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 11097 22.15 - 44.31: 311 44.31 - 66.46: 47 66.46 - 88.62: 51 88.62 - 110.77: 25 Dihedral angle restraints: 11531 sinusoidal: 5706 harmonic: 5825 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 142.98 -49.98 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 141.61 -48.61 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CA CYS A 228 " pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " ideal model delta sinusoidal sigma weight residual -73.00 -1.18 -71.82 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 11528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2884 0.130 - 0.259: 56 0.259 - 0.389: 7 0.389 - 0.518: 0 0.518 - 0.648: 1 Chirality restraints: 2948 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.83e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.65e+01 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 338 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2945 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.281 2.00e-02 2.50e+03 2.36e-01 6.93e+02 pdb=" C7 NAG Z 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.398 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.171 2.00e-02 2.50e+03 1.40e-01 2.47e+02 pdb=" C7 NAG Z 1 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.225 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " 0.117 2.00e-02 2.50e+03 9.64e-02 1.16e+02 pdb=" C7 NAG Y 2 " -0.031 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " -0.155 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.018 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2257 2.76 - 3.29: 16300 3.29 - 3.83: 26644 3.83 - 4.36: 30960 4.36 - 4.90: 52070 Nonbonded interactions: 128231 Sorted by model distance: nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.225 3.040 nonbonded pdb=" N UNK L 13 " pdb=" O UNK L 117 " model vdw 2.235 3.120 nonbonded pdb=" OD1 ASN E 280 " pdb=" NH1 ARG E 455 " model vdw 2.252 3.120 nonbonded pdb=" OE2 GLU E 145 " pdb=" NH1 ARG E 418 " model vdw 2.259 3.120 nonbonded pdb=" OD1 ASN D 607 " pdb=" OG SER D 649 " model vdw 2.275 3.040 ... (remaining 128226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 179 or resid 189 through 397 or resid 411 throu \ gh 503 or resid 601 through 608)) selection = (chain 'C' and (resid 35 through 270 or (resid 271 and (name N or name CA or nam \ e C or name O or name CB )) or resid 272 through 503 or resid 601 through 608)) selection = (chain 'E' and (resid 35 through 270 or (resid 271 and (name N or name CA or nam \ e C or name O or name CB )) or resid 272 through 397 or resid 411 through 503 or \ resid 602 through 609)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 521 through 663 or resid 701)) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) } ncs_group { reference = chain 'H' selection = (chain 'L' and resid 16 through 117) } ncs_group { reference = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'g' selection = chain 'k' } 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: 0.010 Normalize map: mean=0, sd=1: 4.430 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: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.950 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.006 0.242 17048 Z= 0.277 Angle : 0.900 40.665 23369 Z= 0.434 Chirality : 0.052 0.648 2948 Planarity : 0.007 0.236 2819 Dihedral : 13.032 110.774 7659 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1763 helix: 1.30 (0.25), residues: 434 sheet: -0.31 (0.25), residues: 402 loop : -0.27 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 96 HIS 0.004 0.001 HIS E 373 PHE 0.015 0.002 PHE A 53 TYR 0.014 0.001 TYR A 191 ARG 0.002 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 61) link_NAG-ASN : angle 2.37452 ( 183) link_ALPHA1-6 : bond 0.00214 ( 2) link_ALPHA1-6 : angle 1.89405 ( 6) link_BETA1-4 : bond 0.01008 ( 36) link_BETA1-4 : angle 3.36171 ( 108) link_ALPHA1-3 : bond 0.00271 ( 3) link_ALPHA1-3 : angle 1.90080 ( 9) hydrogen bonds : bond 0.15010 ( 538) hydrogen bonds : angle 6.20935 ( 1446) SS BOND : bond 0.04581 ( 28) SS BOND : angle 5.92679 ( 56) covalent geometry : bond 0.00528 (16918) covalent geometry : angle 0.79800 (23007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8500 (ptm) cc_final: 0.8283 (ptm) REVERT: A 97 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8548 (mmmt) REVERT: A 102 GLU cc_start: 0.8536 (tp30) cc_final: 0.8157 (mm-30) REVERT: A 142 MET cc_start: 0.8741 (mmm) cc_final: 0.7772 (mmt) REVERT: A 172 ASP cc_start: 0.8849 (m-30) cc_final: 0.8309 (m-30) REVERT: A 232 LYS cc_start: 0.8210 (mttt) cc_final: 0.7730 (ttpt) REVERT: B 522 PHE cc_start: 0.8671 (t80) cc_final: 0.8063 (t80) REVERT: B 529 THR cc_start: 0.8630 (t) cc_final: 0.8326 (m) REVERT: B 530 MET cc_start: 0.7642 (mtp) cc_final: 0.7088 (mtp) REVERT: B 535 MET cc_start: 0.7595 (mtp) cc_final: 0.7387 (mtp) REVERT: B 550 GLN cc_start: 0.7384 (mp10) cc_final: 0.6940 (mp10) REVERT: B 584 GLU cc_start: 0.8509 (tp30) cc_final: 0.8066 (tm-30) REVERT: B 626 MET cc_start: 0.7637 (mmm) cc_final: 0.7346 (tpp) REVERT: B 645 LEU cc_start: 0.9173 (mt) cc_final: 0.8884 (mp) REVERT: B 647 GLU cc_start: 0.8508 (tt0) cc_final: 0.8173 (tt0) REVERT: B 660 LEU cc_start: 0.8497 (tp) cc_final: 0.8260 (tt) REVERT: C 104 MET cc_start: 0.9315 (ttt) cc_final: 0.8993 (tpp) REVERT: C 159 ASP cc_start: 0.8239 (p0) cc_final: 0.7986 (p0) REVERT: C 376 ASN cc_start: 0.9121 (t0) cc_final: 0.7621 (p0) REVERT: C 474 MET cc_start: 0.8503 (mmm) cc_final: 0.8160 (mmt) REVERT: C 483 TYR cc_start: 0.8806 (p90) cc_final: 0.8601 (p90) REVERT: D 641 ILE cc_start: 0.8821 (mt) cc_final: 0.8613 (mp) REVERT: D 648 GLU cc_start: 0.7965 (tp30) cc_final: 0.7727 (tp30) REVERT: E 35 TRP cc_start: 0.7800 (m100) cc_final: 0.7206 (m100) REVERT: E 99 ASN cc_start: 0.8598 (p0) cc_final: 0.8243 (t0) REVERT: E 145 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7810 (tp30) REVERT: E 161 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8416 (ptmm) REVERT: E 369 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7698 (mm-30) REVERT: E 376 ASN cc_start: 0.8893 (t0) cc_final: 0.7909 (p0) REVERT: F 565 LEU cc_start: 0.6445 (mt) cc_final: 0.5895 (mt) REVERT: F 631 TRP cc_start: 0.8730 (t-100) cc_final: 0.8457 (t-100) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.3187 time to fit residues: 220.5347 Evaluate side-chains 282 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 421 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN D 564 HIS E 329 HIS F 543 ASN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099520 restraints weight = 36618.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102179 restraints weight = 23149.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103970 restraints weight = 17232.760| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17048 Z= 0.159 Angle : 0.726 12.252 23369 Z= 0.345 Chirality : 0.046 0.461 2948 Planarity : 0.004 0.044 2819 Dihedral : 10.208 85.260 4259 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.45 % Allowed : 10.00 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1763 helix: 1.48 (0.25), residues: 444 sheet: -0.07 (0.24), residues: 433 loop : -0.23 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 35 HIS 0.005 0.001 HIS B 564 PHE 0.017 0.002 PHE E 53 TYR 0.022 0.002 TYR A 217 ARG 0.006 0.000 ARG C 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 61) link_NAG-ASN : angle 2.78146 ( 183) link_ALPHA1-6 : bond 0.00504 ( 2) link_ALPHA1-6 : angle 1.85211 ( 6) link_BETA1-4 : bond 0.00705 ( 36) link_BETA1-4 : angle 2.45100 ( 108) link_ALPHA1-3 : bond 0.00524 ( 3) link_ALPHA1-3 : angle 2.37256 ( 9) hydrogen bonds : bond 0.05170 ( 538) hydrogen bonds : angle 5.16440 ( 1446) SS BOND : bond 0.00258 ( 28) SS BOND : angle 0.87619 ( 56) covalent geometry : bond 0.00356 (16918) covalent geometry : angle 0.66433 (23007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 1.665 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 97 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8586 (mmmt) REVERT: A 102 GLU cc_start: 0.8595 (tp30) cc_final: 0.8196 (mm-30) REVERT: A 142 MET cc_start: 0.8785 (mmm) cc_final: 0.7936 (mmt) REVERT: A 172 ASP cc_start: 0.8716 (m-30) cc_final: 0.8243 (m-30) REVERT: A 295 ASN cc_start: 0.8191 (m-40) cc_final: 0.7820 (p0) REVERT: B 522 PHE cc_start: 0.8733 (t80) cc_final: 0.8361 (t80) REVERT: B 530 MET cc_start: 0.8035 (mtp) cc_final: 0.7573 (mtp) REVERT: B 535 MET cc_start: 0.7609 (mtp) cc_final: 0.7267 (mtp) REVERT: B 536 THR cc_start: 0.7943 (p) cc_final: 0.7578 (t) REVERT: B 543 ASN cc_start: 0.8305 (t0) cc_final: 0.7543 (t0) REVERT: B 660 LEU cc_start: 0.8663 (tp) cc_final: 0.8438 (tt) REVERT: C 66 HIS cc_start: 0.7805 (m90) cc_final: 0.7258 (m90) REVERT: C 113 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8758 (t0) REVERT: C 159 ASP cc_start: 0.8293 (p0) cc_final: 0.8091 (p0) REVERT: C 320 ASP cc_start: 0.8277 (t0) cc_final: 0.8002 (m-30) REVERT: C 376 ASN cc_start: 0.9019 (t0) cc_final: 0.7610 (p0) REVERT: C 473 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7290 (p0) REVERT: C 483 TYR cc_start: 0.8815 (p90) cc_final: 0.8582 (p90) REVERT: D 530 MET cc_start: 0.7529 (mtm) cc_final: 0.7285 (mtp) REVERT: D 535 MET cc_start: 0.8666 (mpp) cc_final: 0.8435 (mpp) REVERT: D 626 MET cc_start: 0.7999 (tmm) cc_final: 0.7497 (tmm) REVERT: D 631 TRP cc_start: 0.8315 (t-100) cc_final: 0.7557 (t-100) REVERT: D 632 ASP cc_start: 0.8251 (t0) cc_final: 0.8032 (t0) REVERT: E 83 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6809 (mt-10) REVERT: E 99 ASN cc_start: 0.8715 (p0) cc_final: 0.8225 (t0) REVERT: E 161 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8443 (ptmm) REVERT: E 210 PHE cc_start: 0.7671 (m-80) cc_final: 0.7459 (m-80) REVERT: E 376 ASN cc_start: 0.8922 (t0) cc_final: 0.7926 (p0) REVERT: E 425 MET cc_start: 0.7625 (mtt) cc_final: 0.7196 (mmm) REVERT: F 631 TRP cc_start: 0.8635 (t-100) cc_final: 0.7983 (t-100) REVERT: F 656 ASN cc_start: 0.9156 (m-40) cc_final: 0.8682 (t0) outliers start: 39 outliers final: 21 residues processed: 325 average time/residue: 0.2840 time to fit residues: 137.6887 Evaluate side-chains 278 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 616 ASN C 72 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 HIS D 543 ASN E 329 HIS E 397 ASN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS F 577 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094686 restraints weight = 36767.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097121 restraints weight = 23788.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098749 restraints weight = 18052.317| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.006 0.056 17048 Z= 0.263 Angle : 0.800 13.058 23369 Z= 0.379 Chirality : 0.048 0.498 2948 Planarity : 0.004 0.045 2819 Dihedral : 8.969 78.011 4259 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.52 % Allowed : 11.32 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1763 helix: 1.32 (0.25), residues: 450 sheet: -0.32 (0.24), residues: 441 loop : -0.32 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 112 HIS 0.006 0.001 HIS E 329 PHE 0.018 0.002 PHE F 522 TYR 0.026 0.002 TYR D 643 ARG 0.008 0.001 ARG C 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 61) link_NAG-ASN : angle 2.91284 ( 183) link_ALPHA1-6 : bond 0.00597 ( 2) link_ALPHA1-6 : angle 2.05355 ( 6) link_BETA1-4 : bond 0.00686 ( 36) link_BETA1-4 : angle 2.46984 ( 108) link_ALPHA1-3 : bond 0.00759 ( 3) link_ALPHA1-3 : angle 2.19251 ( 9) hydrogen bonds : bond 0.04898 ( 538) hydrogen bonds : angle 5.12749 ( 1446) SS BOND : bond 0.00442 ( 28) SS BOND : angle 1.04553 ( 56) covalent geometry : bond 0.00596 (16918) covalent geometry : angle 0.74058 (23007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8826 (tp30) cc_final: 0.8396 (mm-30) REVERT: A 104 MET cc_start: 0.9237 (ttm) cc_final: 0.8626 (tpp) REVERT: A 172 ASP cc_start: 0.8817 (m-30) cc_final: 0.8346 (m-30) REVERT: A 295 ASN cc_start: 0.8233 (m-40) cc_final: 0.7522 (p0) REVERT: B 530 MET cc_start: 0.8116 (mtp) cc_final: 0.7778 (mtp) REVERT: B 535 MET cc_start: 0.7686 (mtp) cc_final: 0.7319 (mtp) REVERT: B 567 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8594 (mmtm) REVERT: B 606 THR cc_start: 0.9393 (m) cc_final: 0.9095 (p) REVERT: B 629 LEU cc_start: 0.7905 (mt) cc_final: 0.7667 (mt) REVERT: B 660 LEU cc_start: 0.8698 (tp) cc_final: 0.8416 (tt) REVERT: C 104 MET cc_start: 0.9394 (tpp) cc_final: 0.9136 (tpp) REVERT: C 217 TYR cc_start: 0.8854 (m-80) cc_final: 0.8512 (m-80) REVERT: C 376 ASN cc_start: 0.9151 (t0) cc_final: 0.7705 (p0) REVERT: C 473 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7835 (p0) REVERT: C 483 TYR cc_start: 0.8861 (p90) cc_final: 0.8492 (p90) REVERT: D 530 MET cc_start: 0.7709 (mtm) cc_final: 0.7152 (mtt) REVERT: D 626 MET cc_start: 0.8345 (tmm) cc_final: 0.7643 (tmm) REVERT: D 631 TRP cc_start: 0.8374 (t-100) cc_final: 0.7977 (t-100) REVERT: D 632 ASP cc_start: 0.8528 (t0) cc_final: 0.8325 (t0) REVERT: D 655 LYS cc_start: 0.8709 (pttt) cc_final: 0.8164 (pttm) REVERT: D 661 LEU cc_start: 0.9059 (mt) cc_final: 0.8823 (tt) REVERT: E 35 TRP cc_start: 0.7817 (m100) cc_final: 0.7516 (m100) REVERT: E 74 CYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8872 (p) REVERT: E 99 ASN cc_start: 0.8838 (p0) cc_final: 0.8280 (t0) REVERT: E 107 ASP cc_start: 0.8481 (t0) cc_final: 0.8110 (t0) REVERT: E 376 ASN cc_start: 0.8961 (t0) cc_final: 0.7914 (p0) REVERT: F 621 GLU cc_start: 0.6301 (tp30) cc_final: 0.5788 (tp30) REVERT: F 656 ASN cc_start: 0.9121 (m-40) cc_final: 0.8745 (t0) outliers start: 56 outliers final: 42 residues processed: 304 average time/residue: 0.2949 time to fit residues: 134.3316 Evaluate side-chains 279 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 351 HIS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 27 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 136 optimal weight: 0.0050 chunk 180 optimal weight: 9.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 258 GLN C 351 HIS D 543 ASN E 329 HIS ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096628 restraints weight = 36494.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099171 restraints weight = 22643.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100883 restraints weight = 16697.106| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17048 Z= 0.153 Angle : 0.710 18.960 23369 Z= 0.331 Chirality : 0.046 0.470 2948 Planarity : 0.003 0.049 2819 Dihedral : 8.037 73.011 4259 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.14 % Allowed : 12.77 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1763 helix: 1.40 (0.25), residues: 456 sheet: -0.21 (0.24), residues: 443 loop : -0.25 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 112 HIS 0.010 0.001 HIS C 351 PHE 0.014 0.001 PHE F 522 TYR 0.015 0.001 TYR D 643 ARG 0.005 0.000 ARG C 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 61) link_NAG-ASN : angle 3.29310 ( 183) link_ALPHA1-6 : bond 0.00762 ( 2) link_ALPHA1-6 : angle 2.00168 ( 6) link_BETA1-4 : bond 0.00633 ( 36) link_BETA1-4 : angle 2.22496 ( 108) link_ALPHA1-3 : bond 0.00812 ( 3) link_ALPHA1-3 : angle 2.26449 ( 9) hydrogen bonds : bond 0.04354 ( 538) hydrogen bonds : angle 4.88298 ( 1446) SS BOND : bond 0.00274 ( 28) SS BOND : angle 0.84646 ( 56) covalent geometry : bond 0.00340 (16918) covalent geometry : angle 0.63055 (23007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8251 (pt0) cc_final: 0.7639 (pp20) REVERT: A 97 LYS cc_start: 0.8665 (tppt) cc_final: 0.8444 (tttp) REVERT: A 102 GLU cc_start: 0.8695 (tp30) cc_final: 0.8311 (mm-30) REVERT: A 104 MET cc_start: 0.9269 (ttm) cc_final: 0.8539 (tpp) REVERT: A 142 MET cc_start: 0.8886 (mmm) cc_final: 0.8448 (mmt) REVERT: A 172 ASP cc_start: 0.8732 (m-30) cc_final: 0.8527 (m-30) REVERT: A 295 ASN cc_start: 0.8221 (m-40) cc_final: 0.7550 (p0) REVERT: B 530 MET cc_start: 0.8130 (mtp) cc_final: 0.7726 (mtp) REVERT: B 535 MET cc_start: 0.7562 (mtp) cc_final: 0.7228 (mtp) REVERT: B 536 THR cc_start: 0.7932 (p) cc_final: 0.7668 (t) REVERT: B 606 THR cc_start: 0.9335 (m) cc_final: 0.9016 (p) REVERT: B 631 TRP cc_start: 0.8166 (t60) cc_final: 0.7770 (t60) REVERT: C 104 MET cc_start: 0.9307 (tpp) cc_final: 0.8954 (tpp) REVERT: C 153 MET cc_start: 0.8479 (tpp) cc_final: 0.7994 (ttm) REVERT: C 217 TYR cc_start: 0.8826 (m-80) cc_final: 0.8405 (m-80) REVERT: C 376 ASN cc_start: 0.9091 (t0) cc_final: 0.7688 (p0) REVERT: C 483 TYR cc_start: 0.8862 (p90) cc_final: 0.8521 (p90) REVERT: D 530 MET cc_start: 0.7556 (mtm) cc_final: 0.7122 (mtm) REVERT: D 557 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.8182 (tpp-160) REVERT: D 626 MET cc_start: 0.8334 (tmm) cc_final: 0.7840 (tmm) REVERT: D 631 TRP cc_start: 0.8342 (t-100) cc_final: 0.7689 (t-100) REVERT: D 661 LEU cc_start: 0.9002 (mt) cc_final: 0.8768 (tt) REVERT: E 35 TRP cc_start: 0.7839 (m100) cc_final: 0.7581 (m100) REVERT: E 99 ASN cc_start: 0.8814 (p0) cc_final: 0.8323 (t0) REVERT: E 107 ASP cc_start: 0.8371 (t0) cc_final: 0.8077 (t0) REVERT: E 153 MET cc_start: 0.8564 (tpt) cc_final: 0.8359 (tpt) REVERT: E 158 ARG cc_start: 0.7493 (mtp-110) cc_final: 0.7196 (ttp-110) REVERT: E 213 ILE cc_start: 0.8458 (pt) cc_final: 0.8254 (mt) REVERT: E 376 ASN cc_start: 0.8937 (t0) cc_final: 0.7895 (p0) REVERT: F 554 ASN cc_start: 0.8448 (m-40) cc_final: 0.8214 (p0) REVERT: F 631 TRP cc_start: 0.8781 (t-100) cc_final: 0.8426 (t-100) REVERT: F 635 ILE cc_start: 0.8581 (pt) cc_final: 0.8253 (mt) REVERT: F 656 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8625 (t0) outliers start: 50 outliers final: 32 residues processed: 293 average time/residue: 0.2872 time to fit residues: 127.0869 Evaluate side-chains 273 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 151 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 283 ASN C 424 ASN ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092491 restraints weight = 37695.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094937 restraints weight = 24200.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096552 restraints weight = 18185.010| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17048 Z= 0.272 Angle : 0.817 17.691 23369 Z= 0.380 Chirality : 0.048 0.528 2948 Planarity : 0.004 0.040 2819 Dihedral : 7.940 68.122 4259 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.96 % Allowed : 13.46 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1763 helix: 1.41 (0.25), residues: 445 sheet: -0.25 (0.25), residues: 429 loop : -0.43 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 112 HIS 0.006 0.001 HIS B 564 PHE 0.014 0.002 PHE C 168 TYR 0.031 0.002 TYR D 643 ARG 0.007 0.001 ARG C 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 61) link_NAG-ASN : angle 3.41915 ( 183) link_ALPHA1-6 : bond 0.00777 ( 2) link_ALPHA1-6 : angle 1.82521 ( 6) link_BETA1-4 : bond 0.00603 ( 36) link_BETA1-4 : angle 2.36456 ( 108) link_ALPHA1-3 : bond 0.00723 ( 3) link_ALPHA1-3 : angle 2.40871 ( 9) hydrogen bonds : bond 0.04704 ( 538) hydrogen bonds : angle 5.04249 ( 1446) SS BOND : bond 0.00499 ( 28) SS BOND : angle 1.05521 ( 56) covalent geometry : bond 0.00620 (16918) covalent geometry : angle 0.74388 (23007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 49 GLU cc_start: 0.8235 (pt0) cc_final: 0.7653 (pp20) REVERT: A 102 GLU cc_start: 0.8785 (tp30) cc_final: 0.8535 (mm-30) REVERT: A 104 MET cc_start: 0.9455 (ttm) cc_final: 0.8651 (tpp) REVERT: A 142 MET cc_start: 0.9002 (mmm) cc_final: 0.7974 (mmt) REVERT: A 172 ASP cc_start: 0.8822 (m-30) cc_final: 0.8428 (m-30) REVERT: A 295 ASN cc_start: 0.8354 (m-40) cc_final: 0.7558 (p0) REVERT: B 530 MET cc_start: 0.8150 (mtp) cc_final: 0.7845 (mtp) REVERT: B 535 MET cc_start: 0.7738 (mtp) cc_final: 0.7397 (mtp) REVERT: B 536 THR cc_start: 0.8065 (p) cc_final: 0.7852 (t) REVERT: B 542 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7724 (ttp-110) REVERT: B 606 THR cc_start: 0.9332 (m) cc_final: 0.8984 (p) REVERT: B 629 LEU cc_start: 0.7824 (mt) cc_final: 0.7578 (mt) REVERT: C 153 MET cc_start: 0.8609 (tpp) cc_final: 0.8049 (ttm) REVERT: C 376 ASN cc_start: 0.9161 (t0) cc_final: 0.7744 (p0) REVERT: D 530 MET cc_start: 0.7465 (mtm) cc_final: 0.6891 (mtt) REVERT: D 626 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7964 (tmm) REVERT: D 655 LYS cc_start: 0.8767 (pttt) cc_final: 0.8414 (pttm) REVERT: E 99 ASN cc_start: 0.8850 (p0) cc_final: 0.8410 (t0) REVERT: E 107 ASP cc_start: 0.8354 (t0) cc_final: 0.8105 (t0) REVERT: E 376 ASN cc_start: 0.8950 (t0) cc_final: 0.7920 (p0) REVERT: F 552 GLN cc_start: 0.6895 (pp30) cc_final: 0.6094 (tp40) REVERT: F 631 TRP cc_start: 0.8844 (t-100) cc_final: 0.8584 (t-100) REVERT: F 656 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8851 (t0) outliers start: 63 outliers final: 38 residues processed: 284 average time/residue: 0.2961 time to fit residues: 127.0807 Evaluate side-chains 263 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 424 ASN ** E 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093506 restraints weight = 36954.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095929 restraints weight = 23020.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097578 restraints weight = 17030.745| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17048 Z= 0.199 Angle : 0.755 21.505 23369 Z= 0.351 Chirality : 0.049 0.995 2948 Planarity : 0.004 0.042 2819 Dihedral : 7.513 64.815 4259 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.71 % Allowed : 15.28 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1763 helix: 1.27 (0.25), residues: 452 sheet: -0.24 (0.25), residues: 431 loop : -0.47 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 112 HIS 0.003 0.001 HIS A 329 PHE 0.011 0.001 PHE A 53 TYR 0.016 0.001 TYR D 643 ARG 0.010 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 61) link_NAG-ASN : angle 3.44318 ( 183) link_ALPHA1-6 : bond 0.00944 ( 2) link_ALPHA1-6 : angle 1.73788 ( 6) link_BETA1-4 : bond 0.00605 ( 36) link_BETA1-4 : angle 2.21694 ( 108) link_ALPHA1-3 : bond 0.00814 ( 3) link_ALPHA1-3 : angle 2.29527 ( 9) hydrogen bonds : bond 0.04352 ( 538) hydrogen bonds : angle 4.83591 ( 1446) SS BOND : bond 0.00352 ( 28) SS BOND : angle 0.87270 ( 56) covalent geometry : bond 0.00454 (16918) covalent geometry : angle 0.67616 (23007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8206 (p) REVERT: A 97 LYS cc_start: 0.8623 (tppt) cc_final: 0.8013 (ttmm) REVERT: A 102 GLU cc_start: 0.8732 (tp30) cc_final: 0.8387 (mm-30) REVERT: A 104 MET cc_start: 0.9426 (ttm) cc_final: 0.8691 (tpp) REVERT: A 142 MET cc_start: 0.9010 (mmm) cc_final: 0.8042 (mmt) REVERT: A 172 ASP cc_start: 0.8769 (m-30) cc_final: 0.8400 (m-30) REVERT: A 295 ASN cc_start: 0.8364 (m-40) cc_final: 0.7535 (p0) REVERT: B 530 MET cc_start: 0.8144 (mtp) cc_final: 0.7837 (mtp) REVERT: B 535 MET cc_start: 0.7621 (mtp) cc_final: 0.7245 (mtp) REVERT: B 536 THR cc_start: 0.8018 (p) cc_final: 0.7812 (t) REVERT: B 606 THR cc_start: 0.9311 (m) cc_final: 0.8961 (p) REVERT: B 631 TRP cc_start: 0.8126 (t60) cc_final: 0.7826 (t60) REVERT: C 153 MET cc_start: 0.8593 (tpp) cc_final: 0.8056 (ttm) REVERT: C 376 ASN cc_start: 0.9134 (t0) cc_final: 0.7743 (p0) REVERT: D 530 MET cc_start: 0.7358 (mtm) cc_final: 0.6927 (mtm) REVERT: D 605 CYS cc_start: 0.8629 (p) cc_final: 0.8248 (m) REVERT: D 626 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: D 655 LYS cc_start: 0.8693 (pttt) cc_final: 0.8444 (pttt) REVERT: E 35 TRP cc_start: 0.7959 (m100) cc_final: 0.7174 (m100) REVERT: E 99 ASN cc_start: 0.8842 (p0) cc_final: 0.8486 (t0) REVERT: E 107 ASP cc_start: 0.8352 (t0) cc_final: 0.8082 (t0) REVERT: E 158 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7464 (ttp-110) REVERT: E 213 ILE cc_start: 0.8526 (pt) cc_final: 0.8321 (mt) REVERT: E 376 ASN cc_start: 0.8943 (t0) cc_final: 0.7922 (p0) REVERT: F 631 TRP cc_start: 0.8735 (t-100) cc_final: 0.8422 (t-100) REVERT: F 656 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8820 (t0) outliers start: 59 outliers final: 38 residues processed: 271 average time/residue: 0.2870 time to fit residues: 116.1878 Evaluate side-chains 265 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 620 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 12 optimal weight: 0.0970 chunk 173 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN E 329 HIS E 431 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095263 restraints weight = 36459.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097805 restraints weight = 22597.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099481 restraints weight = 16597.864| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17048 Z= 0.145 Angle : 0.691 17.034 23369 Z= 0.324 Chirality : 0.051 1.318 2948 Planarity : 0.003 0.048 2819 Dihedral : 7.039 60.751 4259 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.02 % Allowed : 16.67 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1763 helix: 1.37 (0.25), residues: 454 sheet: -0.22 (0.24), residues: 440 loop : -0.37 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 112 HIS 0.007 0.001 HIS E 329 PHE 0.015 0.001 PHE D 522 TYR 0.014 0.001 TYR D 643 ARG 0.004 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 61) link_NAG-ASN : angle 2.87406 ( 183) link_ALPHA1-6 : bond 0.01108 ( 2) link_ALPHA1-6 : angle 1.84347 ( 6) link_BETA1-4 : bond 0.00654 ( 36) link_BETA1-4 : angle 2.09745 ( 108) link_ALPHA1-3 : bond 0.00888 ( 3) link_ALPHA1-3 : angle 2.00971 ( 9) hydrogen bonds : bond 0.03979 ( 538) hydrogen bonds : angle 4.64428 ( 1446) SS BOND : bond 0.00235 ( 28) SS BOND : angle 0.72283 ( 56) covalent geometry : bond 0.00325 (16918) covalent geometry : angle 0.62789 (23007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 97 LYS cc_start: 0.8596 (tppt) cc_final: 0.7982 (ttmm) REVERT: A 102 GLU cc_start: 0.8703 (tp30) cc_final: 0.8353 (mm-30) REVERT: A 104 MET cc_start: 0.9393 (ttm) cc_final: 0.8710 (tpp) REVERT: A 142 MET cc_start: 0.9049 (mmm) cc_final: 0.8198 (mmt) REVERT: A 172 ASP cc_start: 0.8734 (m-30) cc_final: 0.8370 (m-30) REVERT: A 295 ASN cc_start: 0.8329 (m-40) cc_final: 0.7745 (p0) REVERT: B 530 MET cc_start: 0.8149 (mtp) cc_final: 0.7706 (mtp) REVERT: B 535 MET cc_start: 0.7678 (mtp) cc_final: 0.7286 (mtp) REVERT: B 536 THR cc_start: 0.8028 (p) cc_final: 0.7790 (t) REVERT: B 606 THR cc_start: 0.9276 (m) cc_final: 0.8951 (p) REVERT: B 631 TRP cc_start: 0.8157 (t60) cc_final: 0.7811 (t60) REVERT: C 153 MET cc_start: 0.8541 (tpp) cc_final: 0.7957 (ttm) REVERT: C 376 ASN cc_start: 0.9098 (t0) cc_final: 0.7738 (p0) REVERT: D 530 MET cc_start: 0.7408 (mtm) cc_final: 0.6931 (mtm) REVERT: D 605 CYS cc_start: 0.8627 (p) cc_final: 0.8268 (m) REVERT: E 35 TRP cc_start: 0.7940 (m100) cc_final: 0.7263 (m100) REVERT: E 99 ASN cc_start: 0.8796 (p0) cc_final: 0.8396 (t0) REVERT: E 107 ASP cc_start: 0.8281 (t0) cc_final: 0.8004 (t0) REVERT: E 153 MET cc_start: 0.8257 (tpp) cc_final: 0.7971 (ttm) REVERT: E 158 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7462 (ttp-110) REVERT: E 213 ILE cc_start: 0.8511 (pt) cc_final: 0.8302 (mt) REVERT: E 376 ASN cc_start: 0.8885 (t0) cc_final: 0.7895 (p0) REVERT: F 656 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8663 (t0) outliers start: 48 outliers final: 30 residues processed: 269 average time/residue: 0.2672 time to fit residues: 108.7035 Evaluate side-chains 257 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 424 ASN D 543 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.111368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092554 restraints weight = 36912.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094914 restraints weight = 23200.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096564 restraints weight = 17339.398| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17048 Z= 0.254 Angle : 0.785 16.346 23369 Z= 0.368 Chirality : 0.050 0.917 2948 Planarity : 0.004 0.047 2819 Dihedral : 7.173 58.672 4259 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.21 % Allowed : 16.98 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1763 helix: 1.14 (0.25), residues: 461 sheet: -0.16 (0.25), residues: 420 loop : -0.57 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 631 HIS 0.005 0.001 HIS B 564 PHE 0.011 0.002 PHE C 168 TYR 0.013 0.002 TYR D 643 ARG 0.005 0.001 ARG C 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 61) link_NAG-ASN : angle 3.00147 ( 183) link_ALPHA1-6 : bond 0.01014 ( 2) link_ALPHA1-6 : angle 2.06103 ( 6) link_BETA1-4 : bond 0.00556 ( 36) link_BETA1-4 : angle 2.21915 ( 108) link_ALPHA1-3 : bond 0.00747 ( 3) link_ALPHA1-3 : angle 2.10901 ( 9) hydrogen bonds : bond 0.04301 ( 538) hydrogen bonds : angle 4.84135 ( 1446) SS BOND : bond 0.00477 ( 28) SS BOND : angle 1.27680 ( 56) covalent geometry : bond 0.00582 (16918) covalent geometry : angle 0.72442 (23007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8292 (p) REVERT: A 102 GLU cc_start: 0.8790 (tp30) cc_final: 0.8444 (mm-30) REVERT: A 104 MET cc_start: 0.9450 (ttm) cc_final: 0.9084 (ttm) REVERT: A 142 MET cc_start: 0.9036 (mmm) cc_final: 0.8065 (mmt) REVERT: A 172 ASP cc_start: 0.8793 (m-30) cc_final: 0.8403 (m-30) REVERT: A 295 ASN cc_start: 0.8353 (m-40) cc_final: 0.7599 (p0) REVERT: B 530 MET cc_start: 0.8047 (mtp) cc_final: 0.7706 (mtp) REVERT: B 535 MET cc_start: 0.7740 (mtp) cc_final: 0.7342 (mtp) REVERT: B 536 THR cc_start: 0.8137 (p) cc_final: 0.7911 (t) REVERT: B 606 THR cc_start: 0.9296 (m) cc_final: 0.8961 (p) REVERT: C 153 MET cc_start: 0.8623 (tpp) cc_final: 0.8263 (ttm) REVERT: C 376 ASN cc_start: 0.9160 (t0) cc_final: 0.7760 (p0) REVERT: D 626 MET cc_start: 0.8262 (tmm) cc_final: 0.7982 (tmm) REVERT: D 655 LYS cc_start: 0.8634 (pttt) cc_final: 0.8346 (pttm) REVERT: E 35 TRP cc_start: 0.8085 (m100) cc_final: 0.7511 (m100) REVERT: E 99 ASN cc_start: 0.8868 (p0) cc_final: 0.8429 (t0) REVERT: E 107 ASP cc_start: 0.8365 (t0) cc_final: 0.8119 (t0) REVERT: E 153 MET cc_start: 0.8266 (tpp) cc_final: 0.8009 (ttm) REVERT: E 158 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7548 (ttp-110) REVERT: E 376 ASN cc_start: 0.8956 (t0) cc_final: 0.7915 (p0) REVERT: F 656 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8797 (t0) outliers start: 51 outliers final: 39 residues processed: 258 average time/residue: 0.2847 time to fit residues: 111.4109 Evaluate side-chains 263 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 175 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS C 195 ASN C 424 ASN E 329 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094906 restraints weight = 36616.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097420 restraints weight = 22722.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099152 restraints weight = 16636.813| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17048 Z= 0.144 Angle : 0.706 17.453 23369 Z= 0.333 Chirality : 0.048 0.951 2948 Planarity : 0.004 0.047 2819 Dihedral : 6.732 58.066 4259 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.52 % Allowed : 17.61 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1763 helix: 1.33 (0.25), residues: 448 sheet: -0.13 (0.25), residues: 448 loop : -0.42 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 631 HIS 0.006 0.001 HIS E 329 PHE 0.012 0.001 PHE A 53 TYR 0.013 0.001 TYR D 643 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 61) link_NAG-ASN : angle 2.85385 ( 183) link_ALPHA1-6 : bond 0.01064 ( 2) link_ALPHA1-6 : angle 1.94731 ( 6) link_BETA1-4 : bond 0.00626 ( 36) link_BETA1-4 : angle 2.05630 ( 108) link_ALPHA1-3 : bond 0.00874 ( 3) link_ALPHA1-3 : angle 1.94264 ( 9) hydrogen bonds : bond 0.03897 ( 538) hydrogen bonds : angle 4.65802 ( 1446) SS BOND : bond 0.00228 ( 28) SS BOND : angle 0.82783 ( 56) covalent geometry : bond 0.00329 (16918) covalent geometry : angle 0.64593 (23007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 97 LYS cc_start: 0.8705 (tppt) cc_final: 0.8161 (ttmm) REVERT: A 102 GLU cc_start: 0.8683 (tp30) cc_final: 0.8357 (mm-30) REVERT: A 104 MET cc_start: 0.9393 (ttm) cc_final: 0.9055 (ttm) REVERT: A 142 MET cc_start: 0.9058 (mmm) cc_final: 0.8201 (mmt) REVERT: A 172 ASP cc_start: 0.8733 (m-30) cc_final: 0.8382 (m-30) REVERT: A 246 GLN cc_start: 0.8060 (pm20) cc_final: 0.7758 (pm20) REVERT: A 295 ASN cc_start: 0.8317 (m-40) cc_final: 0.7725 (p0) REVERT: B 530 MET cc_start: 0.8095 (mtp) cc_final: 0.7712 (mtp) REVERT: B 535 MET cc_start: 0.7714 (mtp) cc_final: 0.7277 (mtp) REVERT: B 536 THR cc_start: 0.8059 (p) cc_final: 0.7563 (t) REVERT: B 606 THR cc_start: 0.9264 (m) cc_final: 0.8942 (p) REVERT: B 629 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7300 (mt) REVERT: B 631 TRP cc_start: 0.8138 (t60) cc_final: 0.7853 (t60) REVERT: C 153 MET cc_start: 0.8516 (tpp) cc_final: 0.7895 (ttm) REVERT: C 194 ILE cc_start: 0.9300 (tp) cc_final: 0.9080 (tp) REVERT: C 376 ASN cc_start: 0.9108 (t0) cc_final: 0.7773 (p0) REVERT: D 605 CYS cc_start: 0.8501 (p) cc_final: 0.8268 (m) REVERT: D 655 LYS cc_start: 0.8662 (pttt) cc_final: 0.8284 (pttm) REVERT: E 35 TRP cc_start: 0.8033 (m100) cc_final: 0.7467 (m100) REVERT: E 99 ASN cc_start: 0.8826 (p0) cc_final: 0.8425 (t0) REVERT: E 107 ASP cc_start: 0.8282 (t0) cc_final: 0.8029 (t0) REVERT: E 153 MET cc_start: 0.8140 (tpp) cc_final: 0.7910 (ttm) REVERT: E 158 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7493 (ttp-110) REVERT: E 376 ASN cc_start: 0.8895 (t0) cc_final: 0.7903 (p0) REVERT: F 631 TRP cc_start: 0.8846 (t-100) cc_final: 0.8253 (t-100) REVERT: F 656 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8668 (t0) outliers start: 40 outliers final: 32 residues processed: 268 average time/residue: 0.2758 time to fit residues: 112.6940 Evaluate side-chains 262 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 112 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS C 424 ASN F 630 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095163 restraints weight = 36765.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097666 restraints weight = 22876.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099354 restraints weight = 16790.037| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17048 Z= 0.155 Angle : 0.721 15.467 23369 Z= 0.341 Chirality : 0.048 0.813 2948 Planarity : 0.004 0.046 2819 Dihedral : 6.548 58.199 4259 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.26 % Allowed : 18.05 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1763 helix: 1.16 (0.25), residues: 454 sheet: -0.13 (0.25), residues: 445 loop : -0.46 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 631 HIS 0.004 0.001 HIS B 564 PHE 0.010 0.001 PHE A 53 TYR 0.013 0.001 TYR D 643 ARG 0.004 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 61) link_NAG-ASN : angle 2.78578 ( 183) link_ALPHA1-6 : bond 0.01024 ( 2) link_ALPHA1-6 : angle 1.96736 ( 6) link_BETA1-4 : bond 0.00602 ( 36) link_BETA1-4 : angle 2.06262 ( 108) link_ALPHA1-3 : bond 0.00814 ( 3) link_ALPHA1-3 : angle 1.87502 ( 9) hydrogen bonds : bond 0.03960 ( 538) hydrogen bonds : angle 4.65167 ( 1446) SS BOND : bond 0.00254 ( 28) SS BOND : angle 0.79221 ( 56) covalent geometry : bond 0.00357 (16918) covalent geometry : angle 0.66463 (23007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8751 (tppt) cc_final: 0.8223 (ttmm) REVERT: A 102 GLU cc_start: 0.8687 (tp30) cc_final: 0.8331 (mm-30) REVERT: A 104 MET cc_start: 0.9392 (ttm) cc_final: 0.9052 (ttm) REVERT: A 142 MET cc_start: 0.9076 (mmm) cc_final: 0.8215 (mmt) REVERT: A 172 ASP cc_start: 0.8727 (m-30) cc_final: 0.8356 (m-30) REVERT: A 246 GLN cc_start: 0.7943 (pm20) cc_final: 0.7621 (pm20) REVERT: A 295 ASN cc_start: 0.8317 (m-40) cc_final: 0.7729 (p0) REVERT: A 433 MET cc_start: 0.8663 (tmm) cc_final: 0.8398 (ttm) REVERT: B 535 MET cc_start: 0.7695 (mtp) cc_final: 0.7330 (mtp) REVERT: B 536 THR cc_start: 0.7847 (p) cc_final: 0.7387 (t) REVERT: B 542 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7807 (ttp80) REVERT: B 606 THR cc_start: 0.9255 (m) cc_final: 0.8941 (p) REVERT: C 153 MET cc_start: 0.8504 (tpp) cc_final: 0.7900 (ttm) REVERT: C 194 ILE cc_start: 0.9254 (tp) cc_final: 0.8939 (tp) REVERT: C 376 ASN cc_start: 0.9115 (t0) cc_final: 0.7745 (p0) REVERT: D 588 ARG cc_start: 0.8486 (tpt170) cc_final: 0.8053 (ttp-170) REVERT: D 605 CYS cc_start: 0.8510 (p) cc_final: 0.8248 (m) REVERT: D 655 LYS cc_start: 0.8726 (pttt) cc_final: 0.8239 (pttm) REVERT: E 35 TRP cc_start: 0.7987 (m100) cc_final: 0.7372 (m100) REVERT: E 99 ASN cc_start: 0.8838 (p0) cc_final: 0.8472 (t0) REVERT: E 107 ASP cc_start: 0.8286 (t0) cc_final: 0.8038 (t0) REVERT: E 153 MET cc_start: 0.8179 (tpp) cc_final: 0.7922 (ttm) REVERT: E 158 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7458 (ttp-110) REVERT: E 376 ASN cc_start: 0.8904 (t0) cc_final: 0.7921 (p0) REVERT: F 542 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7854 (tpt170) REVERT: F 656 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8674 (t0) outliers start: 36 outliers final: 30 residues processed: 258 average time/residue: 0.3009 time to fit residues: 119.1823 Evaluate side-chains 258 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 53 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 115 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN C 195 ASN C 424 ASN E 329 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094610 restraints weight = 37153.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097143 restraints weight = 23299.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098851 restraints weight = 17310.861| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17048 Z= 0.160 Angle : 0.724 17.522 23369 Z= 0.343 Chirality : 0.047 0.648 2948 Planarity : 0.004 0.047 2819 Dihedral : 6.460 59.314 4259 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.39 % Allowed : 18.55 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1763 helix: 1.16 (0.25), residues: 454 sheet: -0.14 (0.25), residues: 442 loop : -0.47 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 45 HIS 0.007 0.001 HIS E 329 PHE 0.010 0.001 PHE A 53 TYR 0.012 0.001 TYR D 643 ARG 0.003 0.000 ARG C 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 61) link_NAG-ASN : angle 2.81561 ( 183) link_ALPHA1-6 : bond 0.01011 ( 2) link_ALPHA1-6 : angle 2.00593 ( 6) link_BETA1-4 : bond 0.00599 ( 36) link_BETA1-4 : angle 2.04763 ( 108) link_ALPHA1-3 : bond 0.00787 ( 3) link_ALPHA1-3 : angle 1.84672 ( 9) hydrogen bonds : bond 0.03909 ( 538) hydrogen bonds : angle 4.64585 ( 1446) SS BOND : bond 0.00266 ( 28) SS BOND : angle 0.75869 ( 56) covalent geometry : bond 0.00369 (16918) covalent geometry : angle 0.66736 (23007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4844.79 seconds wall clock time: 86 minutes 33.84 seconds (5193.84 seconds total)