Starting phenix.real_space_refine on Sun May 18 15:51:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fk5_29248/05_2025/8fk5_29248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fk5_29248/05_2025/8fk5_29248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fk5_29248/05_2025/8fk5_29248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fk5_29248/05_2025/8fk5_29248.map" model { file = "/net/cci-nas-00/data/ceres_data/8fk5_29248/05_2025/8fk5_29248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fk5_29248/05_2025/8fk5_29248.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.062 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 117 5.16 5 C 10559 2.51 5 N 2802 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 16980 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1102 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 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: 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: "e" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" 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 Time building chain proxies: 9.88, per 1000 atoms: 0.58 Number of scatterers: 16980 At special positions: 0 Unit cell: (131.043, 125.628, 166.782, 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 117 16.00 O 3502 8.00 N 2802 7.00 C 10559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " " MAN e 5 " - " MAN e 6 " " MAN e 8 " - " MAN e 9 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 8 " " MAN e 4 " - " MAN e 7 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA a 3 " - " MAN a 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 137 " " NAG D 1 " - " ASN C 160 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 137 " " NAG G 611 " - " ASN G 276 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 363 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 363 " " NAG T 1 " - " ASN G 386 " " NAG U 1 " - " ASN G 448 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 160 " Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 1.9 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 30 sheets defined 24.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.543A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 removed outlier: 4.158A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.063A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.552A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.585A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.317A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.779A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.367A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.758A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.930A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.504A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.374A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 353 removed outlier: 3.587A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.630A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.018A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.267A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.547A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.071A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.570A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.041A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.577A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.821A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 474 through 484 removed outlier: 3.945A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.223A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.614A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 481 removed outlier: 4.113A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.550A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.102A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.871A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.820A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.306A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 309 removed outlier: 4.020A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR C 303 " --> pdb=" O ASP C 321A" (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'F' and resid 603 through 609 removed outlier: 4.314A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.388A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.652A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.469A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 260 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 395 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 374 through 378 removed outlier: 4.003A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 304 through 312 removed outlier: 3.501A pdb=" N ILE G 309 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.786A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.078A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.741A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 130 through 133 removed outlier: 4.705A pdb=" N PHE H 100J" --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N TYR I 173 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.477A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET I 434 " --> pdb=" O ILE I 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 292 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 292 current: chain 'I' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 393 through 395 current: chain 'I' and resid 466 through 470 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.543A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 301 through 312 removed outlier: 3.985A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.713A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AD2, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 19 through 24 484 hydrogen bonds defined for protein. 1314 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: 5.72 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2659 1.32 - 1.45: 4959 1.45 - 1.57: 9526 1.57 - 1.70: 2 1.70 - 1.83: 154 Bond restraints: 17300 Sorted by residual: bond pdb=" C1 MAN e 9 " pdb=" O5 MAN e 9 " ideal model delta sigma weight residual 1.399 1.552 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C1 MAN e 9 " pdb=" C2 MAN e 9 " ideal model delta sigma weight residual 1.526 1.667 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.573 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.587 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.432 -0.061 2.00e-02 2.50e+03 9.33e+00 ... (remaining 17295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 23054 2.51 - 5.02: 365 5.02 - 7.52: 58 7.52 - 10.03: 2 10.03 - 12.54: 1 Bond angle restraints: 23480 Sorted by residual: angle pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" C THR I 467 " ideal model delta sigma weight residual 108.23 120.77 -12.54 1.72e+00 3.38e-01 5.32e+01 angle pdb=" C THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta sigma weight residual 111.05 119.59 -8.54 1.69e+00 3.50e-01 2.55e+01 angle pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta sigma weight residual 110.24 116.75 -6.51 1.45e+00 4.76e-01 2.02e+01 angle pdb=" CA TYS H 100H" pdb=" C TYS H 100H" pdb=" O TYS H 100H" ideal model delta sigma weight residual 120.80 113.20 7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" N ASP I 457 " pdb=" CA ASP I 457 " pdb=" C ASP I 457 " ideal model delta sigma weight residual 110.28 104.19 6.09 1.48e+00 4.57e-01 1.69e+01 ... (remaining 23475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.33: 11023 22.33 - 44.66: 598 44.66 - 66.98: 118 66.98 - 89.31: 64 89.31 - 111.64: 31 Dihedral angle restraints: 11834 sinusoidal: 6158 harmonic: 5676 Sorted by residual: dihedral pdb=" C THR I 467 " pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta harmonic sigma weight residual -122.00 -160.68 38.68 0 2.50e+00 1.60e-01 2.39e+02 dihedral pdb=" N THR I 467 " pdb=" C THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta harmonic sigma weight residual 123.40 160.13 -36.73 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -159.37 73.37 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 11831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 2956 0.331 - 0.661: 2 0.661 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.653: 1 Chirality restraints: 2959 Sorted by residual: chirality pdb=" CA THR I 467 " pdb=" N THR I 467 " pdb=" C THR I 467 " pdb=" CB THR I 467 " both_signs ideal model delta sigma weight residual False 2.53 0.87 1.65 2.00e-01 2.50e+01 6.83e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 448 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C1 MAN e 9 " pdb=" O2 MAN e 8 " pdb=" C2 MAN e 9 " pdb=" O5 MAN e 9 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 5.34e+00 ... (remaining 2956 not shown) Planarity restraints: 2901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 456 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ARG I 456 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG I 456 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP I 457 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYS H 100H" 0.012 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C TYS H 100H" -0.045 2.00e-02 2.50e+03 pdb=" O TYS H 100H" 0.016 2.00e-02 2.50e+03 pdb=" N ASP H 100I" 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.165 9.50e-02 1.11e+02 7.42e-02 3.38e+00 pdb=" NE ARG H 3 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 3 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 3 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 3 " -0.006 2.00e-02 2.50e+03 ... (remaining 2898 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 203 2.62 - 3.19: 15011 3.19 - 3.76: 23718 3.76 - 4.33: 34615 4.33 - 4.90: 57220 Nonbonded interactions: 130767 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.052 3.040 nonbonded pdb=" OD1 ASP C 457 " pdb=" OG1 THR C 467 " model vdw 2.090 3.040 nonbonded pdb=" NH2 ARG G 350 " pdb=" O ASN G 398 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.168 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.198 3.040 ... (remaining 130762 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 519 through 664 or resid 701 through 702)) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = (chain 'C' and (resid 33 through 505 or resid 601 through 609)) selection = (chain 'G' and (resid 33 through 505 or resid 601 through 609)) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'V' selection = chain 'a' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.770 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 17449 Z= 0.259 Angle : 0.755 12.540 23890 Z= 0.333 Chirality : 0.059 1.653 2959 Planarity : 0.003 0.074 2840 Dihedral : 15.600 111.638 8059 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.05 % 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: 0.37 (0.20), residues: 1932 helix: 0.93 (0.29), residues: 369 sheet: 0.69 (0.24), residues: 505 loop : -0.15 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 PHE 0.006 0.001 PHE C 53 TYR 0.008 0.001 TYR L 49 ARG 0.004 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 61) link_NAG-ASN : angle 1.82595 ( 183) link_ALPHA1-6 : bond 0.00715 ( 8) link_ALPHA1-6 : angle 1.61108 ( 24) link_BETA1-4 : bond 0.00468 ( 30) link_BETA1-4 : angle 1.98412 ( 90) link_ALPHA1-2 : bond 0.02570 ( 5) link_ALPHA1-2 : angle 2.79397 ( 15) link_ALPHA1-3 : bond 0.00838 ( 8) link_ALPHA1-3 : angle 2.29375 ( 24) hydrogen bonds : bond 0.24659 ( 484) hydrogen bonds : angle 8.15189 ( 1314) SS BOND : bond 0.00183 ( 37) SS BOND : angle 0.98692 ( 74) covalent geometry : bond 0.00516 (17300) covalent geometry : angle 0.72261 (23480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 1.695 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: B 536 THR cc_start: 0.8904 (t) cc_final: 0.8562 (p) REVERT: C 38 VAL cc_start: 0.8998 (p) cc_final: 0.8605 (m) REVERT: C 46 LYS cc_start: 0.8449 (pttp) cc_final: 0.8215 (pttp) REVERT: G 39 TYR cc_start: 0.8834 (m-80) cc_final: 0.8569 (m-80) REVERT: H 94 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7246 (ttt180) REVERT: L 36 TYR cc_start: 0.7830 (m-80) cc_final: 0.7506 (m-80) outliers start: 2 outliers final: 0 residues processed: 331 average time/residue: 0.3145 time to fit residues: 150.7167 Evaluate side-chains 190 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 99 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 0.0060 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 651 ASN B 540 GLN B 543 ASN C 105 HIS C 249 HIS C 478 ASN G 249 HIS G 374 HIS I 99 ASN I 374 HIS ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100CASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155556 restraints weight = 20466.135| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.22 r_work: 0.3627 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17449 Z= 0.150 Angle : 0.704 18.590 23890 Z= 0.328 Chirality : 0.047 0.307 2959 Planarity : 0.004 0.047 2840 Dihedral : 12.149 114.850 4403 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.56 % Allowed : 7.05 % Favored : 91.39 % 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: 0.26 (0.19), residues: 1932 helix: 1.06 (0.27), residues: 383 sheet: 0.54 (0.23), residues: 504 loop : -0.28 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 35 HIS 0.005 0.001 HIS G 85 PHE 0.027 0.001 PHE C 53 TYR 0.014 0.001 TYR F 638 ARG 0.004 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 61) link_NAG-ASN : angle 2.63569 ( 183) link_ALPHA1-6 : bond 0.00692 ( 8) link_ALPHA1-6 : angle 1.64656 ( 24) link_BETA1-4 : bond 0.00538 ( 30) link_BETA1-4 : angle 1.67805 ( 90) link_ALPHA1-2 : bond 0.00882 ( 5) link_ALPHA1-2 : angle 2.20403 ( 15) link_ALPHA1-3 : bond 0.01019 ( 8) link_ALPHA1-3 : angle 1.91954 ( 24) hydrogen bonds : bond 0.06093 ( 484) hydrogen bonds : angle 5.65547 ( 1314) SS BOND : bond 0.00344 ( 37) SS BOND : angle 1.56805 ( 74) covalent geometry : bond 0.00326 (17300) covalent geometry : angle 0.64996 (23480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8418 (pt0) cc_final: 0.8088 (mt-10) REVERT: B 536 THR cc_start: 0.9068 (t) cc_final: 0.8779 (p) REVERT: C 46 LYS cc_start: 0.8810 (pttp) cc_final: 0.8577 (pttp) REVERT: C 491 ILE cc_start: 0.8332 (mm) cc_final: 0.7846 (mt) REVERT: G 91 GLU cc_start: 0.7193 (tp30) cc_final: 0.6910 (tt0) REVERT: G 151 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8197 (ttp80) REVERT: G 217 TYR cc_start: 0.8658 (m-80) cc_final: 0.8386 (m-80) REVERT: G 434 MET cc_start: 0.8809 (ttp) cc_final: 0.8580 (ttp) REVERT: H 38 ARG cc_start: 0.7291 (ptt180) cc_final: 0.7079 (ptt180) REVERT: H 94 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7845 (ttt-90) REVERT: L 36 TYR cc_start: 0.7888 (m-80) cc_final: 0.7418 (m-80) outliers start: 27 outliers final: 19 residues processed: 230 average time/residue: 0.3155 time to fit residues: 107.1122 Evaluate side-chains 195 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 78 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN C 374 HIS H 100CASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.175630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145127 restraints weight = 20609.243| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.29 r_work: 0.3508 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17449 Z= 0.176 Angle : 0.688 18.369 23890 Z= 0.318 Chirality : 0.047 0.345 2959 Planarity : 0.004 0.045 2840 Dihedral : 11.260 116.965 4403 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 8.55 % Favored : 88.68 % 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: 0.18 (0.19), residues: 1932 helix: 1.02 (0.28), residues: 388 sheet: 0.53 (0.22), residues: 516 loop : -0.40 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 35 HIS 0.005 0.001 HIS H 100R PHE 0.025 0.002 PHE C 53 TYR 0.014 0.001 TYR L 49 ARG 0.006 0.001 ARG G 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 61) link_NAG-ASN : angle 2.63913 ( 183) link_ALPHA1-6 : bond 0.00697 ( 8) link_ALPHA1-6 : angle 1.69868 ( 24) link_BETA1-4 : bond 0.00513 ( 30) link_BETA1-4 : angle 1.50488 ( 90) link_ALPHA1-2 : bond 0.00975 ( 5) link_ALPHA1-2 : angle 2.00828 ( 15) link_ALPHA1-3 : bond 0.01107 ( 8) link_ALPHA1-3 : angle 1.60942 ( 24) hydrogen bonds : bond 0.05284 ( 484) hydrogen bonds : angle 5.20414 ( 1314) SS BOND : bond 0.00466 ( 37) SS BOND : angle 1.57075 ( 74) covalent geometry : bond 0.00418 (17300) covalent geometry : angle 0.63447 (23480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8151 (tp30) cc_final: 0.7896 (tp30) REVERT: B 536 THR cc_start: 0.9105 (t) cc_final: 0.8777 (p) REVERT: C 95 MET cc_start: 0.8672 (ptm) cc_final: 0.7807 (ttp) REVERT: C 205 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6846 (m) REVERT: C 491 ILE cc_start: 0.8437 (mm) cc_final: 0.7929 (mt) REVERT: G 151 ARG cc_start: 0.9035 (ttm-80) cc_final: 0.8188 (ttp80) REVERT: I 246 GLN cc_start: 0.7594 (pm20) cc_final: 0.7371 (pm20) REVERT: H 94 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7896 (ttt-90) REVERT: L 36 TYR cc_start: 0.7941 (m-80) cc_final: 0.7533 (m-80) outliers start: 48 outliers final: 32 residues processed: 229 average time/residue: 0.3110 time to fit residues: 105.0190 Evaluate side-chains 204 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 97 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN C 82 GLN G 422 GLN I 422 GLN H 100CASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140460 restraints weight = 21674.473| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.29 r_work: 0.3419 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17449 Z= 0.269 Angle : 0.807 19.122 23890 Z= 0.373 Chirality : 0.052 0.380 2959 Planarity : 0.005 0.058 2840 Dihedral : 10.610 114.185 4403 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.58 % Allowed : 9.94 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 1932 helix: 0.58 (0.27), residues: 391 sheet: 0.35 (0.23), residues: 504 loop : -0.65 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 35 HIS 0.005 0.002 HIS G 352 PHE 0.026 0.003 PHE C 391 TYR 0.021 0.002 TYR L 49 ARG 0.011 0.001 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 61) link_NAG-ASN : angle 2.87774 ( 183) link_ALPHA1-6 : bond 0.00780 ( 8) link_ALPHA1-6 : angle 1.80896 ( 24) link_BETA1-4 : bond 0.00534 ( 30) link_BETA1-4 : angle 1.58793 ( 90) link_ALPHA1-2 : bond 0.00958 ( 5) link_ALPHA1-2 : angle 2.40265 ( 15) link_ALPHA1-3 : bond 0.01119 ( 8) link_ALPHA1-3 : angle 1.98625 ( 24) hydrogen bonds : bond 0.05581 ( 484) hydrogen bonds : angle 5.27972 ( 1314) SS BOND : bond 0.00406 ( 37) SS BOND : angle 1.76491 ( 74) covalent geometry : bond 0.00665 (17300) covalent geometry : angle 0.75382 (23480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7212 (mtp180) REVERT: A 584 GLU cc_start: 0.8421 (pt0) cc_final: 0.8117 (pt0) REVERT: A 655 LYS cc_start: 0.7110 (tptp) cc_final: 0.6802 (tptt) REVERT: B 536 THR cc_start: 0.9129 (t) cc_final: 0.8773 (p) REVERT: B 544 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8333 (mt) REVERT: C 46 LYS cc_start: 0.8631 (pttm) cc_final: 0.8388 (pttp) REVERT: C 95 MET cc_start: 0.8867 (ptm) cc_final: 0.7992 (ttp) REVERT: C 292 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8931 (m) REVERT: F 632 ASP cc_start: 0.8825 (t70) cc_final: 0.8563 (t0) REVERT: F 659 ASP cc_start: 0.7121 (m-30) cc_final: 0.6915 (m-30) REVERT: G 151 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8165 (ttp80) REVERT: G 423 ILE cc_start: 0.8891 (mm) cc_final: 0.8646 (mt) REVERT: I 205 CYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6461 (m) REVERT: I 246 GLN cc_start: 0.7562 (pm20) cc_final: 0.7062 (pm20) REVERT: H 72 ASP cc_start: 0.8335 (t0) cc_final: 0.8077 (t0) REVERT: H 94 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7799 (ttt-90) REVERT: H 100 TYR cc_start: 0.8580 (m-80) cc_final: 0.8118 (m-80) REVERT: L 24 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6847 (mt0) outliers start: 62 outliers final: 38 residues processed: 251 average time/residue: 0.3193 time to fit residues: 117.3518 Evaluate side-chains 223 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 112 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN G 428 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140670 restraints weight = 20977.764| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.31 r_work: 0.3459 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17449 Z= 0.140 Angle : 0.702 19.006 23890 Z= 0.319 Chirality : 0.049 0.689 2959 Planarity : 0.004 0.047 2840 Dihedral : 9.951 113.582 4403 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.41 % Allowed : 10.86 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1932 helix: 0.86 (0.27), residues: 389 sheet: 0.37 (0.23), residues: 519 loop : -0.61 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 35 HIS 0.005 0.001 HIS H 100R PHE 0.019 0.001 PHE C 317 TYR 0.013 0.001 TYR L 49 ARG 0.010 0.000 ARG A 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 61) link_NAG-ASN : angle 2.99361 ( 183) link_ALPHA1-6 : bond 0.00867 ( 8) link_ALPHA1-6 : angle 1.64543 ( 24) link_BETA1-4 : bond 0.00459 ( 30) link_BETA1-4 : angle 1.39578 ( 90) link_ALPHA1-2 : bond 0.00859 ( 5) link_ALPHA1-2 : angle 2.17771 ( 15) link_ALPHA1-3 : bond 0.01173 ( 8) link_ALPHA1-3 : angle 1.67586 ( 24) hydrogen bonds : bond 0.04390 ( 484) hydrogen bonds : angle 4.90255 ( 1314) SS BOND : bond 0.00548 ( 37) SS BOND : angle 1.72116 ( 74) covalent geometry : bond 0.00323 (17300) covalent geometry : angle 0.63740 (23480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7413 (t0) cc_final: 0.7159 (t0) REVERT: A 655 LYS cc_start: 0.7016 (tptp) cc_final: 0.6675 (tptt) REVERT: B 536 THR cc_start: 0.9102 (t) cc_final: 0.8758 (p) REVERT: B 540 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: B 544 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8379 (mt) REVERT: C 46 LYS cc_start: 0.8673 (pttm) cc_final: 0.8461 (pttp) REVERT: C 95 MET cc_start: 0.8906 (ptm) cc_final: 0.7956 (ttp) REVERT: F 632 ASP cc_start: 0.8715 (t70) cc_final: 0.8437 (t0) REVERT: G 67 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6805 (p0) REVERT: G 151 ARG cc_start: 0.9004 (ttm-80) cc_final: 0.8141 (ttp80) REVERT: G 423 ILE cc_start: 0.8849 (mm) cc_final: 0.8616 (mt) REVERT: I 57 ASP cc_start: 0.7951 (t0) cc_final: 0.7701 (t0) REVERT: I 205 CYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6323 (m) REVERT: H 72 ASP cc_start: 0.8325 (t0) cc_final: 0.7987 (t0) REVERT: L 24 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6818 (mt0) outliers start: 59 outliers final: 36 residues processed: 241 average time/residue: 0.3004 time to fit residues: 108.7033 Evaluate side-chains 218 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN I 103 GLN H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.171389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140538 restraints weight = 20899.861| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.30 r_work: 0.3445 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17449 Z= 0.145 Angle : 0.690 19.010 23890 Z= 0.313 Chirality : 0.049 0.725 2959 Planarity : 0.004 0.042 2840 Dihedral : 9.420 112.900 4403 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.35 % Allowed : 12.02 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1932 helix: 0.95 (0.28), residues: 387 sheet: 0.23 (0.22), residues: 570 loop : -0.56 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 35 HIS 0.004 0.001 HIS G 66 PHE 0.019 0.001 PHE C 317 TYR 0.013 0.001 TYR H 100E ARG 0.008 0.000 ARG G 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 61) link_NAG-ASN : angle 2.81424 ( 183) link_ALPHA1-6 : bond 0.00857 ( 8) link_ALPHA1-6 : angle 1.67013 ( 24) link_BETA1-4 : bond 0.00477 ( 30) link_BETA1-4 : angle 1.35857 ( 90) link_ALPHA1-2 : bond 0.00920 ( 5) link_ALPHA1-2 : angle 2.24860 ( 15) link_ALPHA1-3 : bond 0.01175 ( 8) link_ALPHA1-3 : angle 1.69135 ( 24) hydrogen bonds : bond 0.04254 ( 484) hydrogen bonds : angle 4.80677 ( 1314) SS BOND : bond 0.00342 ( 37) SS BOND : angle 1.51555 ( 74) covalent geometry : bond 0.00343 (17300) covalent geometry : angle 0.63165 (23480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 1.819 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 651 ASN cc_start: 0.7387 (t0) cc_final: 0.7143 (t0) REVERT: A 655 LYS cc_start: 0.6872 (tptp) cc_final: 0.6534 (tptt) REVERT: B 536 THR cc_start: 0.9075 (t) cc_final: 0.8733 (p) REVERT: B 540 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: B 544 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8408 (mt) REVERT: G 100 MET cc_start: 0.8977 (mtp) cc_final: 0.8691 (mtp) REVERT: G 151 ARG cc_start: 0.9003 (ttm-80) cc_final: 0.8181 (ttp80) REVERT: G 423 ILE cc_start: 0.8853 (mm) cc_final: 0.8622 (mt) REVERT: I 205 CYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6342 (m) REVERT: H 72 ASP cc_start: 0.8385 (t0) cc_final: 0.8075 (t0) REVERT: H 81 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.5678 (mp-120) REVERT: H 94 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7732 (ttt-90) REVERT: L 24 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6840 (mt0) outliers start: 58 outliers final: 45 residues processed: 235 average time/residue: 0.3115 time to fit residues: 110.1803 Evaluate side-chains 229 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 113 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 428 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139999 restraints weight = 20789.820| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.28 r_work: 0.3451 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17449 Z= 0.156 Angle : 0.693 19.012 23890 Z= 0.313 Chirality : 0.048 0.544 2959 Planarity : 0.004 0.041 2840 Dihedral : 8.980 111.727 4403 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.22 % Allowed : 11.21 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1932 helix: 0.93 (0.28), residues: 389 sheet: 0.29 (0.22), residues: 552 loop : -0.63 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 479 HIS 0.004 0.001 HIS H 100R PHE 0.017 0.001 PHE C 317 TYR 0.019 0.001 TYR G 173 ARG 0.006 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 61) link_NAG-ASN : angle 2.75666 ( 183) link_ALPHA1-6 : bond 0.00855 ( 8) link_ALPHA1-6 : angle 1.68782 ( 24) link_BETA1-4 : bond 0.00484 ( 30) link_BETA1-4 : angle 1.34999 ( 90) link_ALPHA1-2 : bond 0.01001 ( 5) link_ALPHA1-2 : angle 2.32608 ( 15) link_ALPHA1-3 : bond 0.01173 ( 8) link_ALPHA1-3 : angle 1.71856 ( 24) hydrogen bonds : bond 0.04241 ( 484) hydrogen bonds : angle 4.75188 ( 1314) SS BOND : bond 0.00338 ( 37) SS BOND : angle 1.50648 ( 74) covalent geometry : bond 0.00374 (17300) covalent geometry : angle 0.63671 (23480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7377 (t0) cc_final: 0.7137 (t0) REVERT: A 655 LYS cc_start: 0.6835 (tptp) cc_final: 0.6518 (tptt) REVERT: B 536 THR cc_start: 0.9073 (t) cc_final: 0.8745 (p) REVERT: B 540 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: B 544 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8461 (mt) REVERT: C 95 MET cc_start: 0.8904 (ptm) cc_final: 0.7820 (ttp) REVERT: C 292 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8898 (m) REVERT: F 632 ASP cc_start: 0.8721 (t70) cc_final: 0.8463 (t0) REVERT: G 100 MET cc_start: 0.8970 (mtp) cc_final: 0.8669 (mtp) REVERT: G 151 ARG cc_start: 0.8998 (ttm-80) cc_final: 0.8149 (ttp80) REVERT: G 423 ILE cc_start: 0.8853 (mm) cc_final: 0.8645 (mt) REVERT: I 151 ARG cc_start: 0.8506 (tpm170) cc_final: 0.7615 (tpp80) REVERT: I 268 GLU cc_start: 0.6788 (pt0) cc_final: 0.6547 (pt0) REVERT: H 72 ASP cc_start: 0.8359 (t0) cc_final: 0.8020 (t0) REVERT: H 82 MET cc_start: 0.6771 (mmm) cc_final: 0.6550 (mmm) REVERT: L 24 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6828 (mt0) outliers start: 73 outliers final: 54 residues processed: 247 average time/residue: 0.3008 time to fit residues: 112.3393 Evaluate side-chains 236 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.179805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151750 restraints weight = 20141.836| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.09 r_work: 0.3605 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17449 Z= 0.137 Angle : 0.675 18.677 23890 Z= 0.306 Chirality : 0.047 0.465 2959 Planarity : 0.003 0.040 2840 Dihedral : 8.031 58.576 4403 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.64 % Allowed : 12.19 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1932 helix: 1.07 (0.28), residues: 387 sheet: 0.31 (0.22), residues: 552 loop : -0.59 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 479 HIS 0.003 0.001 HIS H 100R PHE 0.019 0.001 PHE C 53 TYR 0.017 0.001 TYR G 173 ARG 0.004 0.000 ARG G 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 61) link_NAG-ASN : angle 2.62745 ( 183) link_ALPHA1-6 : bond 0.00795 ( 8) link_ALPHA1-6 : angle 1.55849 ( 24) link_BETA1-4 : bond 0.00480 ( 30) link_BETA1-4 : angle 1.33568 ( 90) link_ALPHA1-2 : bond 0.01097 ( 5) link_ALPHA1-2 : angle 2.40098 ( 15) link_ALPHA1-3 : bond 0.01137 ( 8) link_ALPHA1-3 : angle 1.68042 ( 24) hydrogen bonds : bond 0.03984 ( 484) hydrogen bonds : angle 4.68359 ( 1314) SS BOND : bond 0.00321 ( 37) SS BOND : angle 1.32526 ( 74) covalent geometry : bond 0.00319 (17300) covalent geometry : angle 0.62293 (23480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.7678 (tp30) cc_final: 0.7374 (tp30) REVERT: A 655 LYS cc_start: 0.6842 (tptp) cc_final: 0.6503 (tptt) REVERT: B 540 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: B 544 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8460 (mt) REVERT: C 95 MET cc_start: 0.8894 (ptm) cc_final: 0.7784 (ttp) REVERT: C 205 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6606 (m) REVERT: C 292 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8847 (m) REVERT: C 434 MET cc_start: 0.7822 (tmm) cc_final: 0.7046 (ttp) REVERT: F 617 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7731 (ttm-80) REVERT: G 100 MET cc_start: 0.8953 (mtp) cc_final: 0.8669 (mtp) REVERT: G 151 ARG cc_start: 0.8949 (ttm-80) cc_final: 0.8192 (ttp80) REVERT: G 423 ILE cc_start: 0.8829 (mm) cc_final: 0.8629 (mt) REVERT: I 151 ARG cc_start: 0.8386 (tpm170) cc_final: 0.7586 (tpp80) REVERT: I 161 MET cc_start: 0.8241 (mmm) cc_final: 0.7691 (tpp) REVERT: H 38 ARG cc_start: 0.7699 (ptt180) cc_final: 0.7272 (ptt180) REVERT: H 72 ASP cc_start: 0.8365 (t0) cc_final: 0.8007 (t0) REVERT: L 24 GLN cc_start: 0.7337 (tm-30) cc_final: 0.6981 (mt0) outliers start: 63 outliers final: 55 residues processed: 239 average time/residue: 0.2937 time to fit residues: 105.4285 Evaluate side-chains 239 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 119 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.0030 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 ASN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.180832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153251 restraints weight = 20135.196| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.05 r_work: 0.3637 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17449 Z= 0.142 Angle : 0.677 14.648 23890 Z= 0.308 Chirality : 0.047 0.432 2959 Planarity : 0.004 0.041 2840 Dihedral : 7.756 58.415 4403 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.81 % Allowed : 12.59 % Favored : 83.59 % 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 (0.19), residues: 1932 helix: 1.12 (0.28), residues: 387 sheet: 0.32 (0.22), residues: 552 loop : -0.59 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 479 HIS 0.003 0.001 HIS H 100R PHE 0.017 0.001 PHE C 53 TYR 0.016 0.001 TYR G 173 ARG 0.007 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 61) link_NAG-ASN : angle 2.60141 ( 183) link_ALPHA1-6 : bond 0.00692 ( 8) link_ALPHA1-6 : angle 1.58578 ( 24) link_BETA1-4 : bond 0.00485 ( 30) link_BETA1-4 : angle 1.33122 ( 90) link_ALPHA1-2 : bond 0.01124 ( 5) link_ALPHA1-2 : angle 2.47762 ( 15) link_ALPHA1-3 : bond 0.01076 ( 8) link_ALPHA1-3 : angle 1.65604 ( 24) hydrogen bonds : bond 0.03991 ( 484) hydrogen bonds : angle 4.67913 ( 1314) SS BOND : bond 0.00316 ( 37) SS BOND : angle 1.31714 ( 74) covalent geometry : bond 0.00336 (17300) covalent geometry : angle 0.62622 (23480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.6772 (tptp) cc_final: 0.6440 (tptt) REVERT: B 540 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: B 544 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 95 MET cc_start: 0.8925 (ptm) cc_final: 0.7826 (ttp) REVERT: C 205 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6587 (m) REVERT: C 434 MET cc_start: 0.7922 (tmm) cc_final: 0.7166 (ttp) REVERT: F 632 ASP cc_start: 0.8687 (t70) cc_final: 0.8483 (t0) REVERT: G 95 MET cc_start: 0.8281 (ptm) cc_final: 0.7822 (ttp) REVERT: G 96 TRP cc_start: 0.8494 (m100) cc_final: 0.8096 (m100) REVERT: G 100 MET cc_start: 0.8954 (mtp) cc_final: 0.8662 (mtp) REVERT: G 151 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8187 (ttp80) REVERT: I 151 ARG cc_start: 0.8408 (tpm170) cc_final: 0.7598 (tpp80) REVERT: I 161 MET cc_start: 0.8227 (mmm) cc_final: 0.7671 (tpp) REVERT: H 72 ASP cc_start: 0.8329 (t0) cc_final: 0.7942 (t0) REVERT: L 24 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6935 (mt0) outliers start: 66 outliers final: 54 residues processed: 237 average time/residue: 0.2820 time to fit residues: 100.7927 Evaluate side-chains 235 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 151 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 172 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 658 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.185019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158010 restraints weight = 20101.744| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.14 r_work: 0.3640 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17449 Z= 0.129 Angle : 0.658 14.018 23890 Z= 0.300 Chirality : 0.046 0.405 2959 Planarity : 0.003 0.040 2840 Dihedral : 7.594 58.328 4403 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.41 % Allowed : 13.11 % Favored : 83.48 % 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: 0.03 (0.19), residues: 1932 helix: 1.17 (0.28), residues: 387 sheet: 0.34 (0.22), residues: 552 loop : -0.59 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 479 HIS 0.003 0.001 HIS H 100R PHE 0.018 0.001 PHE C 53 TYR 0.016 0.001 TYR G 173 ARG 0.006 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 61) link_NAG-ASN : angle 2.44861 ( 183) link_ALPHA1-6 : bond 0.00763 ( 8) link_ALPHA1-6 : angle 1.57713 ( 24) link_BETA1-4 : bond 0.00476 ( 30) link_BETA1-4 : angle 1.32186 ( 90) link_ALPHA1-2 : bond 0.01168 ( 5) link_ALPHA1-2 : angle 2.43874 ( 15) link_ALPHA1-3 : bond 0.01094 ( 8) link_ALPHA1-3 : angle 1.62144 ( 24) hydrogen bonds : bond 0.03834 ( 484) hydrogen bonds : angle 4.63411 ( 1314) SS BOND : bond 0.00310 ( 37) SS BOND : angle 1.27451 ( 74) covalent geometry : bond 0.00299 (17300) covalent geometry : angle 0.61058 (23480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.6767 (tptp) cc_final: 0.6460 (tptt) REVERT: B 540 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: B 544 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 95 MET cc_start: 0.8915 (ptm) cc_final: 0.7786 (ttp) REVERT: C 205 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6531 (m) REVERT: C 434 MET cc_start: 0.7920 (tmm) cc_final: 0.7184 (ttp) REVERT: F 632 ASP cc_start: 0.8693 (t70) cc_final: 0.8408 (t0) REVERT: F 656 ASN cc_start: 0.7888 (m-40) cc_final: 0.7478 (t0) REVERT: G 96 TRP cc_start: 0.8418 (m100) cc_final: 0.8052 (m100) REVERT: G 100 MET cc_start: 0.8946 (mtp) cc_final: 0.8694 (mtp) REVERT: G 151 ARG cc_start: 0.8941 (ttm-80) cc_final: 0.8315 (ttm110) REVERT: I 151 ARG cc_start: 0.8415 (tpm170) cc_final: 0.7593 (tpp80) REVERT: I 161 MET cc_start: 0.8202 (mmm) cc_final: 0.7666 (tpp) REVERT: H 72 ASP cc_start: 0.8335 (t0) cc_final: 0.7942 (t0) REVERT: L 24 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6965 (mt0) outliers start: 59 outliers final: 53 residues processed: 229 average time/residue: 0.2904 time to fit residues: 102.0007 Evaluate side-chains 233 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 152 optimal weight: 0.0980 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 428 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157607 restraints weight = 20119.487| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.28 r_work: 0.3602 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17449 Z= 0.130 Angle : 0.654 13.585 23890 Z= 0.299 Chirality : 0.046 0.390 2959 Planarity : 0.003 0.040 2840 Dihedral : 7.489 58.291 4403 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.58 % Allowed : 12.94 % Favored : 83.48 % 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: 0.04 (0.19), residues: 1932 helix: 1.23 (0.28), residues: 384 sheet: 0.29 (0.22), residues: 564 loop : -0.57 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 479 HIS 0.003 0.001 HIS H 100R PHE 0.017 0.001 PHE C 53 TYR 0.016 0.001 TYR G 173 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 61) link_NAG-ASN : angle 2.37486 ( 183) link_ALPHA1-6 : bond 0.00734 ( 8) link_ALPHA1-6 : angle 1.58103 ( 24) link_BETA1-4 : bond 0.00476 ( 30) link_BETA1-4 : angle 1.32060 ( 90) link_ALPHA1-2 : bond 0.01115 ( 5) link_ALPHA1-2 : angle 2.43074 ( 15) link_ALPHA1-3 : bond 0.01075 ( 8) link_ALPHA1-3 : angle 1.60565 ( 24) hydrogen bonds : bond 0.03787 ( 484) hydrogen bonds : angle 4.62314 ( 1314) SS BOND : bond 0.00309 ( 37) SS BOND : angle 1.25915 ( 74) covalent geometry : bond 0.00304 (17300) covalent geometry : angle 0.60911 (23480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8479.42 seconds wall clock time: 147 minutes 50.46 seconds (8870.46 seconds total)