Starting phenix.real_space_refine on Sun Aug 24 05:07:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fk5_29248/08_2025/8fk5_29248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fk5_29248/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fk5_29248/08_2025/8fk5_29248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fk5_29248/08_2025/8fk5_29248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fk5_29248/08_2025/8fk5_29248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fk5_29248/08_2025/8fk5_29248.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.77, per 1000 atoms: 0.22 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: 1.74 Conformation dependent library (CDL) restraints added in 540.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.70 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: 2.40 Time building geometry restraints manager: 2.08 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 702) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 702)) } ncs_group { reference = (chain 'C' and resid 33 through 609) selection = (chain 'G' and resid 33 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: 2.260 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.270 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- 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 : 3.60 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG F 585 TYR 0.008 0.001 TYR L 49 PHE 0.006 0.001 PHE C 53 TRP 0.019 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00516 (17300) covalent geometry : angle 0.72261 (23480) SS BOND : bond 0.00183 ( 37) SS BOND : angle 0.98692 ( 74) hydrogen bonds : bond 0.24659 ( 484) hydrogen bonds : angle 8.15189 ( 1314) 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) 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_NAG-ASN : bond 0.00299 ( 61) link_NAG-ASN : angle 1.82595 ( 183) *********************** 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 : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.1420 time to fit residues: 67.8674 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 : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 374 HIS C 478 ASN G 249 HIS G 374 HIS I 99 ASN I 374 HIS H 100CASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148289 restraints weight = 21563.060| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.24 r_work: 0.3510 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17449 Z= 0.221 Angle : 0.772 13.704 23890 Z= 0.360 Chirality : 0.049 0.368 2959 Planarity : 0.004 0.048 2840 Dihedral : 12.206 114.953 4403 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.02 % Allowed : 6.93 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.19), residues: 1932 helix: 0.85 (0.27), residues: 386 sheet: 0.48 (0.22), residues: 513 loop : -0.39 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 360 TYR 0.016 0.002 TYR F 643 PHE 0.027 0.002 PHE C 53 TRP 0.020 0.002 TRP C 479 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00531 (17300) covalent geometry : angle 0.71784 (23480) SS BOND : bond 0.00397 ( 37) SS BOND : angle 1.75057 ( 74) hydrogen bonds : bond 0.06378 ( 484) hydrogen bonds : angle 5.68522 ( 1314) link_ALPHA1-2 : bond 0.00935 ( 5) link_ALPHA1-2 : angle 2.45475 ( 15) link_ALPHA1-3 : bond 0.01018 ( 8) link_ALPHA1-3 : angle 2.02514 ( 24) link_ALPHA1-6 : bond 0.00619 ( 8) link_ALPHA1-6 : angle 1.70794 ( 24) link_BETA1-4 : bond 0.00519 ( 30) link_BETA1-4 : angle 1.71598 ( 90) link_NAG-ASN : bond 0.00583 ( 61) link_NAG-ASN : angle 2.75718 ( 183) *********************** 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 246 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.8372 (m) cc_final: 0.8061 (t) REVERT: A 584 GLU cc_start: 0.8444 (pt0) cc_final: 0.8135 (mt-10) REVERT: B 536 THR cc_start: 0.9067 (t) cc_final: 0.8781 (p) REVERT: C 349 LEU cc_start: 0.8432 (mt) cc_final: 0.8217 (mt) REVERT: G 151 ARG cc_start: 0.8998 (ttm-80) cc_final: 0.8296 (ttm110) REVERT: G 485 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7635 (tttp) REVERT: I 115 SER cc_start: 0.9076 (t) cc_final: 0.8857 (p) REVERT: I 246 GLN cc_start: 0.7602 (pm20) cc_final: 0.7362 (pm20) REVERT: H 94 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7854 (ttt-90) REVERT: L 36 TYR cc_start: 0.7976 (m-80) cc_final: 0.7540 (m-80) outliers start: 35 outliers final: 25 residues processed: 235 average time/residue: 0.1550 time to fit residues: 53.2505 Evaluate side-chains 205 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 613 SER 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 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain G residue 52 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 132 THR 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 355 ASN Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 32 SER 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 108 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN G 422 GLN I 99 ASN H 100CASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142710 restraints weight = 20874.052| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.30 r_work: 0.3484 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17449 Z= 0.167 Angle : 0.695 18.037 23890 Z= 0.320 Chirality : 0.047 0.323 2959 Planarity : 0.004 0.045 2840 Dihedral : 11.267 117.474 4403 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.43 % Allowed : 8.72 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1932 helix: 0.90 (0.28), residues: 387 sheet: 0.48 (0.22), residues: 519 loop : -0.44 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 500 TYR 0.018 0.001 TYR C 484 PHE 0.027 0.002 PHE C 53 TRP 0.019 0.001 TRP I 35 HIS 0.006 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00398 (17300) covalent geometry : angle 0.63959 (23480) SS BOND : bond 0.00293 ( 37) SS BOND : angle 1.62179 ( 74) hydrogen bonds : bond 0.05285 ( 484) hydrogen bonds : angle 5.19848 ( 1314) link_ALPHA1-2 : bond 0.00875 ( 5) link_ALPHA1-2 : angle 2.03324 ( 15) link_ALPHA1-3 : bond 0.01129 ( 8) link_ALPHA1-3 : angle 1.59531 ( 24) link_ALPHA1-6 : bond 0.00738 ( 8) link_ALPHA1-6 : angle 1.65673 ( 24) link_BETA1-4 : bond 0.00495 ( 30) link_BETA1-4 : angle 1.49512 ( 90) link_NAG-ASN : bond 0.00555 ( 61) link_NAG-ASN : angle 2.69947 ( 183) *********************** 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 242 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9077 (t) cc_final: 0.8770 (p) REVERT: B 654 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6900 (tt0) REVERT: C 95 MET cc_start: 0.8807 (ptm) cc_final: 0.7904 (ttp) REVERT: C 205 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6943 (m) REVERT: C 349 LEU cc_start: 0.8304 (mt) cc_final: 0.8083 (mt) REVERT: F 617 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7574 (ttm170) REVERT: G 151 ARG cc_start: 0.9033 (ttm-80) cc_final: 0.8180 (ttp80) REVERT: G 485 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7582 (tttp) REVERT: I 115 SER cc_start: 0.9092 (t) cc_final: 0.8831 (p) REVERT: I 205 CYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6447 (m) REVERT: I 246 GLN cc_start: 0.7598 (pm20) cc_final: 0.7184 (pm20) REVERT: H 72 ASP cc_start: 0.8178 (t0) cc_final: 0.7977 (t0) REVERT: H 94 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7825 (ttt-90) REVERT: L 24 GLN cc_start: 0.6874 (tm-30) cc_final: 0.6469 (mt0) REVERT: L 36 TYR cc_start: 0.7935 (m-80) cc_final: 0.7530 (m-80) outliers start: 42 outliers final: 27 residues processed: 233 average time/residue: 0.1537 time to fit residues: 52.8191 Evaluate side-chains 212 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 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 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 297 THR 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 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 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 21 optimal weight: 0.0670 chunk 157 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 134 optimal weight: 0.0470 chunk 193 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 103 GLN H 100CASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.175349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144727 restraints weight = 20724.801| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.29 r_work: 0.3505 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17449 Z= 0.120 Angle : 0.652 18.774 23890 Z= 0.297 Chirality : 0.046 0.353 2959 Planarity : 0.003 0.042 2840 Dihedral : 10.306 115.754 4403 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.60 % Allowed : 10.57 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.19), residues: 1932 helix: 0.99 (0.28), residues: 390 sheet: 0.47 (0.22), residues: 526 loop : -0.38 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 327 TYR 0.015 0.001 TYR G 173 PHE 0.020 0.001 PHE C 53 TRP 0.014 0.001 TRP I 35 HIS 0.005 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00266 (17300) covalent geometry : angle 0.59751 (23480) SS BOND : bond 0.00386 ( 37) SS BOND : angle 1.23787 ( 74) hydrogen bonds : bond 0.04391 ( 484) hydrogen bonds : angle 4.87081 ( 1314) link_ALPHA1-2 : bond 0.00874 ( 5) link_ALPHA1-2 : angle 2.05137 ( 15) link_ALPHA1-3 : bond 0.01153 ( 8) link_ALPHA1-3 : angle 1.63499 ( 24) link_ALPHA1-6 : bond 0.00833 ( 8) link_ALPHA1-6 : angle 1.61139 ( 24) link_BETA1-4 : bond 0.00474 ( 30) link_BETA1-4 : angle 1.41481 ( 90) link_NAG-ASN : bond 0.00451 ( 61) link_NAG-ASN : angle 2.64455 ( 183) *********************** 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 240 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.6950 (tptp) cc_final: 0.6608 (tptt) REVERT: B 536 THR cc_start: 0.9091 (t) cc_final: 0.8754 (p) REVERT: C 46 LYS cc_start: 0.8688 (pttm) cc_final: 0.8457 (pttp) REVERT: C 95 MET cc_start: 0.8692 (ptm) cc_final: 0.7921 (ttp) REVERT: C 205 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6941 (m) REVERT: C 349 LEU cc_start: 0.8281 (mt) cc_final: 0.8058 (mt) REVERT: G 100 MET cc_start: 0.8929 (mtp) cc_final: 0.8626 (mtp) REVERT: G 151 ARG cc_start: 0.9031 (ttm-80) cc_final: 0.8179 (ttp80) REVERT: I 115 SER cc_start: 0.9094 (t) cc_final: 0.8787 (p) REVERT: I 205 CYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6478 (m) REVERT: I 246 GLN cc_start: 0.7533 (pm20) cc_final: 0.7092 (pm20) REVERT: H 72 ASP cc_start: 0.8265 (t0) cc_final: 0.7987 (t0) REVERT: H 94 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7875 (ttt-90) REVERT: L 24 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6555 (mt0) REVERT: L 36 TYR cc_start: 0.7945 (m-80) cc_final: 0.7570 (m-80) outliers start: 45 outliers final: 30 residues processed: 226 average time/residue: 0.1597 time to fit residues: 52.6449 Evaluate side-chains 213 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 B residue 648 GLU 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 F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 292 VAL 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 125 LEU 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 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 68 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN I 99 ASN I 103 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 = 0.3984 r_free = 0.3984 target = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139765 restraints weight = 21678.608| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.28 r_work: 0.3419 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17449 Z= 0.253 Angle : 0.787 18.904 23890 Z= 0.360 Chirality : 0.051 0.385 2959 Planarity : 0.005 0.050 2840 Dihedral : 9.995 114.141 4403 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.70 % Allowed : 10.69 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1932 helix: 0.74 (0.28), residues: 387 sheet: 0.22 (0.22), residues: 543 loop : -0.62 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 500 TYR 0.019 0.002 TYR L 49 PHE 0.020 0.002 PHE C 53 TRP 0.015 0.002 TRP H 47 HIS 0.005 0.002 HIS G 352 Details of bonding type rmsd covalent geometry : bond 0.00623 (17300) covalent geometry : angle 0.73395 (23480) SS BOND : bond 0.00399 ( 37) SS BOND : angle 1.60304 ( 74) hydrogen bonds : bond 0.05342 ( 484) hydrogen bonds : angle 5.14960 ( 1314) link_ALPHA1-2 : bond 0.00863 ( 5) link_ALPHA1-2 : angle 2.37934 ( 15) link_ALPHA1-3 : bond 0.01125 ( 8) link_ALPHA1-3 : angle 1.91027 ( 24) link_ALPHA1-6 : bond 0.00775 ( 8) link_ALPHA1-6 : angle 1.83957 ( 24) link_BETA1-4 : bond 0.00536 ( 30) link_BETA1-4 : angle 1.52402 ( 90) link_NAG-ASN : bond 0.00612 ( 61) link_NAG-ASN : angle 2.86369 ( 183) *********************** 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 262 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 523 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 536 THR cc_start: 0.9119 (t) cc_final: 0.8748 (p) REVERT: B 654 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7318 (tt0) REVERT: C 292 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8852 (m) REVERT: G 151 ARG cc_start: 0.9004 (ttm-80) cc_final: 0.8290 (ttm110) REVERT: G 423 ILE cc_start: 0.8896 (mm) cc_final: 0.8669 (mt) REVERT: I 95 MET cc_start: 0.8647 (ptm) cc_final: 0.8235 (ttp) REVERT: I 115 SER cc_start: 0.9210 (t) cc_final: 0.8869 (p) REVERT: I 205 CYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6541 (m) REVERT: H 72 ASP cc_start: 0.8442 (t0) cc_final: 0.8031 (t0) REVERT: H 94 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7782 (ttt-90) REVERT: H 100 TYR cc_start: 0.8592 (m-80) cc_final: 0.8116 (m-80) REVERT: L 24 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6849 (mt0) outliers start: 64 outliers final: 41 residues processed: 244 average time/residue: 0.1578 time to fit residues: 57.0074 Evaluate side-chains 227 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 SER 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 B residue 647 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 199 SER 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 C residue 496 VAL 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 247 CYS Chi-restraints excluded: chain G residue 270 VAL 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 447 SER Chi-restraints excluded: chain I residue 47 ASP 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 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 396 ILE 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 101 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 5 optimal weight: 0.0370 chunk 143 optimal weight: 0.5980 chunk 186 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN G 67 ASN G 428 GLN I 99 ASN I 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.174389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143361 restraints weight = 21593.692| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.29 r_work: 0.3466 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17449 Z= 0.144 Angle : 0.698 18.998 23890 Z= 0.315 Chirality : 0.049 0.820 2959 Planarity : 0.004 0.043 2840 Dihedral : 9.476 113.339 4403 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.87 % Allowed : 11.32 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 1932 helix: 0.98 (0.28), residues: 387 sheet: 0.39 (0.23), residues: 496 loop : -0.64 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 500 TYR 0.013 0.001 TYR L 49 PHE 0.020 0.001 PHE C 53 TRP 0.010 0.001 TRP C 479 HIS 0.003 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00335 (17300) covalent geometry : angle 0.63419 (23480) SS BOND : bond 0.00402 ( 37) SS BOND : angle 1.54234 ( 74) hydrogen bonds : bond 0.04343 ( 484) hydrogen bonds : angle 4.84480 ( 1314) link_ALPHA1-2 : bond 0.00966 ( 5) link_ALPHA1-2 : angle 2.27318 ( 15) link_ALPHA1-3 : bond 0.01178 ( 8) link_ALPHA1-3 : angle 1.69190 ( 24) link_ALPHA1-6 : bond 0.00868 ( 8) link_ALPHA1-6 : angle 1.66202 ( 24) link_BETA1-4 : bond 0.00468 ( 30) link_BETA1-4 : angle 1.35598 ( 90) link_NAG-ASN : bond 0.00582 ( 61) link_NAG-ASN : angle 3.00542 ( 183) *********************** 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 257 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9082 (t) cc_final: 0.8725 (p) REVERT: C 95 MET cc_start: 0.8547 (ptm) cc_final: 0.8332 (ttp) REVERT: C 292 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8893 (m) REVERT: G 67 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6910 (p0) REVERT: G 151 ARG cc_start: 0.8988 (ttm-80) cc_final: 0.8139 (ttp80) REVERT: G 423 ILE cc_start: 0.8828 (mm) cc_final: 0.8624 (mt) REVERT: I 115 SER cc_start: 0.9156 (t) cc_final: 0.8818 (p) REVERT: I 161 MET cc_start: 0.8363 (mmm) cc_final: 0.7754 (tpp) REVERT: I 205 CYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6406 (m) REVERT: H 72 ASP cc_start: 0.8485 (t0) cc_final: 0.8144 (t0) REVERT: H 94 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7761 (ttt-90) REVERT: H 100 TYR cc_start: 0.8529 (m-80) cc_final: 0.8029 (m-80) REVERT: L 24 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6868 (mt0) outliers start: 67 outliers final: 43 residues processed: 239 average time/residue: 0.1496 time to fit residues: 53.8173 Evaluate side-chains 226 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 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 F residue 648 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 67 ASN 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 138 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU 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 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 L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 156 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 GLN G 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144218 restraints weight = 21526.409| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.52 r_work: 0.3456 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3782 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= 0.135 Angle : 0.677 18.997 23890 Z= 0.305 Chirality : 0.047 0.411 2959 Planarity : 0.004 0.042 2840 Dihedral : 8.895 112.610 4403 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.70 % Allowed : 12.02 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.19), residues: 1932 helix: 1.10 (0.28), residues: 387 sheet: 0.26 (0.22), residues: 562 loop : -0.58 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 500 TYR 0.011 0.001 TYR L 49 PHE 0.017 0.001 PHE C 53 TRP 0.013 0.001 TRP G 69 HIS 0.004 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00315 (17300) covalent geometry : angle 0.61859 (23480) SS BOND : bond 0.00323 ( 37) SS BOND : angle 1.43996 ( 74) hydrogen bonds : bond 0.04042 ( 484) hydrogen bonds : angle 4.73192 ( 1314) link_ALPHA1-2 : bond 0.01106 ( 5) link_ALPHA1-2 : angle 2.32861 ( 15) link_ALPHA1-3 : bond 0.01207 ( 8) link_ALPHA1-3 : angle 1.68274 ( 24) link_ALPHA1-6 : bond 0.00849 ( 8) link_ALPHA1-6 : angle 1.62940 ( 24) link_BETA1-4 : bond 0.00477 ( 30) link_BETA1-4 : angle 1.33852 ( 90) link_NAG-ASN : bond 0.00529 ( 61) link_NAG-ASN : angle 2.79448 ( 183) *********************** 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 252 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9026 (t) cc_final: 0.8657 (p) REVERT: C 292 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8783 (m) REVERT: F 540 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: G 100 MET cc_start: 0.8925 (mtp) cc_final: 0.8702 (mtp) REVERT: G 151 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8126 (ttp80) REVERT: G 267 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: I 115 SER cc_start: 0.9098 (t) cc_final: 0.8764 (p) REVERT: I 151 ARG cc_start: 0.8321 (tpm170) cc_final: 0.7571 (tpp80) REVERT: I 161 MET cc_start: 0.8199 (mmm) cc_final: 0.7587 (tpp) REVERT: I 205 CYS cc_start: 0.6232 (OUTLIER) cc_final: 0.6005 (m) REVERT: H 72 ASP cc_start: 0.8354 (t0) cc_final: 0.8076 (t0) REVERT: H 82 MET cc_start: 0.6722 (mmm) cc_final: 0.6380 (mmm) REVERT: L 24 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6951 (mt0) REVERT: L 36 TYR cc_start: 0.7984 (m-80) cc_final: 0.7699 (m-80) outliers start: 64 outliers final: 47 residues processed: 240 average time/residue: 0.1485 time to fit residues: 53.2704 Evaluate side-chains 228 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR 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 138 ILE Chi-restraints excluded: chain C residue 203 GLN 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 494 LEU Chi-restraints excluded: chain F residue 540 GLN 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 F residue 648 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR 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 213 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 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 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 L residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 35 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 12 optimal weight: 0.0370 chunk 79 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.174835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145174 restraints weight = 20654.060| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.20 r_work: 0.3519 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3906 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= 0.128 Angle : 0.679 19.003 23890 Z= 0.306 Chirality : 0.049 0.786 2959 Planarity : 0.003 0.041 2840 Dihedral : 8.301 112.039 4403 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.52 % Allowed : 12.13 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.19), residues: 1932 helix: 1.17 (0.28), residues: 387 sheet: 0.31 (0.22), residues: 557 loop : -0.55 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 500 TYR 0.014 0.001 TYR H 100E PHE 0.020 0.001 PHE C 53 TRP 0.013 0.001 TRP C 338 HIS 0.004 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00296 (17300) covalent geometry : angle 0.62276 (23480) SS BOND : bond 0.00290 ( 37) SS BOND : angle 1.31047 ( 74) hydrogen bonds : bond 0.03934 ( 484) hydrogen bonds : angle 4.66477 ( 1314) link_ALPHA1-2 : bond 0.01155 ( 5) link_ALPHA1-2 : angle 2.43636 ( 15) link_ALPHA1-3 : bond 0.01144 ( 8) link_ALPHA1-3 : angle 1.66524 ( 24) link_ALPHA1-6 : bond 0.00838 ( 8) link_ALPHA1-6 : angle 1.57963 ( 24) link_BETA1-4 : bond 0.00483 ( 30) link_BETA1-4 : angle 1.32303 ( 90) link_NAG-ASN : bond 0.00479 ( 61) link_NAG-ASN : angle 2.78791 ( 183) *********************** 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 255 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 194 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9090 (t) cc_final: 0.8729 (p) REVERT: C 292 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8779 (m) REVERT: F 540 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: G 95 MET cc_start: 0.8246 (ptm) cc_final: 0.8027 (ttp) REVERT: G 96 TRP cc_start: 0.8383 (m100) cc_final: 0.7975 (m100) REVERT: G 151 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8209 (ttp80) REVERT: G 267 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: I 115 SER cc_start: 0.9137 (t) cc_final: 0.8814 (p) REVERT: I 151 ARG cc_start: 0.8504 (tpm170) cc_final: 0.7622 (tpp80) REVERT: I 161 MET cc_start: 0.8328 (mmm) cc_final: 0.7775 (tpp) REVERT: I 205 CYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6425 (m) REVERT: H 72 ASP cc_start: 0.8440 (t0) cc_final: 0.8150 (t0) REVERT: L 24 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6849 (mt0) REVERT: L 36 TYR cc_start: 0.8003 (m-80) cc_final: 0.7730 (m-80) outliers start: 61 outliers final: 51 residues processed: 243 average time/residue: 0.1292 time to fit residues: 47.8103 Evaluate side-chains 231 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR 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 137 ASN Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 GLN 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 494 LEU Chi-restraints excluded: chain F residue 540 GLN 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 F residue 648 GLU 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 247 CYS Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 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 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 L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 60 optimal weight: 0.3980 chunk 176 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 110 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.183819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156501 restraints weight = 20155.618| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.06 r_work: 0.3634 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4007 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= 0.140 Angle : 0.672 15.489 23890 Z= 0.306 Chirality : 0.048 0.687 2959 Planarity : 0.003 0.041 2840 Dihedral : 7.638 58.364 4403 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.76 % Allowed : 12.13 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.19), residues: 1932 helix: 1.19 (0.28), residues: 387 sheet: 0.25 (0.22), residues: 559 loop : -0.59 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 500 TYR 0.011 0.001 TYR L 49 PHE 0.018 0.001 PHE C 53 TRP 0.009 0.001 TRP C 96 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd covalent geometry : bond 0.00331 (17300) covalent geometry : angle 0.62149 (23480) SS BOND : bond 0.00292 ( 37) SS BOND : angle 1.32682 ( 74) hydrogen bonds : bond 0.03922 ( 484) hydrogen bonds : angle 4.67233 ( 1314) link_ALPHA1-2 : bond 0.01215 ( 5) link_ALPHA1-2 : angle 2.45943 ( 15) link_ALPHA1-3 : bond 0.01108 ( 8) link_ALPHA1-3 : angle 1.67648 ( 24) link_ALPHA1-6 : bond 0.00741 ( 8) link_ALPHA1-6 : angle 1.60160 ( 24) link_BETA1-4 : bond 0.00484 ( 30) link_BETA1-4 : angle 1.32296 ( 90) link_NAG-ASN : bond 0.00422 ( 61) link_NAG-ASN : angle 2.58379 ( 183) *********************** 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 258 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9054 (t) cc_final: 0.8713 (p) REVERT: C 113 ASP cc_start: 0.8611 (m-30) cc_final: 0.8348 (m-30) REVERT: F 540 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: F 632 ASP cc_start: 0.8519 (t70) cc_final: 0.8304 (t0) REVERT: G 95 MET cc_start: 0.8287 (ptm) cc_final: 0.7735 (ttp) REVERT: G 96 TRP cc_start: 0.8436 (m100) cc_final: 0.8044 (m100) REVERT: G 151 ARG cc_start: 0.8929 (ttm-80) cc_final: 0.8333 (ttm110) REVERT: G 217 TYR cc_start: 0.8798 (m-80) cc_final: 0.8534 (m-80) REVERT: I 95 MET cc_start: 0.8419 (ptm) cc_final: 0.7967 (ttp) REVERT: I 115 SER cc_start: 0.9169 (t) cc_final: 0.8857 (p) REVERT: I 151 ARG cc_start: 0.8407 (tpm170) cc_final: 0.7648 (tpp80) REVERT: H 72 ASP cc_start: 0.8456 (t0) cc_final: 0.8193 (t0) REVERT: H 82 MET cc_start: 0.6727 (mmm) cc_final: 0.6489 (mmm) REVERT: L 24 GLN cc_start: 0.7357 (tm-30) cc_final: 0.7000 (mt0) outliers start: 65 outliers final: 55 residues processed: 247 average time/residue: 0.1348 time to fit residues: 51.0494 Evaluate side-chains 242 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR 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 199 SER Chi-restraints excluded: chain C residue 203 GLN 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 494 LEU Chi-restraints excluded: chain F residue 540 GLN 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 636 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 648 GLU 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 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 259 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 144 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 133 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 62 optimal weight: 0.0050 chunk 140 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 658 GLN I 428 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 = 0.4172 r_free = 0.4172 target = 0.185546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158571 restraints weight = 19903.358| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.14 r_work: 0.3627 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4060 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= 0.123 Angle : 0.656 14.631 23890 Z= 0.298 Chirality : 0.047 0.617 2959 Planarity : 0.003 0.040 2840 Dihedral : 7.454 58.208 4403 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.18 % Allowed : 12.77 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1932 helix: 1.25 (0.28), residues: 387 sheet: 0.29 (0.22), residues: 565 loop : -0.56 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 500 TYR 0.011 0.001 TYR H 100E PHE 0.017 0.001 PHE C 53 TRP 0.010 0.001 TRP C 338 HIS 0.004 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00284 (17300) covalent geometry : angle 0.60754 (23480) SS BOND : bond 0.00298 ( 37) SS BOND : angle 1.36259 ( 74) hydrogen bonds : bond 0.03773 ( 484) hydrogen bonds : angle 4.61904 ( 1314) link_ALPHA1-2 : bond 0.01125 ( 5) link_ALPHA1-2 : angle 2.43765 ( 15) link_ALPHA1-3 : bond 0.01085 ( 8) link_ALPHA1-3 : angle 1.60268 ( 24) link_ALPHA1-6 : bond 0.00747 ( 8) link_ALPHA1-6 : angle 1.56399 ( 24) link_BETA1-4 : bond 0.00472 ( 30) link_BETA1-4 : angle 1.31481 ( 90) link_NAG-ASN : bond 0.00482 ( 61) link_NAG-ASN : angle 2.44826 ( 183) ********************** 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 241 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 ASP cc_start: 0.8612 (m-30) cc_final: 0.8349 (m-30) REVERT: F 540 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7062 (mt0) REVERT: G 95 MET cc_start: 0.8185 (ptm) cc_final: 0.7837 (ttp) REVERT: G 96 TRP cc_start: 0.8384 (m100) cc_final: 0.8021 (m100) REVERT: G 151 ARG cc_start: 0.8934 (ttm-80) cc_final: 0.8324 (ttm110) REVERT: G 217 TYR cc_start: 0.8778 (m-80) cc_final: 0.8512 (m-80) REVERT: G 267 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: I 95 MET cc_start: 0.8356 (ptm) cc_final: 0.8011 (ttp) REVERT: I 115 SER cc_start: 0.9093 (t) cc_final: 0.8826 (p) REVERT: I 151 ARG cc_start: 0.8402 (tpm170) cc_final: 0.7618 (tpp80) REVERT: I 161 MET cc_start: 0.8116 (mmm) cc_final: 0.7680 (tpp) REVERT: H 72 ASP cc_start: 0.8403 (t0) cc_final: 0.8157 (t0) REVERT: L 24 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7029 (mt0) REVERT: L 36 TYR cc_start: 0.7942 (m-80) cc_final: 0.7681 (m-80) outliers start: 55 outliers final: 53 residues processed: 231 average time/residue: 0.1299 time to fit residues: 45.7392 Evaluate side-chains 238 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 545 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR 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 203 GLN 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 494 LEU Chi-restraints excluded: chain F residue 540 GLN 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 F residue 648 GLU 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 247 CYS Chi-restraints excluded: chain G residue 267 GLU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 259 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.185597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.158628 restraints weight = 19976.011| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.15 r_work: 0.3651 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.035 17449 Z= 0.123 Angle : 0.650 14.218 23890 Z= 0.296 Chirality : 0.047 0.565 2959 Planarity : 0.003 0.040 2840 Dihedral : 7.376 58.131 4403 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.41 % Allowed : 12.82 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1932 helix: 1.31 (0.28), residues: 384 sheet: 0.29 (0.22), residues: 565 loop : -0.54 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 500 TYR 0.011 0.001 TYR H 100E PHE 0.017 0.001 PHE C 53 TRP 0.011 0.001 TRP C 96 HIS 0.004 0.001 HIS H 100R Details of bonding type rmsd covalent geometry : bond 0.00286 (17300) covalent geometry : angle 0.60391 (23480) SS BOND : bond 0.00272 ( 37) SS BOND : angle 1.29104 ( 74) hydrogen bonds : bond 0.03736 ( 484) hydrogen bonds : angle 4.60255 ( 1314) link_ALPHA1-2 : bond 0.01127 ( 5) link_ALPHA1-2 : angle 2.40429 ( 15) link_ALPHA1-3 : bond 0.01077 ( 8) link_ALPHA1-3 : angle 1.59679 ( 24) link_ALPHA1-6 : bond 0.00742 ( 8) link_ALPHA1-6 : angle 1.56748 ( 24) link_BETA1-4 : bond 0.00473 ( 30) link_BETA1-4 : angle 1.31089 ( 90) link_NAG-ASN : bond 0.00473 ( 61) link_NAG-ASN : angle 2.37777 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4385.32 seconds wall clock time: 76 minutes 1.74 seconds (4561.74 seconds total)