Starting phenix.real_space_refine on Sun May 18 21:07:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtd_36641/05_2025/8jtd_36641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtd_36641/05_2025/8jtd_36641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtd_36641/05_2025/8jtd_36641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtd_36641/05_2025/8jtd_36641.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtd_36641/05_2025/8jtd_36641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtd_36641/05_2025/8jtd_36641.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 111 5.16 5 C 10755 2.51 5 N 2830 2.21 5 O 3579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17275 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3545 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1094 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 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: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "0" 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: "1" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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 Residues with excluded nonbonded symmetry interactions: 63 residue: pdb=" C1 NAG P 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 1 " occ=0.00 residue: pdb=" C1 NAG P 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG P 2 " occ=0.00 residue: pdb=" C1 NAG R 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 1 " occ=0.00 residue: pdb=" C1 NAG R 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG R 2 " occ=0.00 residue: pdb=" C1 NAG S 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 1 " occ=0.00 residue: pdb=" C1 NAG S 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG S 2 " occ=0.00 residue: pdb=" C1 BMA S 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA S 3 " occ=0.00 residue: pdb=" C1 NAG T 1 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 1 " occ=0.00 residue: pdb=" C1 NAG T 2 " occ=0.00 ... (12 atoms not shown) pdb=" O7 NAG T 2 " occ=0.00 residue: pdb=" C1 BMA T 3 " occ=0.00 ... (9 atoms not shown) pdb=" O6 BMA T 3 " occ=0.00 residue: pdb=" C1 MAN T 4 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 4 " occ=0.00 residue: pdb=" C1 MAN T 5 " occ=0.00 ... (9 atoms not shown) pdb=" O6 MAN T 5 " occ=0.00 ... (remaining 51 not shown) Time building chain proxies: 10.04, per 1000 atoms: 0.58 Number of scatterers: 17275 At special positions: 0 Unit cell: (129, 137.6, 166.84, 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 111 16.00 O 3579 8.00 N 2830 7.00 C 10755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 Atom "HETATM17035 O5 NAG A 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " " MAN f 4 " - " MAN f 5 " " MAN q 4 " - " MAN q 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA k 3 " - " MAN k 4 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " " BMA x 3 " - " MAN x 4 " ALPHA1-6 " BMA T 3 " - " MAN T 6 " " BMA Y 3 " - " MAN Y 5 " " BMA f 3 " - " MAN f 6 " " BMA k 3 " - " MAN k 5 " " BMA q 3 " - " MAN q 6 " " MAN q 6 " - " MAN q 8 " " BMA s 3 " - " MAN s 6 " " BMA x 3 " - " MAN x 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN E 637 " " NAG 1 1 " - " ASN F 611 " " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 355 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 339 " " NAG D 604 " - " ASN D 355 " " NAG D 605 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 133 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 363 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN C 133 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 363 " " NAG l 1 " - " ASN C 386 " " NAG m 1 " - " ASN C 392 " " NAG n 1 " - " ASN C 448 " " NAG o 1 " - " ASN D 88 " " NAG p 1 " - " ASN D 156 " " NAG q 1 " - " ASN D 160 " " NAG r 1 " - " ASN D 197 " " NAG s 1 " - " ASN D 262 " " NAG u 1 " - " ASN D 295 " " NAG v 1 " - " ASN D 301 " " NAG w 1 " - " ASN D 332 " " NAG x 1 " - " ASN D 363 " " NAG y 1 " - " ASN D 386 " " NAG z 1 " - " ASN D 448 " Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 2.2 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3686 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 33 sheets defined 27.1% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.695A pdb=" N THR A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.646A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.654A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.654A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.422A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.841A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.219A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.886A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.922A pdb=" N THR C 63 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.927A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 127 " --> pdb=" O PRO C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 127' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.667A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.682A pdb=" N SER C 463 " --> pdb=" O SER C 460 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 464 " --> pdb=" O THR C 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 464' Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.505A pdb=" N ARG D 151 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.668A pdb=" N GLU D 381 " --> pdb=" O CYS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 removed outlier: 3.660A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 392 " --> pdb=" O GLY D 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 392' Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.918A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 3.705A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.954A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.303A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 650 through 664 removed outlier: 3.728A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 3.614A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.882A pdb=" N SER F 534 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 531 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.170A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.111A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.596A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 31 removed outlier: 5.831A pdb=" N PHE J 29 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 removed outlier: 3.791A pdb=" N GLN J 62 " --> pdb=" O GLN J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.603A pdb=" N VAL N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.655A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.120A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.691A pdb=" N VAL A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 159 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.404A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.414A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 361 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.632A pdb=" N VAL C 489 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 224 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.179A pdb=" N GLN C 130 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.853A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 416 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.050A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'D' and resid 76 through 77 removed outlier: 7.381A pdb=" N THR D 77 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 56 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.302A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 489 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 removed outlier: 3.700A pdb=" N MET D 161 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 159 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN D 156 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.843A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.521A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.521A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 359 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 374 through 376 removed outlier: 3.900A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 6 removed outlier: 5.814A pdb=" N SER J 16 " --> pdb=" O GLY J 82B" (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.168A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.168A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS J 92 " --> pdb=" O TRP J 108 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP J 108 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR J 94 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS J 98 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU J 102 " --> pdb=" O HIS J 98 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU J 100 " --> pdb=" O ASP J 100R" (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP J 100R" --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP J 100B" --> pdb=" O TRP J 100P" (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP J 100P" --> pdb=" O ASP J 100B" (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE J 100D" --> pdb=" O GLU J 100N" (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU J 100N" --> pdb=" O PHE J 100D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 7 removed outlier: 5.139A pdb=" N GLU N 17 " --> pdb=" O ARG N 77 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG N 77 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.509A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS N 53 " --> pdb=" O HIS N 49 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5323 1.34 - 1.47: 4536 1.47 - 1.60: 7588 1.60 - 1.73: 0 1.73 - 1.85: 151 Bond restraints: 17598 Sorted by residual: bond pdb=" C1 NAG D 603 " pdb=" O5 NAG D 603 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG l 1 " pdb=" O5 NAG l 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 ... (remaining 17593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 23207 2.53 - 5.06: 586 5.06 - 7.59: 88 7.59 - 10.12: 6 10.12 - 12.65: 3 Bond angle restraints: 23890 Sorted by residual: angle pdb=" C LYS C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta sigma weight residual 121.70 134.35 -12.65 1.80e+00 3.09e-01 4.94e+01 angle pdb=" CA ASN A 355 " pdb=" CB ASN A 355 " pdb=" CG ASN A 355 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.06e+01 angle pdb=" C LYS A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta sigma weight residual 121.70 131.26 -9.56 1.80e+00 3.09e-01 2.82e+01 angle pdb=" C TRP A 427 " pdb=" CA TRP A 427 " pdb=" CB TRP A 427 " ideal model delta sigma weight residual 115.79 109.67 6.12 1.19e+00 7.06e-01 2.65e+01 angle pdb=" N ALA D 362 " pdb=" CA ALA D 362 " pdb=" C ALA D 362 " ideal model delta sigma weight residual 108.24 114.96 -6.72 1.32e+00 5.74e-01 2.59e+01 ... (remaining 23885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 11370 24.62 - 49.24: 610 49.24 - 73.87: 110 73.87 - 98.49: 78 98.49 - 123.11: 49 Dihedral angle restraints: 12217 sinusoidal: 6513 harmonic: 5704 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 5.43 87.57 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -6.88 -79.12 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CA CYS C 385 " pdb=" C CYS C 385 " pdb=" N ASN C 386 " pdb=" CA ASN C 386 " ideal model delta harmonic sigma weight residual -180.00 -137.97 -42.03 0 5.00e+00 4.00e-02 7.07e+01 ... (remaining 12214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 3040 0.226 - 0.451: 23 0.451 - 0.677: 4 0.677 - 0.902: 2 0.902 - 1.128: 1 Chirality restraints: 3070 Sorted by residual: chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN D 262 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 3067 not shown) Planarity restraints: 2917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 355 " 0.083 2.00e-02 2.50e+03 7.33e-02 6.71e+01 pdb=" CG ASN A 355 " -0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN A 355 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 355 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " -0.007 2.00e-02 2.50e+03 4.88e-02 2.97e+01 pdb=" CG ASN B 637 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 339 " 0.005 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN D 339 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN D 339 " 0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN D 339 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG D 603 " 0.040 2.00e-02 2.50e+03 ... (remaining 2914 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 360 2.62 - 3.19: 16069 3.19 - 3.76: 27137 3.76 - 4.33: 35865 4.33 - 4.90: 56131 Nonbonded interactions: 135562 Sorted by model distance: nonbonded pdb=" O ILE F 595 " pdb=" ND2 ASN F 651 " model vdw 2.048 3.120 nonbonded pdb=" O ILE C 491 " pdb=" NH2 ARG F 585 " model vdw 2.068 3.120 nonbonded pdb=" OE1 GLU C 102 " pdb=" NH1 ARG C 476 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR J 83 " pdb=" OD1 ASP J 85 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR J 70 " pdb=" O TYR J 79 " model vdw 2.185 3.040 ... (remaining 135557 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 '0' selection = chain '1' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 398 or resid 412 through 506 or resid 601 throu \ gh 604)) selection = (chain 'D' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 506 or resid 601 through 604)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'E' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 520 through 545 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'd' selection = chain 'l' selection = chain 'y' } ncs_group { reference = (chain 'T' and (resid 1 or resid 4 through 6)) selection = (chain 'f' and (resid 2 or resid 5 through 7)) selection = (chain 's' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Y' selection = chain 'k' selection = chain 'x' } 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=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.070 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 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 0.100 17761 Z= 0.267 Angle : 1.116 27.182 24344 Z= 0.488 Chirality : 0.067 1.128 3070 Planarity : 0.004 0.054 2860 Dihedral : 17.494 123.110 8426 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1944 helix: 0.11 (0.26), residues: 418 sheet: 0.00 (0.22), residues: 509 loop : -0.31 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 45 HIS 0.007 0.001 HIS N 53 PHE 0.041 0.002 PHE D 288 TYR 0.030 0.002 TYR F 643 ARG 0.010 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 57) link_NAG-ASN : angle 6.95287 ( 171) link_ALPHA1-6 : bond 0.00450 ( 8) link_ALPHA1-6 : angle 1.72791 ( 24) link_BETA1-4 : bond 0.00628 ( 49) link_BETA1-4 : angle 2.59209 ( 147) link_ALPHA1-2 : bond 0.00286 ( 4) link_ALPHA1-2 : angle 1.87362 ( 12) link_ALPHA1-3 : bond 0.00542 ( 10) link_ALPHA1-3 : angle 1.58806 ( 30) hydrogen bonds : bond 0.21968 ( 571) hydrogen bonds : angle 8.74648 ( 1542) SS BOND : bond 0.00564 ( 35) SS BOND : angle 1.86257 ( 70) covalent geometry : bond 0.00541 (17598) covalent geometry : angle 0.92955 (23890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7063 (p-80) cc_final: 0.6635 (p-80) REVERT: A 108 ILE cc_start: 0.8499 (mp) cc_final: 0.7595 (mp) REVERT: A 190 GLU cc_start: 0.6156 (pm20) cc_final: 0.5276 (pm20) REVERT: C 271 MET cc_start: 0.4814 (tpt) cc_final: 0.4506 (mmm) REVERT: C 298 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7314 (tmm-80) REVERT: C 423 ILE cc_start: 0.7945 (mt) cc_final: 0.7674 (mt) REVERT: D 216 HIS cc_start: 0.6996 (m-70) cc_final: 0.6430 (m170) REVERT: D 318 TYR cc_start: 0.7514 (m-10) cc_final: 0.7118 (m-80) REVERT: D 391 PHE cc_start: 0.7661 (m-80) cc_final: 0.7394 (m-80) REVERT: D 434 MET cc_start: 0.5241 (ptm) cc_final: 0.4438 (ppp) REVERT: D 484 TYR cc_start: 0.7944 (p90) cc_final: 0.7482 (p90) REVERT: F 590 GLN cc_start: 0.8914 (tt0) cc_final: 0.8446 (pt0) REVERT: F 601 LYS cc_start: 0.7682 (mppt) cc_final: 0.7429 (mmtm) REVERT: F 643 TYR cc_start: 0.8122 (m-80) cc_final: 0.7676 (m-80) REVERT: F 656 ASN cc_start: 0.9130 (t0) cc_final: 0.8889 (t0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2774 time to fit residues: 156.5387 Evaluate side-chains 299 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN A 425 ASN A 428 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 72 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 315 GLN E 540 GLN E 651 ASN F 540 GLN F 575 GLN F 591 GLN F 650 GLN J 32 HIS ** J 52AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.140396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.105993 restraints weight = 55830.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109580 restraints weight = 41434.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112041 restraints weight = 30771.971| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17761 Z= 0.199 Angle : 0.958 20.190 24344 Z= 0.432 Chirality : 0.056 0.846 3070 Planarity : 0.005 0.061 2860 Dihedral : 14.141 103.867 4728 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.52 % Allowed : 6.03 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 1944 helix: -0.01 (0.25), residues: 423 sheet: -0.09 (0.21), residues: 517 loop : -0.54 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 45 HIS 0.007 0.001 HIS J 35 PHE 0.024 0.002 PHE C 159 TYR 0.030 0.002 TYR B 638 ARG 0.025 0.001 ARG E 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 57) link_NAG-ASN : angle 5.39627 ( 171) link_ALPHA1-6 : bond 0.00651 ( 8) link_ALPHA1-6 : angle 1.80015 ( 24) link_BETA1-4 : bond 0.00658 ( 49) link_BETA1-4 : angle 2.36530 ( 147) link_ALPHA1-2 : bond 0.00140 ( 4) link_ALPHA1-2 : angle 2.04172 ( 12) link_ALPHA1-3 : bond 0.01026 ( 10) link_ALPHA1-3 : angle 1.90348 ( 30) hydrogen bonds : bond 0.05136 ( 571) hydrogen bonds : angle 6.90467 ( 1542) SS BOND : bond 0.00480 ( 35) SS BOND : angle 1.47628 ( 70) covalent geometry : bond 0.00415 (17598) covalent geometry : angle 0.82260 (23890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 385 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8363 (p-80) cc_final: 0.7823 (p-80) REVERT: A 104 MET cc_start: 0.8722 (tpt) cc_final: 0.8002 (tpp) REVERT: A 108 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 190 GLU cc_start: 0.7902 (pm20) cc_final: 0.7018 (pm20) REVERT: A 252 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8180 (mmtm) REVERT: A 271 MET cc_start: -0.1021 (ttt) cc_final: -0.1511 (ttt) REVERT: A 298 ARG cc_start: 0.8949 (ptm160) cc_final: 0.8575 (tpt-90) REVERT: A 383 PHE cc_start: 0.9039 (m-80) cc_final: 0.8564 (m-80) REVERT: A 435 TYR cc_start: 0.7850 (t80) cc_final: 0.7568 (t80) REVERT: C 47 ASP cc_start: 0.8713 (t0) cc_final: 0.8456 (t0) REVERT: C 271 MET cc_start: 0.5862 (tpt) cc_final: 0.5428 (tpt) REVERT: C 288 PHE cc_start: 0.7395 (m-10) cc_final: 0.7019 (m-10) REVERT: C 298 ARG cc_start: 0.8544 (tmm-80) cc_final: 0.7795 (tmm-80) REVERT: C 423 ILE cc_start: 0.8295 (mt) cc_final: 0.8031 (mt) REVERT: C 434 MET cc_start: 0.5368 (tmm) cc_final: 0.4835 (ttm) REVERT: D 45 TRP cc_start: 0.6939 (p90) cc_final: 0.6596 (p90) REVERT: D 130 GLN cc_start: 0.9288 (mp10) cc_final: 0.8836 (pm20) REVERT: D 176 PHE cc_start: 0.8512 (m-10) cc_final: 0.8153 (m-10) REVERT: D 216 HIS cc_start: 0.8419 (m-70) cc_final: 0.8186 (m-70) REVERT: D 260 LEU cc_start: 0.8494 (mt) cc_final: 0.8197 (mt) REVERT: D 271 MET cc_start: 0.7559 (tmm) cc_final: 0.6433 (ttt) REVERT: D 288 PHE cc_start: 0.8345 (m-10) cc_final: 0.8019 (m-10) REVERT: D 302 ASN cc_start: 0.9330 (m110) cc_final: 0.9113 (m110) REVERT: D 318 TYR cc_start: 0.8106 (m-10) cc_final: 0.7657 (m-80) REVERT: D 342 LEU cc_start: 0.9195 (mp) cc_final: 0.8901 (mt) REVERT: D 384 TYR cc_start: 0.8387 (m-10) cc_final: 0.8177 (m-10) REVERT: D 391 PHE cc_start: 0.9337 (m-80) cc_final: 0.8714 (m-80) REVERT: D 475 MET cc_start: 0.8664 (pmm) cc_final: 0.8399 (pmm) REVERT: F 591 GLN cc_start: 0.9211 (mt0) cc_final: 0.8717 (mt0) REVERT: F 643 TYR cc_start: 0.9061 (m-80) cc_final: 0.8440 (m-80) REVERT: J 51 MET cc_start: 0.8513 (ttt) cc_final: 0.8143 (ttt) REVERT: J 69 ILE cc_start: 0.7545 (tp) cc_final: 0.6423 (tp) REVERT: N 27 LEU cc_start: 0.8335 (tp) cc_final: 0.8120 (tp) REVERT: N 27 HIS cc_start: 0.8819 (t-90) cc_final: 0.8379 (t-90) REVERT: N 39 ARG cc_start: 0.6804 (mmt180) cc_final: 0.6294 (mmt180) REVERT: N 87 TYR cc_start: 0.8661 (m-80) cc_final: 0.8385 (m-80) outliers start: 9 outliers final: 3 residues processed: 391 average time/residue: 0.2791 time to fit residues: 164.5403 Evaluate side-chains 309 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 305 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 195 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 HIS ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.138659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104307 restraints weight = 55841.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107723 restraints weight = 41845.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.109948 restraints weight = 31481.194| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17761 Z= 0.187 Angle : 0.920 20.236 24344 Z= 0.419 Chirality : 0.053 0.820 3070 Planarity : 0.004 0.048 2860 Dihedral : 12.679 106.097 4728 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.34 % Allowed : 4.71 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 1944 helix: 0.03 (0.26), residues: 417 sheet: -0.17 (0.22), residues: 494 loop : -0.60 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 631 HIS 0.010 0.001 HIS A 216 PHE 0.022 0.002 PHE C 159 TYR 0.022 0.002 TYR F 643 ARG 0.010 0.001 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 57) link_NAG-ASN : angle 5.26520 ( 171) link_ALPHA1-6 : bond 0.00877 ( 8) link_ALPHA1-6 : angle 1.78094 ( 24) link_BETA1-4 : bond 0.00606 ( 49) link_BETA1-4 : angle 2.28897 ( 147) link_ALPHA1-2 : bond 0.00357 ( 4) link_ALPHA1-2 : angle 1.66547 ( 12) link_ALPHA1-3 : bond 0.01155 ( 10) link_ALPHA1-3 : angle 1.41497 ( 30) hydrogen bonds : bond 0.04865 ( 571) hydrogen bonds : angle 6.76007 ( 1542) SS BOND : bond 0.00464 ( 35) SS BOND : angle 1.50608 ( 70) covalent geometry : bond 0.00396 (17598) covalent geometry : angle 0.78566 (23890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 381 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8720 (p-80) cc_final: 0.8426 (p-80) REVERT: A 104 MET cc_start: 0.8795 (tpt) cc_final: 0.8025 (tpp) REVERT: A 108 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 190 GLU cc_start: 0.7901 (pm20) cc_final: 0.7274 (pm20) REVERT: A 216 HIS cc_start: 0.8955 (m-70) cc_final: 0.8463 (m-70) REVERT: A 248 THR cc_start: 0.8972 (m) cc_final: 0.8522 (t) REVERT: A 271 MET cc_start: -0.0604 (ttt) cc_final: -0.1079 (ttt) REVERT: A 298 ARG cc_start: 0.8790 (ptm160) cc_final: 0.8205 (ptm-80) REVERT: A 383 PHE cc_start: 0.9032 (m-80) cc_final: 0.8594 (m-80) REVERT: A 435 TYR cc_start: 0.8257 (t80) cc_final: 0.7688 (t80) REVERT: C 47 ASP cc_start: 0.8829 (t0) cc_final: 0.8584 (t0) REVERT: C 150 MET cc_start: 0.4997 (tmm) cc_final: 0.4550 (ppp) REVERT: C 271 MET cc_start: 0.6002 (tpt) cc_final: 0.5676 (tpt) REVERT: C 288 PHE cc_start: 0.7460 (m-10) cc_final: 0.7012 (m-10) REVERT: C 298 ARG cc_start: 0.8655 (tmm-80) cc_final: 0.8020 (tmm-80) REVERT: C 308 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7792 (tpp80) REVERT: C 423 ILE cc_start: 0.8116 (mt) cc_final: 0.7892 (mt) REVERT: C 434 MET cc_start: 0.6122 (tmm) cc_final: 0.5669 (ttm) REVERT: C 446 VAL cc_start: 0.7276 (p) cc_final: 0.6975 (t) REVERT: D 130 GLN cc_start: 0.9354 (mp10) cc_final: 0.8983 (mp10) REVERT: D 176 PHE cc_start: 0.7926 (m-10) cc_final: 0.7443 (m-10) REVERT: D 191 TYR cc_start: 0.8537 (m-80) cc_final: 0.8039 (m-80) REVERT: D 216 HIS cc_start: 0.8927 (m-70) cc_final: 0.8676 (m-70) REVERT: D 271 MET cc_start: 0.7583 (tmm) cc_final: 0.6601 (ttt) REVERT: D 288 PHE cc_start: 0.8309 (m-10) cc_final: 0.7938 (m-10) REVERT: D 318 TYR cc_start: 0.8262 (m-10) cc_final: 0.7813 (m-80) REVERT: D 384 TYR cc_start: 0.8469 (m-10) cc_final: 0.8267 (m-10) REVERT: D 391 PHE cc_start: 0.9337 (m-80) cc_final: 0.8785 (m-80) REVERT: D 475 MET cc_start: 0.8611 (pmm) cc_final: 0.8328 (pmm) REVERT: D 487 LYS cc_start: 0.8237 (mttt) cc_final: 0.7850 (mttt) REVERT: F 588 ARG cc_start: 0.8138 (mmt180) cc_final: 0.7727 (mmt180) REVERT: F 643 TYR cc_start: 0.8891 (m-80) cc_final: 0.8387 (m-80) REVERT: J 46 GLU cc_start: 0.7151 (pm20) cc_final: 0.6608 (pm20) REVERT: J 48 MET cc_start: 0.8926 (mtm) cc_final: 0.7756 (mmm) REVERT: J 51 MET cc_start: 0.8573 (ttt) cc_final: 0.8202 (ttt) REVERT: J 69 ILE cc_start: 0.7666 (tp) cc_final: 0.6555 (tp) REVERT: N 27 LEU cc_start: 0.8376 (tp) cc_final: 0.8151 (tp) REVERT: N 27 HIS cc_start: 0.8910 (t-90) cc_final: 0.8434 (t-90) REVERT: N 39 ARG cc_start: 0.6354 (mmt180) cc_final: 0.5778 (mmt180) REVERT: N 53 HIS cc_start: 0.8635 (t-90) cc_final: 0.8426 (t70) REVERT: N 87 TYR cc_start: 0.8656 (m-80) cc_final: 0.8441 (m-80) outliers start: 6 outliers final: 1 residues processed: 385 average time/residue: 0.2887 time to fit residues: 168.1865 Evaluate side-chains 305 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 72 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 300 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN D 103 GLN E 651 ASN F 540 GLN F 575 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.136622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103151 restraints weight = 56601.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106142 restraints weight = 42859.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108020 restraints weight = 33401.851| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17761 Z= 0.195 Angle : 0.935 20.094 24344 Z= 0.421 Chirality : 0.055 0.795 3070 Planarity : 0.005 0.058 2860 Dihedral : 11.783 104.235 4728 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1944 helix: -0.11 (0.26), residues: 423 sheet: -0.25 (0.21), residues: 520 loop : -0.61 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 596 HIS 0.006 0.001 HIS A 216 PHE 0.017 0.002 PHE C 382 TYR 0.022 0.002 TYR F 643 ARG 0.006 0.001 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00874 ( 57) link_NAG-ASN : angle 5.27991 ( 171) link_ALPHA1-6 : bond 0.00912 ( 8) link_ALPHA1-6 : angle 1.85674 ( 24) link_BETA1-4 : bond 0.00579 ( 49) link_BETA1-4 : angle 2.32289 ( 147) link_ALPHA1-2 : bond 0.00275 ( 4) link_ALPHA1-2 : angle 1.71851 ( 12) link_ALPHA1-3 : bond 0.01148 ( 10) link_ALPHA1-3 : angle 1.55102 ( 30) hydrogen bonds : bond 0.04685 ( 571) hydrogen bonds : angle 6.65687 ( 1542) SS BOND : bond 0.00485 ( 35) SS BOND : angle 1.42071 ( 70) covalent geometry : bond 0.00413 (17598) covalent geometry : angle 0.80295 (23890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8803 (tmm) cc_final: 0.8552 (ttt) REVERT: A 104 MET cc_start: 0.8724 (tpt) cc_final: 0.7917 (tpp) REVERT: A 108 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.7628 (mp) REVERT: A 190 GLU cc_start: 0.7821 (pm20) cc_final: 0.7184 (pm20) REVERT: A 216 HIS cc_start: 0.8703 (m-70) cc_final: 0.8209 (m-70) REVERT: A 248 THR cc_start: 0.8778 (m) cc_final: 0.8231 (t) REVERT: A 271 MET cc_start: -0.0034 (ttt) cc_final: -0.0604 (ttt) REVERT: A 317 PHE cc_start: 0.7383 (t80) cc_final: 0.7032 (t80) REVERT: A 383 PHE cc_start: 0.8633 (m-80) cc_final: 0.8310 (m-80) REVERT: A 423 ILE cc_start: 0.8317 (mm) cc_final: 0.8074 (mm) REVERT: A 435 TYR cc_start: 0.8404 (t80) cc_final: 0.7843 (t80) REVERT: A 480 ARG cc_start: 0.8400 (mtp180) cc_final: 0.8054 (ptm160) REVERT: C 47 ASP cc_start: 0.8817 (t0) cc_final: 0.8544 (t0) REVERT: C 150 MET cc_start: 0.5035 (tmm) cc_final: 0.4726 (ppp) REVERT: C 271 MET cc_start: 0.6298 (tpt) cc_final: 0.5966 (tpt) REVERT: C 288 PHE cc_start: 0.7888 (m-10) cc_final: 0.7559 (m-10) REVERT: C 298 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.7900 (tmm-80) REVERT: C 446 VAL cc_start: 0.7149 (p) cc_final: 0.6913 (t) REVERT: D 130 GLN cc_start: 0.9450 (mp10) cc_final: 0.9080 (pm20) REVERT: D 176 PHE cc_start: 0.7762 (m-10) cc_final: 0.7399 (m-10) REVERT: D 216 HIS cc_start: 0.8281 (m-70) cc_final: 0.8064 (m-70) REVERT: D 288 PHE cc_start: 0.8174 (m-10) cc_final: 0.7905 (m-10) REVERT: D 302 ASN cc_start: 0.9186 (m110) cc_final: 0.8978 (m-40) REVERT: D 318 TYR cc_start: 0.8091 (m-10) cc_final: 0.7597 (m-80) REVERT: D 342 LEU cc_start: 0.9239 (mp) cc_final: 0.9022 (mp) REVERT: D 391 PHE cc_start: 0.9179 (m-80) cc_final: 0.8477 (m-80) REVERT: D 453 ILE cc_start: 0.8813 (tp) cc_final: 0.8600 (tp) REVERT: D 475 MET cc_start: 0.8595 (pmm) cc_final: 0.8263 (pmm) REVERT: E 607 ASN cc_start: 0.8193 (m-40) cc_final: 0.7992 (m-40) REVERT: F 584 GLU cc_start: 0.9220 (pt0) cc_final: 0.8880 (pt0) REVERT: F 601 LYS cc_start: 0.7527 (mppt) cc_final: 0.6723 (pttt) REVERT: F 643 TYR cc_start: 0.8901 (m-80) cc_final: 0.8576 (m-80) REVERT: J 51 MET cc_start: 0.8537 (ttt) cc_final: 0.8293 (ttt) REVERT: J 69 ILE cc_start: 0.7522 (tp) cc_final: 0.6355 (tp) REVERT: N 27 LEU cc_start: 0.8358 (tp) cc_final: 0.8122 (tp) REVERT: N 27 HIS cc_start: 0.8900 (t-90) cc_final: 0.8383 (t-90) REVERT: N 39 ARG cc_start: 0.6467 (mmt180) cc_final: 0.5806 (mmt180) REVERT: N 53 HIS cc_start: 0.8604 (t-90) cc_final: 0.8377 (t70) REVERT: N 87 TYR cc_start: 0.8600 (m-80) cc_final: 0.8166 (m-80) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.2852 time to fit residues: 157.4880 Evaluate side-chains 297 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 186 optimal weight: 0.0170 chunk 0 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 315 GLN C 348 GLN C 374 HIS C 425 ASN D 348 GLN E 651 ASN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.139532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105229 restraints weight = 54942.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109050 restraints weight = 40160.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110601 restraints weight = 30405.688| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17761 Z= 0.143 Angle : 0.881 19.554 24344 Z= 0.395 Chirality : 0.053 0.761 3070 Planarity : 0.004 0.061 2860 Dihedral : 11.041 106.295 4728 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1944 helix: 0.27 (0.26), residues: 410 sheet: -0.09 (0.22), residues: 530 loop : -0.56 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 631 HIS 0.004 0.001 HIS A 216 PHE 0.011 0.001 PHE A 382 TYR 0.024 0.001 TYR A 484 ARG 0.009 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 57) link_NAG-ASN : angle 5.06226 ( 171) link_ALPHA1-6 : bond 0.00933 ( 8) link_ALPHA1-6 : angle 1.79179 ( 24) link_BETA1-4 : bond 0.00544 ( 49) link_BETA1-4 : angle 2.16816 ( 147) link_ALPHA1-2 : bond 0.00324 ( 4) link_ALPHA1-2 : angle 1.63582 ( 12) link_ALPHA1-3 : bond 0.01130 ( 10) link_ALPHA1-3 : angle 1.37812 ( 30) hydrogen bonds : bond 0.04256 ( 571) hydrogen bonds : angle 6.35066 ( 1542) SS BOND : bond 0.00418 ( 35) SS BOND : angle 1.51506 ( 70) covalent geometry : bond 0.00306 (17598) covalent geometry : angle 0.75101 (23890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8732 (tpt) cc_final: 0.7994 (tpp) REVERT: A 108 ILE cc_start: 0.8824 (mp) cc_final: 0.7540 (mp) REVERT: A 164 GLU cc_start: 0.7689 (mp0) cc_final: 0.7330 (tt0) REVERT: A 190 GLU cc_start: 0.7902 (pm20) cc_final: 0.7421 (pm20) REVERT: A 216 HIS cc_start: 0.8882 (m-70) cc_final: 0.8414 (m-70) REVERT: A 225 ILE cc_start: 0.7691 (mt) cc_final: 0.7310 (mp) REVERT: A 248 THR cc_start: 0.8774 (m) cc_final: 0.8111 (t) REVERT: A 271 MET cc_start: 0.0042 (ttt) cc_final: -0.0800 (ttt) REVERT: A 381 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 383 PHE cc_start: 0.8645 (m-80) cc_final: 0.8354 (m-80) REVERT: A 482 GLU cc_start: 0.8656 (pm20) cc_final: 0.8392 (pm20) REVERT: B 590 GLN cc_start: 0.9262 (pm20) cc_final: 0.8861 (pm20) REVERT: C 47 ASP cc_start: 0.8793 (t0) cc_final: 0.8479 (t0) REVERT: C 150 MET cc_start: 0.4843 (tmm) cc_final: 0.4624 (ppp) REVERT: C 271 MET cc_start: 0.6833 (tpt) cc_final: 0.6496 (tpt) REVERT: C 288 PHE cc_start: 0.7729 (m-10) cc_final: 0.7474 (m-10) REVERT: C 298 ARG cc_start: 0.8524 (tmm-80) cc_final: 0.7860 (tmm-80) REVERT: C 423 ILE cc_start: 0.8038 (mt) cc_final: 0.7820 (mt) REVERT: C 446 VAL cc_start: 0.7369 (p) cc_final: 0.7135 (t) REVERT: D 93 PHE cc_start: 0.8838 (m-10) cc_final: 0.8475 (m-10) REVERT: D 109 ILE cc_start: 0.9462 (pt) cc_final: 0.9030 (pt) REVERT: D 111 LEU cc_start: 0.9289 (mt) cc_final: 0.8895 (mt) REVERT: D 130 GLN cc_start: 0.9493 (mp10) cc_final: 0.9127 (pm20) REVERT: D 176 PHE cc_start: 0.7730 (m-10) cc_final: 0.7340 (m-10) REVERT: D 191 TYR cc_start: 0.8814 (m-10) cc_final: 0.7931 (m-80) REVERT: D 271 MET cc_start: 0.6970 (tmm) cc_final: 0.6752 (tmm) REVERT: D 288 PHE cc_start: 0.8262 (m-10) cc_final: 0.7924 (m-10) REVERT: D 318 TYR cc_start: 0.8059 (m-10) cc_final: 0.7586 (m-80) REVERT: D 342 LEU cc_start: 0.9257 (mp) cc_final: 0.8984 (mp) REVERT: D 391 PHE cc_start: 0.9280 (m-80) cc_final: 0.8647 (m-80) REVERT: D 434 MET cc_start: 0.3487 (ptm) cc_final: 0.2396 (tmm) REVERT: D 453 ILE cc_start: 0.8744 (tp) cc_final: 0.8541 (tp) REVERT: D 475 MET cc_start: 0.8603 (pmm) cc_final: 0.8303 (pmm) REVERT: E 536 THR cc_start: 0.9181 (p) cc_final: 0.8956 (p) REVERT: E 545 LEU cc_start: 0.9160 (tp) cc_final: 0.8957 (tp) REVERT: E 585 ARG cc_start: 0.9428 (mmm-85) cc_final: 0.9182 (mmm-85) REVERT: E 588 ARG cc_start: 0.8889 (mtm110) cc_final: 0.8632 (mtm110) REVERT: F 575 GLN cc_start: 0.8441 (pp30) cc_final: 0.7590 (mp10) REVERT: F 584 GLU cc_start: 0.9322 (pt0) cc_final: 0.9079 (pt0) REVERT: F 588 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7093 (mmt180) REVERT: F 642 ILE cc_start: 0.8690 (mt) cc_final: 0.8484 (mt) REVERT: F 643 TYR cc_start: 0.8894 (m-80) cc_final: 0.8432 (m-80) REVERT: J 61 PHE cc_start: 0.8645 (m-80) cc_final: 0.8412 (m-10) REVERT: J 100 GLU cc_start: 0.7722 (tp30) cc_final: 0.7499 (tm-30) REVERT: N 27 HIS cc_start: 0.8902 (t-90) cc_final: 0.8458 (t-90) REVERT: N 39 ARG cc_start: 0.6283 (mmt180) cc_final: 0.5575 (mmt180) REVERT: N 53 HIS cc_start: 0.8623 (t-90) cc_final: 0.8367 (t70) REVERT: N 81 ASP cc_start: 0.8521 (t0) cc_final: 0.8256 (t0) REVERT: N 87 TYR cc_start: 0.8602 (m-80) cc_final: 0.8185 (m-80) outliers start: 1 outliers final: 1 residues processed: 380 average time/residue: 0.2914 time to fit residues: 166.2078 Evaluate side-chains 299 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 7 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN D 377 ASN E 651 ASN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.137061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103892 restraints weight = 55943.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106680 restraints weight = 41177.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109126 restraints weight = 31731.482| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17761 Z= 0.157 Angle : 0.890 19.305 24344 Z= 0.398 Chirality : 0.054 0.737 3070 Planarity : 0.004 0.054 2860 Dihedral : 10.268 106.953 4728 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1944 helix: 0.27 (0.26), residues: 417 sheet: -0.16 (0.21), residues: 535 loop : -0.58 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 631 HIS 0.005 0.001 HIS J 35 PHE 0.018 0.002 PHE C 233 TYR 0.014 0.002 TYR A 484 ARG 0.006 0.001 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 57) link_NAG-ASN : angle 5.08324 ( 171) link_ALPHA1-6 : bond 0.01018 ( 8) link_ALPHA1-6 : angle 1.77341 ( 24) link_BETA1-4 : bond 0.00571 ( 49) link_BETA1-4 : angle 2.21472 ( 147) link_ALPHA1-2 : bond 0.00282 ( 4) link_ALPHA1-2 : angle 1.63217 ( 12) link_ALPHA1-3 : bond 0.01087 ( 10) link_ALPHA1-3 : angle 1.43798 ( 30) hydrogen bonds : bond 0.04169 ( 571) hydrogen bonds : angle 6.32505 ( 1542) SS BOND : bond 0.00459 ( 35) SS BOND : angle 1.51575 ( 70) covalent geometry : bond 0.00334 (17598) covalent geometry : angle 0.76072 (23890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8743 (mp) cc_final: 0.8524 (mp) REVERT: A 164 GLU cc_start: 0.7653 (mp0) cc_final: 0.7304 (tt0) REVERT: A 216 HIS cc_start: 0.8631 (m-70) cc_final: 0.8092 (m-70) REVERT: A 225 ILE cc_start: 0.7608 (mt) cc_final: 0.7357 (mt) REVERT: A 248 THR cc_start: 0.8628 (m) cc_final: 0.8103 (t) REVERT: A 271 MET cc_start: 0.1304 (ttt) cc_final: 0.0358 (ttt) REVERT: A 383 PHE cc_start: 0.8682 (m-80) cc_final: 0.8385 (m-80) REVERT: A 435 TYR cc_start: 0.8209 (t80) cc_final: 0.7774 (t80) REVERT: A 483 LEU cc_start: 0.9451 (mp) cc_final: 0.8405 (mp) REVERT: B 586 TYR cc_start: 0.8749 (t80) cc_final: 0.8548 (t80) REVERT: C 47 ASP cc_start: 0.8681 (t0) cc_final: 0.8255 (t0) REVERT: C 180 ASP cc_start: 0.7483 (m-30) cc_final: 0.6670 (m-30) REVERT: C 271 MET cc_start: 0.6685 (tpt) cc_final: 0.6304 (tpt) REVERT: C 298 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.7814 (tmm-80) REVERT: C 423 ILE cc_start: 0.7911 (mt) cc_final: 0.7250 (mt) REVERT: C 490 LYS cc_start: 0.7645 (tptp) cc_final: 0.7137 (tptp) REVERT: D 93 PHE cc_start: 0.8828 (m-10) cc_final: 0.8527 (m-10) REVERT: D 130 GLN cc_start: 0.9439 (mp10) cc_final: 0.9070 (pm20) REVERT: D 176 PHE cc_start: 0.7776 (m-80) cc_final: 0.7449 (m-10) REVERT: D 216 HIS cc_start: 0.8034 (m-70) cc_final: 0.7693 (m-70) REVERT: D 288 PHE cc_start: 0.8244 (m-10) cc_final: 0.7895 (m-10) REVERT: D 302 ASN cc_start: 0.9238 (m-40) cc_final: 0.8962 (m-40) REVERT: D 318 TYR cc_start: 0.8078 (m-10) cc_final: 0.7596 (m-80) REVERT: D 342 LEU cc_start: 0.9222 (mp) cc_final: 0.8960 (mp) REVERT: D 391 PHE cc_start: 0.9074 (m-80) cc_final: 0.8328 (m-80) REVERT: D 434 MET cc_start: 0.3704 (ptm) cc_final: 0.2632 (tmm) REVERT: D 475 MET cc_start: 0.8600 (pmm) cc_final: 0.8282 (pmm) REVERT: E 635 ILE cc_start: 0.8976 (mm) cc_final: 0.8546 (tp) REVERT: F 588 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7718 (mmt180) REVERT: F 601 LYS cc_start: 0.7134 (mppt) cc_final: 0.6438 (pttt) REVERT: F 643 TYR cc_start: 0.8940 (m-80) cc_final: 0.8536 (m-80) REVERT: J 51 MET cc_start: 0.8534 (tpt) cc_final: 0.8004 (mmm) REVERT: J 61 PHE cc_start: 0.8577 (m-80) cc_final: 0.8243 (m-10) REVERT: J 69 ILE cc_start: 0.7905 (tp) cc_final: 0.7588 (tp) REVERT: J 97 LYS cc_start: 0.9306 (pttp) cc_final: 0.8761 (pttp) REVERT: J 100 GLU cc_start: 0.7976 (tp30) cc_final: 0.7534 (tp30) REVERT: N 27 HIS cc_start: 0.8869 (t-90) cc_final: 0.8305 (t-90) REVERT: N 39 ARG cc_start: 0.6491 (mmt180) cc_final: 0.5780 (mmt180) REVERT: N 53 HIS cc_start: 0.8544 (t-90) cc_final: 0.8284 (t70) REVERT: N 70 ASP cc_start: 0.8023 (p0) cc_final: 0.7814 (p0) REVERT: N 81 ASP cc_start: 0.8395 (t0) cc_final: 0.8186 (t0) REVERT: N 87 TYR cc_start: 0.8529 (m-80) cc_final: 0.8132 (m-80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2772 time to fit residues: 150.9616 Evaluate side-chains 290 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.137229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103792 restraints weight = 55514.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.106992 restraints weight = 40576.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.109022 restraints weight = 31481.199| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17761 Z= 0.155 Angle : 0.894 19.125 24344 Z= 0.402 Chirality : 0.053 0.728 3070 Planarity : 0.004 0.062 2860 Dihedral : 9.775 104.441 4728 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1944 helix: 0.26 (0.27), residues: 416 sheet: -0.20 (0.21), residues: 541 loop : -0.64 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP J 47 HIS 0.010 0.001 HIS J 52A PHE 0.013 0.002 PHE D 382 TYR 0.026 0.002 TYR C 486 ARG 0.015 0.001 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 57) link_NAG-ASN : angle 5.10599 ( 171) link_ALPHA1-6 : bond 0.00898 ( 8) link_ALPHA1-6 : angle 1.57822 ( 24) link_BETA1-4 : bond 0.00600 ( 49) link_BETA1-4 : angle 2.17794 ( 147) link_ALPHA1-2 : bond 0.00312 ( 4) link_ALPHA1-2 : angle 1.71166 ( 12) link_ALPHA1-3 : bond 0.01057 ( 10) link_ALPHA1-3 : angle 1.36952 ( 30) hydrogen bonds : bond 0.04186 ( 571) hydrogen bonds : angle 6.31046 ( 1542) SS BOND : bond 0.00452 ( 35) SS BOND : angle 1.50036 ( 70) covalent geometry : bond 0.00333 (17598) covalent geometry : angle 0.76553 (23890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8803 (mp) cc_final: 0.8587 (mp) REVERT: A 164 GLU cc_start: 0.7754 (mp0) cc_final: 0.7412 (tt0) REVERT: A 216 HIS cc_start: 0.8673 (m-70) cc_final: 0.8168 (m-70) REVERT: A 225 ILE cc_start: 0.7278 (mt) cc_final: 0.6941 (mt) REVERT: A 248 THR cc_start: 0.8740 (m) cc_final: 0.8157 (t) REVERT: A 252 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8413 (mmtt) REVERT: A 271 MET cc_start: 0.1446 (ttt) cc_final: 0.0561 (ttt) REVERT: A 383 PHE cc_start: 0.8450 (m-80) cc_final: 0.8137 (m-80) REVERT: A 423 ILE cc_start: 0.8418 (mm) cc_final: 0.8074 (mm) REVERT: A 435 TYR cc_start: 0.8159 (t80) cc_final: 0.7818 (t80) REVERT: B 590 GLN cc_start: 0.9257 (pm20) cc_final: 0.8908 (pm20) REVERT: C 47 ASP cc_start: 0.8706 (t0) cc_final: 0.8263 (t0) REVERT: C 116 LEU cc_start: 0.8856 (mt) cc_final: 0.8645 (mt) REVERT: C 271 MET cc_start: 0.6619 (tpt) cc_final: 0.6211 (tpt) REVERT: C 298 ARG cc_start: 0.8528 (tmm-80) cc_final: 0.7955 (tmm-80) REVERT: D 93 PHE cc_start: 0.8950 (m-10) cc_final: 0.8622 (m-10) REVERT: D 130 GLN cc_start: 0.9434 (mp10) cc_final: 0.9116 (pm20) REVERT: D 176 PHE cc_start: 0.7860 (m-80) cc_final: 0.7472 (m-80) REVERT: D 180 ASP cc_start: 0.7863 (m-30) cc_final: 0.7471 (m-30) REVERT: D 191 TYR cc_start: 0.8628 (m-80) cc_final: 0.6783 (m-80) REVERT: D 216 HIS cc_start: 0.8084 (m-70) cc_final: 0.7771 (m-70) REVERT: D 271 MET cc_start: 0.5308 (tmm) cc_final: 0.5102 (tmm) REVERT: D 288 PHE cc_start: 0.8272 (m-10) cc_final: 0.7969 (m-10) REVERT: D 318 TYR cc_start: 0.8113 (m-10) cc_final: 0.7638 (m-80) REVERT: D 342 LEU cc_start: 0.9504 (mp) cc_final: 0.9235 (mp) REVERT: D 391 PHE cc_start: 0.9171 (m-80) cc_final: 0.8422 (m-80) REVERT: D 434 MET cc_start: 0.3629 (ptm) cc_final: 0.2659 (tmm) REVERT: E 635 ILE cc_start: 0.9018 (mm) cc_final: 0.8614 (tp) REVERT: F 588 ARG cc_start: 0.8021 (mmt180) cc_final: 0.7473 (mmt180) REVERT: F 601 LYS cc_start: 0.6802 (mppt) cc_final: 0.6207 (pttt) REVERT: F 643 TYR cc_start: 0.8937 (m-80) cc_final: 0.8543 (m-80) REVERT: J 51 MET cc_start: 0.8486 (tpt) cc_final: 0.8240 (tpt) REVERT: J 61 PHE cc_start: 0.8657 (m-80) cc_final: 0.8332 (m-10) REVERT: J 100 GLU cc_start: 0.7936 (tp30) cc_final: 0.7414 (tp30) REVERT: N 27 LEU cc_start: 0.8720 (tp) cc_final: 0.8515 (tp) REVERT: N 27 HIS cc_start: 0.8931 (t-90) cc_final: 0.8387 (t-90) REVERT: N 39 ARG cc_start: 0.6383 (mmt180) cc_final: 0.5671 (mmt180) REVERT: N 53 HIS cc_start: 0.8580 (t-90) cc_final: 0.8314 (t70) REVERT: N 87 TYR cc_start: 0.8604 (m-80) cc_final: 0.8236 (m-80) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.2896 time to fit residues: 162.1330 Evaluate side-chains 294 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 75 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 183 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS E 540 GLN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.128216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.095837 restraints weight = 57836.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098859 restraints weight = 42560.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101633 restraints weight = 31881.152| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 17761 Z= 0.297 Angle : 1.102 20.303 24344 Z= 0.508 Chirality : 0.058 0.802 3070 Planarity : 0.006 0.077 2860 Dihedral : 10.436 99.620 4728 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 1944 helix: -0.76 (0.24), residues: 423 sheet: -0.63 (0.21), residues: 519 loop : -0.94 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 631 HIS 0.012 0.003 HIS D 216 PHE 0.041 0.003 PHE C 382 TYR 0.020 0.003 TYR D 484 ARG 0.018 0.001 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.01168 ( 57) link_NAG-ASN : angle 5.49928 ( 171) link_ALPHA1-6 : bond 0.00994 ( 8) link_ALPHA1-6 : angle 1.52421 ( 24) link_BETA1-4 : bond 0.00770 ( 49) link_BETA1-4 : angle 2.47670 ( 147) link_ALPHA1-2 : bond 0.00368 ( 4) link_ALPHA1-2 : angle 1.87010 ( 12) link_ALPHA1-3 : bond 0.00995 ( 10) link_ALPHA1-3 : angle 1.66712 ( 30) hydrogen bonds : bond 0.05316 ( 571) hydrogen bonds : angle 7.15843 ( 1542) SS BOND : bond 0.00796 ( 35) SS BOND : angle 2.41534 ( 70) covalent geometry : bond 0.00635 (17598) covalent geometry : angle 0.97933 (23890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 HIS cc_start: 0.8733 (m-70) cc_final: 0.8216 (m-70) REVERT: A 271 MET cc_start: 0.2265 (ttt) cc_final: 0.1293 (ttt) REVERT: A 298 ARG cc_start: 0.8733 (ptm-80) cc_final: 0.8374 (ptm-80) REVERT: A 317 PHE cc_start: 0.7552 (t80) cc_final: 0.7206 (t80) REVERT: A 383 PHE cc_start: 0.8528 (m-80) cc_final: 0.8327 (m-80) REVERT: A 395 TRP cc_start: 0.6118 (t-100) cc_final: 0.5895 (t-100) REVERT: A 423 ILE cc_start: 0.8594 (mm) cc_final: 0.8383 (mm) REVERT: A 435 TYR cc_start: 0.8774 (t80) cc_final: 0.8135 (t80) REVERT: B 586 TYR cc_start: 0.8676 (t80) cc_final: 0.8386 (t80) REVERT: B 631 TRP cc_start: 0.8555 (t-100) cc_final: 0.8328 (t-100) REVERT: C 45 TRP cc_start: 0.7785 (p-90) cc_final: 0.7568 (p-90) REVERT: C 150 MET cc_start: 0.5203 (tmm) cc_final: 0.4654 (ppp) REVERT: C 180 ASP cc_start: 0.7603 (m-30) cc_final: 0.7083 (m-30) REVERT: C 271 MET cc_start: 0.6975 (tpt) cc_final: 0.6623 (tpt) REVERT: C 298 ARG cc_start: 0.8629 (tmm-80) cc_final: 0.7973 (tmm-80) REVERT: C 423 ILE cc_start: 0.8305 (mt) cc_final: 0.7835 (mt) REVERT: D 93 PHE cc_start: 0.9163 (m-10) cc_final: 0.8883 (m-10) REVERT: D 130 GLN cc_start: 0.9437 (mp10) cc_final: 0.9158 (pm20) REVERT: D 176 PHE cc_start: 0.8002 (m-80) cc_final: 0.7595 (m-80) REVERT: D 191 TYR cc_start: 0.8720 (m-80) cc_final: 0.6612 (m-80) REVERT: D 288 PHE cc_start: 0.8336 (m-10) cc_final: 0.8025 (m-10) REVERT: D 318 TYR cc_start: 0.8131 (m-10) cc_final: 0.7687 (m-80) REVERT: D 391 PHE cc_start: 0.8626 (m-80) cc_final: 0.8106 (m-80) REVERT: D 434 MET cc_start: 0.3637 (ptm) cc_final: 0.2823 (tmm) REVERT: D 475 MET cc_start: 0.8818 (pmm) cc_final: 0.8182 (pmm) REVERT: E 523 LEU cc_start: 0.8457 (mt) cc_final: 0.8208 (mt) REVERT: E 574 LYS cc_start: 0.9156 (mttt) cc_final: 0.8954 (mmmt) REVERT: E 588 ARG cc_start: 0.8854 (mtm110) cc_final: 0.8287 (mtm110) REVERT: E 635 ILE cc_start: 0.8998 (mm) cc_final: 0.8765 (tp) REVERT: F 601 LYS cc_start: 0.7146 (mppt) cc_final: 0.6458 (pttt) REVERT: F 619 LEU cc_start: 0.9213 (tp) cc_final: 0.8308 (tt) REVERT: F 643 TYR cc_start: 0.8894 (m-80) cc_final: 0.8342 (m-80) REVERT: J 51 MET cc_start: 0.8835 (tpt) cc_final: 0.8404 (mmm) REVERT: J 55 THR cc_start: 0.6859 (m) cc_final: 0.6420 (t) REVERT: J 61 PHE cc_start: 0.8659 (m-80) cc_final: 0.8387 (m-10) REVERT: J 69 ILE cc_start: 0.8031 (tp) cc_final: 0.7785 (tp) REVERT: J 97 LYS cc_start: 0.9344 (pttp) cc_final: 0.9005 (pttp) REVERT: N 27 LEU cc_start: 0.8693 (tp) cc_final: 0.8438 (tp) REVERT: N 39 ARG cc_start: 0.6602 (mmt180) cc_final: 0.5863 (mmt180) REVERT: N 53 HIS cc_start: 0.8752 (t-90) cc_final: 0.8528 (t70) REVERT: N 85 THR cc_start: 0.6299 (p) cc_final: 0.5551 (p) REVERT: N 87 TYR cc_start: 0.8576 (m-80) cc_final: 0.8294 (m-80) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2960 time to fit residues: 150.8982 Evaluate side-chains 280 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 302 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 330 HIS E 651 ASN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.134256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101262 restraints weight = 57182.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104803 restraints weight = 41362.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107531 restraints weight = 30734.674| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17761 Z= 0.166 Angle : 0.963 19.346 24344 Z= 0.439 Chirality : 0.055 0.765 3070 Planarity : 0.005 0.083 2860 Dihedral : 9.793 114.659 4728 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 1944 helix: -0.19 (0.26), residues: 413 sheet: -0.48 (0.22), residues: 505 loop : -0.88 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 596 HIS 0.004 0.001 HIS D 216 PHE 0.053 0.002 PHE D 382 TYR 0.014 0.002 TYR C 177 ARG 0.014 0.001 ARG C 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 57) link_NAG-ASN : angle 5.28600 ( 171) link_ALPHA1-6 : bond 0.00926 ( 8) link_ALPHA1-6 : angle 1.38363 ( 24) link_BETA1-4 : bond 0.00559 ( 49) link_BETA1-4 : angle 2.19632 ( 147) link_ALPHA1-2 : bond 0.00335 ( 4) link_ALPHA1-2 : angle 1.69539 ( 12) link_ALPHA1-3 : bond 0.01099 ( 10) link_ALPHA1-3 : angle 1.37778 ( 30) hydrogen bonds : bond 0.04689 ( 571) hydrogen bonds : angle 6.56442 ( 1542) SS BOND : bond 0.00549 ( 35) SS BOND : angle 2.00102 ( 70) covalent geometry : bond 0.00360 (17598) covalent geometry : angle 0.83589 (23890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7732 (mp0) cc_final: 0.7464 (tt0) REVERT: A 216 HIS cc_start: 0.8645 (m-70) cc_final: 0.8101 (m-70) REVERT: A 225 ILE cc_start: 0.7797 (mt) cc_final: 0.7498 (mp) REVERT: A 246 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7323 (mm110) REVERT: A 248 THR cc_start: 0.8878 (m) cc_final: 0.8153 (t) REVERT: A 317 PHE cc_start: 0.7567 (t80) cc_final: 0.7210 (t80) REVERT: A 383 PHE cc_start: 0.8507 (m-80) cc_final: 0.8286 (m-80) REVERT: A 423 ILE cc_start: 0.8471 (mm) cc_final: 0.8264 (mm) REVERT: A 435 TYR cc_start: 0.8708 (t80) cc_final: 0.8063 (t80) REVERT: B 593 LEU cc_start: 0.9459 (tp) cc_final: 0.9127 (tp) REVERT: B 596 TRP cc_start: 0.8996 (m-90) cc_final: 0.8695 (m-90) REVERT: B 646 LEU cc_start: 0.9209 (mt) cc_final: 0.8986 (mt) REVERT: C 59 LYS cc_start: 0.6645 (tptt) cc_final: 0.5935 (ttmt) REVERT: C 133 ASN cc_start: 0.8225 (m-40) cc_final: 0.7181 (t0) REVERT: C 150 MET cc_start: 0.5305 (tmm) cc_final: 0.4816 (ppp) REVERT: C 180 ASP cc_start: 0.7401 (m-30) cc_final: 0.6777 (m-30) REVERT: C 271 MET cc_start: 0.6791 (tpt) cc_final: 0.6372 (tpt) REVERT: C 298 ARG cc_start: 0.8637 (tmm-80) cc_final: 0.8009 (tmm-80) REVERT: C 423 ILE cc_start: 0.8195 (mt) cc_final: 0.7709 (mt) REVERT: C 434 MET cc_start: 0.5579 (tmm) cc_final: 0.4699 (ttm) REVERT: C 453 ILE cc_start: 0.7557 (mm) cc_final: 0.7309 (mm) REVERT: D 93 PHE cc_start: 0.9119 (m-10) cc_final: 0.8781 (m-10) REVERT: D 130 GLN cc_start: 0.9437 (mp10) cc_final: 0.9145 (pm20) REVERT: D 176 PHE cc_start: 0.8064 (m-80) cc_final: 0.7624 (m-80) REVERT: D 191 TYR cc_start: 0.8653 (m-80) cc_final: 0.6553 (m-80) REVERT: D 260 LEU cc_start: 0.8893 (mt) cc_final: 0.8665 (mt) REVERT: D 288 PHE cc_start: 0.8283 (m-10) cc_final: 0.7961 (m-10) REVERT: D 318 TYR cc_start: 0.8247 (m-10) cc_final: 0.7846 (m-80) REVERT: D 342 LEU cc_start: 0.9275 (mp) cc_final: 0.9049 (mp) REVERT: D 391 PHE cc_start: 0.9067 (m-80) cc_final: 0.8434 (m-80) REVERT: D 434 MET cc_start: 0.3650 (ptm) cc_final: 0.3104 (tmm) REVERT: D 453 ILE cc_start: 0.9130 (mp) cc_final: 0.8747 (mp) REVERT: D 475 MET cc_start: 0.8726 (pmm) cc_final: 0.8328 (pmm) REVERT: E 635 ILE cc_start: 0.8931 (mm) cc_final: 0.8704 (tp) REVERT: F 575 GLN cc_start: 0.8218 (pp30) cc_final: 0.6898 (mp10) REVERT: F 581 LEU cc_start: 0.9267 (mt) cc_final: 0.9031 (mt) REVERT: F 588 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7938 (mmt180) REVERT: F 601 LYS cc_start: 0.6966 (mppt) cc_final: 0.6296 (pttt) REVERT: F 643 TYR cc_start: 0.8899 (m-80) cc_final: 0.8539 (m-80) REVERT: J 48 MET cc_start: 0.9271 (mtm) cc_final: 0.8460 (mmm) REVERT: J 51 MET cc_start: 0.8737 (tpt) cc_final: 0.8485 (tpt) REVERT: J 55 THR cc_start: 0.6524 (m) cc_final: 0.5886 (t) REVERT: J 97 LYS cc_start: 0.9453 (pttp) cc_final: 0.9007 (pttp) REVERT: J 100 GLU cc_start: 0.7998 (tp30) cc_final: 0.7720 (tp30) REVERT: N 27 LEU cc_start: 0.8620 (tp) cc_final: 0.8390 (tp) REVERT: N 39 ARG cc_start: 0.6590 (mmt180) cc_final: 0.5737 (mmt180) REVERT: N 53 HIS cc_start: 0.8676 (t-90) cc_final: 0.8381 (t70) REVERT: N 79 GLU cc_start: 0.6055 (mm-30) cc_final: 0.4810 (pm20) REVERT: N 81 ASP cc_start: 0.8631 (t0) cc_final: 0.8261 (t0) REVERT: N 87 TYR cc_start: 0.8536 (m-80) cc_final: 0.8318 (m-80) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2766 time to fit residues: 152.7026 Evaluate side-chains 300 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN E 650 GLN F 540 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.135116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102455 restraints weight = 56641.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.105817 restraints weight = 42213.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108059 restraints weight = 31524.422| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17761 Z= 0.151 Angle : 0.923 18.796 24344 Z= 0.419 Chirality : 0.053 0.710 3070 Planarity : 0.004 0.075 2860 Dihedral : 9.281 115.528 4728 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 1944 helix: 0.05 (0.26), residues: 418 sheet: -0.43 (0.22), residues: 504 loop : -0.82 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 596 HIS 0.003 0.001 HIS D 374 PHE 0.028 0.002 PHE C 382 TYR 0.016 0.001 TYR J 100C ARG 0.008 0.001 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 57) link_NAG-ASN : angle 5.07606 ( 171) link_ALPHA1-6 : bond 0.00912 ( 8) link_ALPHA1-6 : angle 1.34207 ( 24) link_BETA1-4 : bond 0.00573 ( 49) link_BETA1-4 : angle 2.13429 ( 147) link_ALPHA1-2 : bond 0.00353 ( 4) link_ALPHA1-2 : angle 1.64855 ( 12) link_ALPHA1-3 : bond 0.01010 ( 10) link_ALPHA1-3 : angle 1.38929 ( 30) hydrogen bonds : bond 0.04513 ( 571) hydrogen bonds : angle 6.31732 ( 1542) SS BOND : bond 0.00531 ( 35) SS BOND : angle 1.70000 ( 70) covalent geometry : bond 0.00328 (17598) covalent geometry : angle 0.80099 (23890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7933 (mppt) cc_final: 0.7222 (tmtt) REVERT: A 216 HIS cc_start: 0.8380 (m-70) cc_final: 0.7893 (m-70) REVERT: A 225 ILE cc_start: 0.7330 (mt) cc_final: 0.7033 (mp) REVERT: A 248 THR cc_start: 0.8706 (m) cc_final: 0.7992 (t) REVERT: A 252 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8478 (mmtt) REVERT: A 271 MET cc_start: 0.1673 (ttt) cc_final: 0.0664 (ttt) REVERT: A 298 ARG cc_start: 0.8596 (ptm-80) cc_final: 0.8380 (ptm-80) REVERT: A 423 ILE cc_start: 0.8415 (mm) cc_final: 0.8201 (mm) REVERT: B 586 TYR cc_start: 0.8767 (t80) cc_final: 0.8267 (t80) REVERT: B 596 TRP cc_start: 0.8979 (m-90) cc_final: 0.8498 (m-90) REVERT: C 47 ASP cc_start: 0.8849 (t0) cc_final: 0.8577 (t0) REVERT: C 150 MET cc_start: 0.5232 (tmm) cc_final: 0.4735 (ppp) REVERT: C 180 ASP cc_start: 0.7325 (m-30) cc_final: 0.6548 (m-30) REVERT: C 191 TYR cc_start: 0.7926 (m-80) cc_final: 0.7683 (m-80) REVERT: C 271 MET cc_start: 0.6368 (tpt) cc_final: 0.5957 (tpt) REVERT: C 298 ARG cc_start: 0.8651 (tmm-80) cc_final: 0.8059 (tmm-80) REVERT: C 423 ILE cc_start: 0.8150 (mt) cc_final: 0.7548 (mt) REVERT: C 434 MET cc_start: 0.5975 (tmm) cc_final: 0.4966 (ttm) REVERT: C 453 ILE cc_start: 0.7573 (mm) cc_final: 0.7318 (mm) REVERT: D 93 PHE cc_start: 0.9055 (m-10) cc_final: 0.8632 (m-10) REVERT: D 130 GLN cc_start: 0.9392 (mp10) cc_final: 0.9099 (pm20) REVERT: D 176 PHE cc_start: 0.7986 (m-80) cc_final: 0.7549 (m-80) REVERT: D 191 TYR cc_start: 0.8624 (m-80) cc_final: 0.6566 (m-80) REVERT: D 216 HIS cc_start: 0.7625 (m-70) cc_final: 0.7289 (m-70) REVERT: D 260 LEU cc_start: 0.8891 (mt) cc_final: 0.8653 (mt) REVERT: D 288 PHE cc_start: 0.8186 (m-10) cc_final: 0.7925 (m-10) REVERT: D 318 TYR cc_start: 0.8215 (m-10) cc_final: 0.7800 (m-80) REVERT: D 342 LEU cc_start: 0.9250 (mp) cc_final: 0.9014 (mp) REVERT: D 391 PHE cc_start: 0.9021 (m-80) cc_final: 0.8298 (m-80) REVERT: D 434 MET cc_start: 0.3563 (ptm) cc_final: 0.3110 (tmm) REVERT: D 475 MET cc_start: 0.8579 (pmm) cc_final: 0.8169 (pmm) REVERT: E 545 LEU cc_start: 0.9029 (tp) cc_final: 0.8747 (tp) REVERT: E 635 ILE cc_start: 0.8889 (mm) cc_final: 0.8673 (tp) REVERT: F 588 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7495 (mmt180) REVERT: F 643 TYR cc_start: 0.8859 (m-80) cc_final: 0.8431 (m-80) REVERT: J 48 MET cc_start: 0.9267 (mtm) cc_final: 0.8324 (mmm) REVERT: J 51 MET cc_start: 0.8617 (tpt) cc_final: 0.8191 (tpt) REVERT: J 97 LYS cc_start: 0.9356 (pttp) cc_final: 0.8825 (pttp) REVERT: J 100 GLU cc_start: 0.7704 (tp30) cc_final: 0.7307 (tp30) REVERT: N 39 ARG cc_start: 0.6407 (mmt180) cc_final: 0.5609 (mmt180) REVERT: N 53 HIS cc_start: 0.8513 (t-90) cc_final: 0.8209 (t70) REVERT: N 70 ASP cc_start: 0.8039 (p0) cc_final: 0.7812 (p0) REVERT: N 79 GLU cc_start: 0.5346 (mm-30) cc_final: 0.4211 (pm20) REVERT: N 81 ASP cc_start: 0.8532 (t0) cc_final: 0.8177 (t0) REVERT: N 87 TYR cc_start: 0.8522 (m-80) cc_final: 0.8170 (m-80) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.2928 time to fit residues: 161.7396 Evaluate side-chains 293 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 0.2980 chunk 166 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 173 optimal weight: 0.2980 chunk 192 optimal weight: 10.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN F 540 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.136946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104099 restraints weight = 55420.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107271 restraints weight = 40172.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109182 restraints weight = 30947.860| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17761 Z= 0.145 Angle : 0.915 18.265 24344 Z= 0.421 Chirality : 0.053 0.696 3070 Planarity : 0.004 0.076 2860 Dihedral : 8.935 115.289 4728 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 1944 helix: 0.02 (0.26), residues: 416 sheet: -0.25 (0.23), residues: 477 loop : -0.85 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 596 HIS 0.003 0.001 HIS C 374 PHE 0.024 0.002 PHE C 382 TYR 0.014 0.001 TYR C 486 ARG 0.010 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 57) link_NAG-ASN : angle 4.89917 ( 171) link_ALPHA1-6 : bond 0.00915 ( 8) link_ALPHA1-6 : angle 1.34470 ( 24) link_BETA1-4 : bond 0.00536 ( 49) link_BETA1-4 : angle 2.11125 ( 147) link_ALPHA1-2 : bond 0.00399 ( 4) link_ALPHA1-2 : angle 1.60689 ( 12) link_ALPHA1-3 : bond 0.00935 ( 10) link_ALPHA1-3 : angle 1.37887 ( 30) hydrogen bonds : bond 0.04453 ( 571) hydrogen bonds : angle 6.24670 ( 1542) SS BOND : bond 0.00535 ( 35) SS BOND : angle 1.64513 ( 70) covalent geometry : bond 0.00310 (17598) covalent geometry : angle 0.80063 (23890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5310.11 seconds wall clock time: 94 minutes 22.68 seconds (5662.68 seconds total)