Starting phenix.real_space_refine on Sun Aug 24 06:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtd_36641/08_2025/8jtd_36641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtd_36641/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jtd_36641/08_2025/8jtd_36641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtd_36641/08_2025/8jtd_36641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtd_36641/08_2025/8jtd_36641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtd_36641/08_2025/8jtd_36641.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.63, per 1000 atoms: 0.27 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: 1.77 Conformation dependent library (CDL) restraints added in 739.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.73 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: 2.86 Time building geometry restraints manager: 2.30 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 604)) selection = (chain 'D' and (resid 32 through 185 or resid 189 through 398 or resid 412 throu \ gh 604)) } ncs_group { reference = (chain 'B' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'E' and (resid 520 through 545 or resid 569 through 702)) selection = (chain 'F' and (resid 520 through 545 or resid 569 through 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.470 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- 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 : 20.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (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 ARG 0.010 0.000 ARG F 585 TYR 0.030 0.002 TYR F 643 PHE 0.041 0.002 PHE D 288 TRP 0.053 0.002 TRP D 45 HIS 0.007 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00541 (17598) covalent geometry : angle 0.92955 (23890) SS BOND : bond 0.00564 ( 35) SS BOND : angle 1.86257 ( 70) hydrogen bonds : bond 0.21968 ( 571) hydrogen bonds : angle 8.74648 ( 1542) 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) 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_NAG-ASN : bond 0.00681 ( 57) link_NAG-ASN : angle 6.95287 ( 171) *********************** 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 : 0.519 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: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7063 (p-80) cc_final: 0.6653 (p-80) REVERT: A 108 ILE cc_start: 0.8499 (mp) cc_final: 0.7592 (mp) REVERT: A 117 LYS cc_start: 0.9052 (tttt) cc_final: 0.8740 (ptmt) REVERT: A 190 GLU cc_start: 0.6156 (pm20) cc_final: 0.5270 (pm20) REVERT: B 646 LEU cc_start: 0.9119 (mt) cc_final: 0.8877 (mt) REVERT: C 271 MET cc_start: 0.4814 (tpt) cc_final: 0.4499 (mmm) REVERT: C 298 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7321 (tmm-80) REVERT: C 423 ILE cc_start: 0.7945 (mt) cc_final: 0.7676 (mt) REVERT: D 216 HIS cc_start: 0.6996 (m-70) cc_final: 0.6427 (m170) REVERT: D 391 PHE cc_start: 0.7661 (m-80) cc_final: 0.7393 (m-80) REVERT: D 434 MET cc_start: 0.5241 (ptm) cc_final: 0.4427 (ppp) REVERT: D 484 TYR cc_start: 0.7944 (p90) cc_final: 0.7486 (p90) REVERT: F 590 GLN cc_start: 0.8914 (tt0) cc_final: 0.8457 (pt0) REVERT: F 591 GLN cc_start: 0.9049 (mt0) cc_final: 0.8825 (mt0) REVERT: F 601 LYS cc_start: 0.7682 (mppt) cc_final: 0.7418 (mmtm) REVERT: F 606 THR cc_start: 0.8112 (m) cc_final: 0.7839 (m) REVERT: F 642 ILE cc_start: 0.8420 (mt) cc_final: 0.8049 (mt) REVERT: F 643 TYR cc_start: 0.8122 (m-80) cc_final: 0.7573 (m-80) REVERT: F 656 ASN cc_start: 0.9130 (t0) cc_final: 0.8880 (t0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1098 time to fit residues: 62.6691 Evaluate side-chains 301 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 428 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 72 HIS ** 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 D 103 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 ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.145151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110734 restraints weight = 54914.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114080 restraints weight = 40849.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.116887 restraints weight = 30864.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.118453 restraints weight = 25133.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.118790 restraints weight = 22789.935| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17761 Z= 0.149 Angle : 0.898 19.796 24344 Z= 0.403 Chirality : 0.054 0.848 3070 Planarity : 0.004 0.065 2860 Dihedral : 14.789 110.093 4728 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.34 % Allowed : 5.23 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 1944 helix: 0.18 (0.26), residues: 424 sheet: 0.00 (0.21), residues: 512 loop : -0.45 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 585 TYR 0.027 0.002 TYR F 643 PHE 0.021 0.002 PHE C 159 TRP 0.029 0.002 TRP D 45 HIS 0.006 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00304 (17598) covalent geometry : angle 0.75333 (23890) SS BOND : bond 0.00397 ( 35) SS BOND : angle 1.37572 ( 70) hydrogen bonds : bond 0.05079 ( 571) hydrogen bonds : angle 6.86908 ( 1542) link_ALPHA1-2 : bond 0.00241 ( 4) link_ALPHA1-2 : angle 1.77821 ( 12) link_ALPHA1-3 : bond 0.01141 ( 10) link_ALPHA1-3 : angle 1.85667 ( 30) link_ALPHA1-6 : bond 0.00713 ( 8) link_ALPHA1-6 : angle 1.80083 ( 24) link_BETA1-4 : bond 0.00605 ( 49) link_BETA1-4 : angle 2.31106 ( 147) link_NAG-ASN : bond 0.00990 ( 57) link_NAG-ASN : angle 5.36213 ( 171) *********************** 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 393 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 387 time to evaluate : 0.537 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 66 HIS cc_start: 0.8091 (p-80) cc_final: 0.7626 (p-80) REVERT: A 104 MET cc_start: 0.8612 (tpt) cc_final: 0.7961 (tpp) REVERT: A 108 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 117 LYS cc_start: 0.8837 (tttt) cc_final: 0.8614 (tttt) REVERT: A 190 GLU cc_start: 0.7686 (pm20) cc_final: 0.6822 (pm20) REVERT: A 271 MET cc_start: -0.1690 (ttt) cc_final: -0.2259 (ttt) REVERT: A 298 ARG cc_start: 0.8996 (ptm160) cc_final: 0.8701 (tpt-90) REVERT: A 423 ILE cc_start: 0.7554 (mm) cc_final: 0.7308 (mm) REVERT: B 635 ILE cc_start: 0.7647 (tt) cc_final: 0.6922 (tt) REVERT: C 271 MET cc_start: 0.5680 (tpt) cc_final: 0.5302 (mmm) REVERT: C 288 PHE cc_start: 0.7251 (m-10) cc_final: 0.6807 (m-80) REVERT: C 298 ARG cc_start: 0.8502 (tmm-80) cc_final: 0.7766 (tmm-80) REVERT: C 423 ILE cc_start: 0.8133 (mt) cc_final: 0.7873 (mt) REVERT: C 434 MET cc_start: 0.4989 (tmm) cc_final: 0.3413 (ttm) REVERT: D 45 TRP cc_start: 0.6448 (p90) cc_final: 0.6247 (p90) REVERT: D 130 GLN cc_start: 0.9285 (mp10) cc_final: 0.8952 (pm20) REVERT: D 159 PHE cc_start: 0.4457 (p90) cc_final: 0.4112 (p90) REVERT: D 176 PHE cc_start: 0.8430 (m-10) cc_final: 0.8093 (m-10) REVERT: D 191 TYR cc_start: 0.8585 (m-10) cc_final: 0.8119 (m-80) REVERT: D 216 HIS cc_start: 0.8242 (m-70) cc_final: 0.7800 (m170) REVERT: D 260 LEU cc_start: 0.8445 (mt) cc_final: 0.8120 (mt) REVERT: D 271 MET cc_start: 0.7409 (tmm) cc_final: 0.6172 (ttt) REVERT: D 342 LEU cc_start: 0.9152 (mp) cc_final: 0.8845 (mt) REVERT: D 391 PHE cc_start: 0.9272 (m-80) cc_final: 0.8613 (m-80) REVERT: D 475 MET cc_start: 0.8446 (pmm) cc_final: 0.8241 (pmm) REVERT: F 588 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7569 (mmt180) REVERT: F 591 GLN cc_start: 0.9142 (mt0) cc_final: 0.8789 (mt0) REVERT: F 643 TYR cc_start: 0.8988 (m-80) cc_final: 0.8251 (m-80) REVERT: J 51 MET cc_start: 0.8265 (ttt) cc_final: 0.7781 (mmm) REVERT: J 69 ILE cc_start: 0.7529 (tp) cc_final: 0.7305 (tp) REVERT: J 100 TYR cc_start: 0.8460 (t80) cc_final: 0.8250 (t80) REVERT: N 27 HIS cc_start: 0.8668 (t-90) cc_final: 0.8259 (t-90) REVERT: N 39 ARG cc_start: 0.7195 (mmt180) cc_final: 0.6727 (mmt180) REVERT: N 87 TYR cc_start: 0.8591 (m-80) cc_final: 0.8294 (m-80) outliers start: 6 outliers final: 2 residues processed: 390 average time/residue: 0.1125 time to fit residues: 67.4032 Evaluate side-chains 309 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 306 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 45 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- 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 130 GLN A 136 ASN C 82 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN E 651 ASN F 540 GLN F 575 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.142488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107616 restraints weight = 56359.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.111319 restraints weight = 41670.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.113837 restraints weight = 30925.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.115312 restraints weight = 25765.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115719 restraints weight = 23439.155| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.1861 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= 0.163 Angle : 0.879 19.639 24344 Z= 0.398 Chirality : 0.053 0.787 3070 Planarity : 0.004 0.068 2860 Dihedral : 12.910 107.895 4728 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.34 % Allowed : 4.08 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 1944 helix: 0.25 (0.26), residues: 423 sheet: -0.08 (0.21), residues: 527 loop : -0.47 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 273 TYR 0.024 0.002 TYR F 643 PHE 0.022 0.002 PHE C 159 TRP 0.020 0.002 TRP B 631 HIS 0.009 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00342 (17598) covalent geometry : angle 0.74698 (23890) SS BOND : bond 0.00479 ( 35) SS BOND : angle 1.39904 ( 70) hydrogen bonds : bond 0.04583 ( 571) hydrogen bonds : angle 6.61678 ( 1542) link_ALPHA1-2 : bond 0.00341 ( 4) link_ALPHA1-2 : angle 1.62326 ( 12) link_ALPHA1-3 : bond 0.01138 ( 10) link_ALPHA1-3 : angle 1.35143 ( 30) link_ALPHA1-6 : bond 0.00820 ( 8) link_ALPHA1-6 : angle 1.76564 ( 24) link_BETA1-4 : bond 0.00592 ( 49) link_BETA1-4 : angle 2.26825 ( 147) link_NAG-ASN : bond 0.00894 ( 57) link_NAG-ASN : angle 5.09886 ( 171) *********************** 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 393 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 387 time to evaluate : 0.625 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8619 (p-80) cc_final: 0.8377 (p-80) REVERT: A 104 MET cc_start: 0.8776 (tpt) cc_final: 0.8089 (tpp) REVERT: A 108 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.7495 (mp) REVERT: A 190 GLU cc_start: 0.7891 (pm20) cc_final: 0.7237 (pm20) REVERT: A 216 HIS cc_start: 0.8839 (m-70) cc_final: 0.8287 (m-70) REVERT: A 298 ARG cc_start: 0.8798 (ptm160) cc_final: 0.8466 (ptm-80) REVERT: A 383 PHE cc_start: 0.9149 (m-10) cc_final: 0.8945 (m-80) REVERT: A 423 ILE cc_start: 0.7512 (mm) cc_final: 0.7239 (mm) REVERT: A 435 TYR cc_start: 0.7778 (t80) cc_final: 0.7482 (t80) REVERT: B 588 ARG cc_start: 0.9123 (mtt180) cc_final: 0.8749 (ttm170) REVERT: C 47 ASP cc_start: 0.8517 (t0) cc_final: 0.8128 (t0) REVERT: C 59 LYS cc_start: 0.7479 (tppt) cc_final: 0.7179 (ttmt) REVERT: C 150 MET cc_start: 0.5160 (tmm) cc_final: 0.4700 (ppp) REVERT: C 271 MET cc_start: 0.5992 (tpt) cc_final: 0.5750 (tpt) REVERT: C 288 PHE cc_start: 0.7380 (m-10) cc_final: 0.6871 (m-10) REVERT: C 298 ARG cc_start: 0.8578 (tmm-80) cc_final: 0.7842 (tmm-80) REVERT: D 130 GLN cc_start: 0.9312 (mp10) cc_final: 0.8916 (pm20) REVERT: D 176 PHE cc_start: 0.7912 (m-10) cc_final: 0.7557 (m-10) REVERT: D 191 TYR cc_start: 0.8710 (m-10) cc_final: 0.8008 (m-80) REVERT: D 216 HIS cc_start: 0.8928 (m-70) cc_final: 0.8638 (m-70) REVERT: D 244 THR cc_start: 0.8866 (t) cc_final: 0.8541 (t) REVERT: D 260 LEU cc_start: 0.8491 (mt) cc_final: 0.8185 (mt) REVERT: D 271 MET cc_start: 0.7435 (tmm) cc_final: 0.6481 (ttt) REVERT: D 288 PHE cc_start: 0.8240 (m-10) cc_final: 0.7975 (m-10) REVERT: D 302 ASN cc_start: 0.9193 (m110) cc_final: 0.8959 (m110) REVERT: D 342 LEU cc_start: 0.9174 (mp) cc_final: 0.8875 (mt) REVERT: D 391 PHE cc_start: 0.9372 (m-80) cc_final: 0.8743 (m-80) REVERT: D 475 MET cc_start: 0.8670 (pmm) cc_final: 0.8353 (pmm) REVERT: D 487 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7979 (mtpt) REVERT: F 584 GLU cc_start: 0.9361 (pt0) cc_final: 0.9112 (pt0) REVERT: F 591 GLN cc_start: 0.9134 (mt0) cc_final: 0.8712 (mt0) REVERT: F 643 TYR cc_start: 0.8954 (m-80) cc_final: 0.8457 (m-80) REVERT: J 51 MET cc_start: 0.8319 (ttt) cc_final: 0.7935 (ttt) REVERT: J 69 ILE cc_start: 0.7647 (tp) cc_final: 0.6460 (tp) REVERT: J 100 TYR cc_start: 0.8586 (t80) cc_final: 0.8358 (t80) REVERT: N 27 LEU cc_start: 0.8313 (tp) cc_final: 0.8111 (tp) REVERT: N 27 HIS cc_start: 0.8845 (t-90) cc_final: 0.8376 (t-90) REVERT: N 87 TYR cc_start: 0.8646 (m-80) cc_final: 0.8387 (m-80) outliers start: 6 outliers final: 1 residues processed: 391 average time/residue: 0.1139 time to fit residues: 67.4282 Evaluate side-chains 306 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 300 ASN D 103 GLN D 105 HIS D 377 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.143036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108393 restraints weight = 56055.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111957 restraints weight = 40921.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.114718 restraints weight = 30234.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116209 restraints weight = 24805.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116834 restraints weight = 22205.684| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17761 Z= 0.139 Angle : 0.871 19.234 24344 Z= 0.389 Chirality : 0.054 0.768 3070 Planarity : 0.004 0.047 2860 Dihedral : 11.668 109.342 4728 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.19), residues: 1944 helix: 0.37 (0.27), residues: 416 sheet: -0.05 (0.21), residues: 531 loop : -0.40 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 588 TYR 0.021 0.001 TYR F 643 PHE 0.018 0.002 PHE C 159 TRP 0.051 0.002 TRP B 596 HIS 0.007 0.001 HIS N 53 Details of bonding type rmsd covalent geometry : bond 0.00289 (17598) covalent geometry : angle 0.73564 (23890) SS BOND : bond 0.00420 ( 35) SS BOND : angle 1.29460 ( 70) hydrogen bonds : bond 0.04175 ( 571) hydrogen bonds : angle 6.35994 ( 1542) link_ALPHA1-2 : bond 0.00359 ( 4) link_ALPHA1-2 : angle 1.62566 ( 12) link_ALPHA1-3 : bond 0.01160 ( 10) link_ALPHA1-3 : angle 1.41528 ( 30) link_ALPHA1-6 : bond 0.00874 ( 8) link_ALPHA1-6 : angle 1.83819 ( 24) link_BETA1-4 : bond 0.00535 ( 49) link_BETA1-4 : angle 2.21220 ( 147) link_NAG-ASN : bond 0.00693 ( 57) link_NAG-ASN : angle 5.14885 ( 171) *********************** 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 383 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 380 time to evaluate : 0.444 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: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8735 (tpt) cc_final: 0.8113 (tpp) REVERT: A 108 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.7508 (mp) REVERT: A 190 GLU cc_start: 0.7850 (pm20) cc_final: 0.7175 (pm20) REVERT: A 216 HIS cc_start: 0.8788 (m-70) cc_final: 0.8215 (m-70) REVERT: A 271 MET cc_start: -0.1763 (ttt) cc_final: -0.2011 (ttt) REVERT: A 298 ARG cc_start: 0.8849 (ptm160) cc_final: 0.8452 (ptm-80) REVERT: A 370 GLU cc_start: 0.7250 (pt0) cc_final: 0.6646 (pm20) REVERT: A 423 ILE cc_start: 0.7519 (mm) cc_final: 0.7293 (mm) REVERT: B 590 GLN cc_start: 0.9184 (pm20) cc_final: 0.8812 (pm20) REVERT: B 635 ILE cc_start: 0.7993 (tt) cc_final: 0.7227 (tt) REVERT: C 47 ASP cc_start: 0.8493 (t0) cc_final: 0.8143 (t0) REVERT: C 59 LYS cc_start: 0.7372 (tppt) cc_final: 0.7057 (tppt) REVERT: C 150 MET cc_start: 0.4763 (tmm) cc_final: 0.4477 (ppp) REVERT: C 271 MET cc_start: 0.5969 (tpt) cc_final: 0.5714 (tpt) REVERT: C 288 PHE cc_start: 0.7397 (m-10) cc_final: 0.6958 (m-10) REVERT: C 298 ARG cc_start: 0.8527 (tmm-80) cc_final: 0.7899 (tmm-80) REVERT: C 446 VAL cc_start: 0.7179 (p) cc_final: 0.6961 (t) REVERT: D 130 GLN cc_start: 0.9422 (mp10) cc_final: 0.9057 (pm20) REVERT: D 176 PHE cc_start: 0.7862 (m-10) cc_final: 0.7541 (m-10) REVERT: D 191 TYR cc_start: 0.8674 (m-10) cc_final: 0.7850 (m-80) REVERT: D 216 HIS cc_start: 0.8275 (m-70) cc_final: 0.8041 (m-70) REVERT: D 244 THR cc_start: 0.8828 (t) cc_final: 0.8475 (t) REVERT: D 252 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8630 (tptt) REVERT: D 260 LEU cc_start: 0.8492 (mt) cc_final: 0.8203 (mt) REVERT: D 288 PHE cc_start: 0.8227 (m-10) cc_final: 0.7954 (m-10) REVERT: D 342 LEU cc_start: 0.9399 (mp) cc_final: 0.9186 (mt) REVERT: D 391 PHE cc_start: 0.9352 (m-80) cc_final: 0.8710 (m-80) REVERT: D 475 MET cc_start: 0.8600 (pmm) cc_final: 0.8276 (pmm) REVERT: D 487 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7991 (mtpt) REVERT: F 575 GLN cc_start: 0.8474 (pp30) cc_final: 0.7456 (mp10) REVERT: F 584 GLU cc_start: 0.9355 (pt0) cc_final: 0.9067 (pt0) REVERT: F 591 GLN cc_start: 0.9056 (mt0) cc_final: 0.8709 (mt0) REVERT: F 643 TYR cc_start: 0.8949 (m-80) cc_final: 0.8486 (m-80) REVERT: J 51 MET cc_start: 0.8241 (ttt) cc_final: 0.8006 (ttt) REVERT: J 69 ILE cc_start: 0.7420 (tp) cc_final: 0.6227 (tp) REVERT: N 27 LEU cc_start: 0.8318 (tp) cc_final: 0.8111 (tp) REVERT: N 27 HIS cc_start: 0.8846 (t-90) cc_final: 0.8322 (t-90) REVERT: N 39 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5696 (mmt180) REVERT: N 53 HIS cc_start: 0.8535 (t-90) cc_final: 0.8291 (t70) REVERT: N 87 TYR cc_start: 0.8594 (m-80) cc_final: 0.8376 (m-80) outliers start: 3 outliers final: 0 residues processed: 381 average time/residue: 0.1178 time to fit residues: 68.1246 Evaluate side-chains 308 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 190 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.140714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.107680 restraints weight = 56652.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110432 restraints weight = 43155.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.112603 restraints weight = 32794.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.113373 restraints weight = 28501.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114140 restraints weight = 26066.605| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17761 Z= 0.161 Angle : 0.881 19.196 24344 Z= 0.399 Chirality : 0.053 0.751 3070 Planarity : 0.004 0.068 2860 Dihedral : 10.834 108.648 4728 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.19), residues: 1944 helix: 0.26 (0.26), residues: 429 sheet: -0.06 (0.21), residues: 532 loop : -0.46 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 273 TYR 0.017 0.001 TYR A 484 PHE 0.018 0.002 PHE C 159 TRP 0.034 0.002 TRP J 47 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00343 (17598) covalent geometry : angle 0.75159 (23890) SS BOND : bond 0.00419 ( 35) SS BOND : angle 1.58292 ( 70) hydrogen bonds : bond 0.04175 ( 571) hydrogen bonds : angle 6.35270 ( 1542) link_ALPHA1-2 : bond 0.00317 ( 4) link_ALPHA1-2 : angle 1.63523 ( 12) link_ALPHA1-3 : bond 0.01075 ( 10) link_ALPHA1-3 : angle 1.45981 ( 30) link_ALPHA1-6 : bond 0.00898 ( 8) link_ALPHA1-6 : angle 1.72652 ( 24) link_BETA1-4 : bond 0.00572 ( 49) link_BETA1-4 : angle 2.18074 ( 147) link_NAG-ASN : bond 0.00728 ( 57) link_NAG-ASN : angle 5.05862 ( 171) *********************** 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 370 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.610 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: symmetry clash REVERT: A 101 VAL cc_start: 0.9389 (m) cc_final: 0.9013 (m) REVERT: A 190 GLU cc_start: 0.7657 (pm20) cc_final: 0.6991 (pm20) REVERT: A 216 HIS cc_start: 0.8694 (m-70) cc_final: 0.8176 (m-70) REVERT: A 252 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8126 (mmtm) REVERT: A 271 MET cc_start: -0.0761 (ttt) cc_final: -0.1369 (ttt) REVERT: A 298 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8391 (ptm-80) REVERT: A 383 PHE cc_start: 0.8842 (m-80) cc_final: 0.8450 (m-80) REVERT: A 423 ILE cc_start: 0.7809 (mm) cc_final: 0.7560 (mm) REVERT: A 435 TYR cc_start: 0.7870 (t80) cc_final: 0.7615 (t80) REVERT: A 483 LEU cc_start: 0.9373 (mp) cc_final: 0.8523 (mp) REVERT: B 590 GLN cc_start: 0.9214 (pm20) cc_final: 0.8793 (pm20) REVERT: C 47 ASP cc_start: 0.8359 (t0) cc_final: 0.7953 (t0) REVERT: C 59 LYS cc_start: 0.7239 (tppt) cc_final: 0.6801 (tppt) REVERT: C 99 ASN cc_start: 0.7443 (t0) cc_final: 0.7150 (t0) REVERT: C 122 LEU cc_start: 0.9570 (tt) cc_final: 0.9347 (tt) REVERT: C 150 MET cc_start: 0.4796 (tmm) cc_final: 0.4536 (ppp) REVERT: C 271 MET cc_start: 0.5926 (tpt) cc_final: 0.5442 (tpt) REVERT: C 288 PHE cc_start: 0.7883 (m-10) cc_final: 0.7618 (m-10) REVERT: C 298 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.7951 (tmm-80) REVERT: C 423 ILE cc_start: 0.7916 (mt) cc_final: 0.7656 (mt) REVERT: C 446 VAL cc_start: 0.7076 (p) cc_final: 0.6836 (t) REVERT: C 490 LYS cc_start: 0.7780 (tptt) cc_final: 0.7451 (tptm) REVERT: D 130 GLN cc_start: 0.9422 (mp10) cc_final: 0.8995 (pm20) REVERT: D 176 PHE cc_start: 0.7896 (m-10) cc_final: 0.7613 (m-10) REVERT: D 191 TYR cc_start: 0.8652 (m-10) cc_final: 0.8025 (m-80) REVERT: D 216 HIS cc_start: 0.8236 (m-70) cc_final: 0.8032 (m-70) REVERT: D 244 THR cc_start: 0.8812 (t) cc_final: 0.8475 (t) REVERT: D 252 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8648 (tptt) REVERT: D 288 PHE cc_start: 0.8124 (m-10) cc_final: 0.7819 (m-10) REVERT: D 342 LEU cc_start: 0.9435 (mp) cc_final: 0.9201 (mt) REVERT: D 391 PHE cc_start: 0.9275 (m-80) cc_final: 0.8711 (m-80) REVERT: D 434 MET cc_start: 0.3417 (ptm) cc_final: 0.2424 (tmm) REVERT: D 475 MET cc_start: 0.8377 (pmm) cc_final: 0.8144 (pmm) REVERT: E 585 ARG cc_start: 0.9379 (mmm-85) cc_final: 0.9028 (mmm-85) REVERT: E 588 ARG cc_start: 0.8879 (mtm110) cc_final: 0.8601 (mtm110) REVERT: F 575 GLN cc_start: 0.8259 (pp30) cc_final: 0.7380 (mp10) REVERT: F 584 GLU cc_start: 0.9150 (pt0) cc_final: 0.8844 (pt0) REVERT: F 588 ARG cc_start: 0.8126 (mmt180) cc_final: 0.7797 (mmt180) REVERT: F 643 TYR cc_start: 0.8870 (m-80) cc_final: 0.8437 (m-80) REVERT: J 51 MET cc_start: 0.8340 (ttt) cc_final: 0.8115 (ttt) REVERT: J 69 ILE cc_start: 0.7904 (tp) cc_final: 0.7422 (tp) REVERT: N 27 HIS cc_start: 0.8832 (t-90) cc_final: 0.8384 (t-90) REVERT: N 53 HIS cc_start: 0.8470 (t-90) cc_final: 0.8227 (t70) REVERT: N 79 GLU cc_start: 0.5359 (pp20) cc_final: 0.5154 (pm20) REVERT: N 87 TYR cc_start: 0.8483 (m-80) cc_final: 0.8276 (m-80) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1161 time to fit residues: 65.3044 Evaluate side-chains 298 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 36 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 139 optimal weight: 0.0010 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.0000 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 348 GLN C 478 ASN D 103 GLN D 203 GLN D 377 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.143501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110160 restraints weight = 56648.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.113307 restraints weight = 41763.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.115566 restraints weight = 31414.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.116435 restraints weight = 27080.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.116952 restraints weight = 24817.030| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17761 Z= 0.130 Angle : 0.860 18.661 24344 Z= 0.382 Chirality : 0.053 0.723 3070 Planarity : 0.004 0.049 2860 Dihedral : 9.895 103.391 4728 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.19), residues: 1944 helix: 0.51 (0.27), residues: 418 sheet: 0.13 (0.22), residues: 526 loop : -0.46 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 273 TYR 0.017 0.001 TYR F 643 PHE 0.015 0.001 PHE D 382 TRP 0.020 0.001 TRP B 631 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00271 (17598) covalent geometry : angle 0.73462 (23890) SS BOND : bond 0.00319 ( 35) SS BOND : angle 1.37241 ( 70) hydrogen bonds : bond 0.03938 ( 571) hydrogen bonds : angle 6.03221 ( 1542) link_ALPHA1-2 : bond 0.00374 ( 4) link_ALPHA1-2 : angle 1.59464 ( 12) link_ALPHA1-3 : bond 0.01141 ( 10) link_ALPHA1-3 : angle 1.30387 ( 30) link_ALPHA1-6 : bond 0.00939 ( 8) link_ALPHA1-6 : angle 1.73069 ( 24) link_BETA1-4 : bond 0.00547 ( 49) link_BETA1-4 : angle 2.13921 ( 147) link_NAG-ASN : bond 0.00783 ( 57) link_NAG-ASN : angle 4.93514 ( 171) *********************** 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 382 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.464 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8335 (m-30) cc_final: 0.7818 (m-30) REVERT: A 108 ILE cc_start: 0.8643 (mp) cc_final: 0.8400 (mp) REVERT: A 190 GLU cc_start: 0.7664 (pm20) cc_final: 0.7008 (pm20) REVERT: A 216 HIS cc_start: 0.8701 (m-70) cc_final: 0.8205 (m-70) REVERT: A 271 MET cc_start: -0.1224 (ttt) cc_final: -0.1878 (ttt) REVERT: A 298 ARG cc_start: 0.8734 (ptm160) cc_final: 0.8463 (ptm-80) REVERT: A 381 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 383 PHE cc_start: 0.9075 (m-80) cc_final: 0.8645 (m-80) REVERT: C 47 ASP cc_start: 0.8373 (t0) cc_final: 0.7956 (t0) REVERT: C 59 LYS cc_start: 0.7005 (tppt) cc_final: 0.6703 (tppt) REVERT: C 176 PHE cc_start: 0.8730 (m-80) cc_final: 0.8506 (m-80) REVERT: C 298 ARG cc_start: 0.8484 (tmm-80) cc_final: 0.7882 (tmm-80) REVERT: C 423 ILE cc_start: 0.7933 (mt) cc_final: 0.7716 (mt) REVERT: C 446 VAL cc_start: 0.6975 (p) cc_final: 0.6775 (t) REVERT: D 93 PHE cc_start: 0.8710 (m-10) cc_final: 0.8254 (m-10) REVERT: D 111 LEU cc_start: 0.9248 (mt) cc_final: 0.8501 (mt) REVERT: D 130 GLN cc_start: 0.9457 (mp10) cc_final: 0.9107 (pm20) REVERT: D 176 PHE cc_start: 0.7917 (m-10) cc_final: 0.7590 (m-10) REVERT: D 216 HIS cc_start: 0.8280 (m-70) cc_final: 0.7883 (m-70) REVERT: D 244 THR cc_start: 0.8877 (t) cc_final: 0.8576 (t) REVERT: D 252 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8598 (tptt) REVERT: D 271 MET cc_start: 0.5379 (tmm) cc_final: 0.5151 (tmm) REVERT: D 288 PHE cc_start: 0.8282 (m-10) cc_final: 0.8018 (m-10) REVERT: D 342 LEU cc_start: 0.9429 (mp) cc_final: 0.9224 (mt) REVERT: D 391 PHE cc_start: 0.9230 (m-80) cc_final: 0.8679 (m-80) REVERT: D 434 MET cc_start: 0.3325 (ptm) cc_final: 0.2409 (tmm) REVERT: E 635 ILE cc_start: 0.9212 (mm) cc_final: 0.8717 (tp) REVERT: F 584 GLU cc_start: 0.9214 (pt0) cc_final: 0.8928 (pt0) REVERT: F 588 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7898 (mmt180) REVERT: F 591 GLN cc_start: 0.9197 (mt0) cc_final: 0.8637 (mt0) REVERT: F 643 TYR cc_start: 0.8924 (m-80) cc_final: 0.8506 (m-80) REVERT: J 51 MET cc_start: 0.8371 (ttt) cc_final: 0.8067 (mmm) REVERT: J 100 GLU cc_start: 0.8056 (tp30) cc_final: 0.7296 (tm-30) REVERT: N 27 HIS cc_start: 0.8819 (t-90) cc_final: 0.8243 (t-90) REVERT: N 39 ARG cc_start: 0.6418 (mmt180) cc_final: 0.5656 (mmt180) REVERT: N 53 HIS cc_start: 0.8380 (t-90) cc_final: 0.8138 (t70) REVERT: N 70 ASP cc_start: 0.7829 (p0) cc_final: 0.7617 (p0) outliers start: 2 outliers final: 1 residues processed: 382 average time/residue: 0.1117 time to fit residues: 64.8433 Evaluate side-chains 307 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 187 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 95 optimal weight: 0.0270 chunk 39 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 425 ASN D 103 GLN D 289 ASN D 348 GLN D 377 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108388 restraints weight = 55409.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111248 restraints weight = 39579.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114152 restraints weight = 30368.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115380 restraints weight = 24516.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.115854 restraints weight = 22271.662| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.3159 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= 0.133 Angle : 0.858 18.452 24344 Z= 0.387 Chirality : 0.052 0.709 3070 Planarity : 0.004 0.054 2860 Dihedral : 9.545 110.129 4728 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.19), residues: 1944 helix: 0.46 (0.27), residues: 417 sheet: 0.08 (0.22), residues: 535 loop : -0.47 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 588 TYR 0.017 0.001 TYR D 486 PHE 0.018 0.002 PHE A 159 TRP 0.025 0.002 TRP B 631 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00282 (17598) covalent geometry : angle 0.73430 (23890) SS BOND : bond 0.00322 ( 35) SS BOND : angle 1.45137 ( 70) hydrogen bonds : bond 0.03914 ( 571) hydrogen bonds : angle 6.05938 ( 1542) link_ALPHA1-2 : bond 0.00331 ( 4) link_ALPHA1-2 : angle 1.58854 ( 12) link_ALPHA1-3 : bond 0.01080 ( 10) link_ALPHA1-3 : angle 1.33146 ( 30) link_ALPHA1-6 : bond 0.00951 ( 8) link_ALPHA1-6 : angle 1.44877 ( 24) link_BETA1-4 : bond 0.00530 ( 49) link_BETA1-4 : angle 2.10178 ( 147) link_NAG-ASN : bond 0.00632 ( 57) link_NAG-ASN : angle 4.90817 ( 171) *********************** 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 384 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.511 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 107 ASP cc_start: 0.8436 (m-30) cc_final: 0.7973 (m-30) REVERT: A 108 ILE cc_start: 0.8740 (mp) cc_final: 0.8494 (mp) REVERT: A 190 GLU cc_start: 0.7788 (pm20) cc_final: 0.7136 (pm20) REVERT: A 216 HIS cc_start: 0.8777 (m-70) cc_final: 0.8288 (m-70) REVERT: A 225 ILE cc_start: 0.7157 (mt) cc_final: 0.6888 (mp) REVERT: A 271 MET cc_start: -0.1268 (ttt) cc_final: -0.1827 (ttt) REVERT: A 298 ARG cc_start: 0.8811 (ptm160) cc_final: 0.8490 (ptm-80) REVERT: A 381 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 383 PHE cc_start: 0.9126 (m-80) cc_final: 0.8643 (m-80) REVERT: A 435 TYR cc_start: 0.7118 (t80) cc_final: 0.6911 (t80) REVERT: B 590 GLN cc_start: 0.9260 (pm20) cc_final: 0.8879 (pm20) REVERT: B 635 ILE cc_start: 0.7979 (tt) cc_final: 0.7259 (tt) REVERT: C 47 ASP cc_start: 0.8481 (t0) cc_final: 0.8065 (t0) REVERT: C 59 LYS cc_start: 0.7019 (tppt) cc_final: 0.6499 (ttmt) REVERT: C 99 ASN cc_start: 0.7538 (t0) cc_final: 0.7141 (t0) REVERT: C 150 MET cc_start: 0.4828 (tmm) cc_final: 0.4322 (ppp) REVERT: C 176 PHE cc_start: 0.8730 (m-80) cc_final: 0.8512 (m-80) REVERT: C 298 ARG cc_start: 0.8526 (tmm-80) cc_final: 0.7852 (tmm-80) REVERT: C 423 ILE cc_start: 0.8042 (mt) cc_final: 0.7770 (mt) REVERT: D 93 PHE cc_start: 0.8454 (m-10) cc_final: 0.8238 (m-10) REVERT: D 130 GLN cc_start: 0.9465 (mp10) cc_final: 0.9146 (pm20) REVERT: D 176 PHE cc_start: 0.8020 (m-80) cc_final: 0.7621 (m-10) REVERT: D 216 HIS cc_start: 0.8343 (m-70) cc_final: 0.7924 (m-70) REVERT: D 244 THR cc_start: 0.8895 (t) cc_final: 0.8535 (t) REVERT: D 271 MET cc_start: 0.5230 (tmm) cc_final: 0.4969 (tmm) REVERT: D 288 PHE cc_start: 0.8371 (m-10) cc_final: 0.8116 (m-10) REVERT: D 342 LEU cc_start: 0.9271 (mp) cc_final: 0.9036 (mt) REVERT: D 391 PHE cc_start: 0.9279 (m-80) cc_final: 0.8609 (m-80) REVERT: D 434 MET cc_start: 0.3344 (ptm) cc_final: 0.2480 (tmm) REVERT: E 575 GLN cc_start: 0.9282 (pm20) cc_final: 0.8996 (mp10) REVERT: E 635 ILE cc_start: 0.9039 (mm) cc_final: 0.8566 (tp) REVERT: F 584 GLU cc_start: 0.9267 (pt0) cc_final: 0.8909 (pt0) REVERT: F 588 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7726 (mmt180) REVERT: F 591 GLN cc_start: 0.9199 (mt0) cc_final: 0.8702 (mt0) REVERT: F 643 TYR cc_start: 0.9015 (m-80) cc_final: 0.8598 (m-80) REVERT: J 100 GLU cc_start: 0.8194 (tp30) cc_final: 0.7553 (tm-30) REVERT: N 27 HIS cc_start: 0.8885 (t-90) cc_final: 0.8306 (t-90) REVERT: N 39 ARG cc_start: 0.6120 (mmt180) cc_final: 0.5378 (mmt180) REVERT: N 53 HIS cc_start: 0.8438 (t-90) cc_final: 0.8190 (t70) REVERT: N 87 TYR cc_start: 0.8556 (m-80) cc_final: 0.8344 (m-80) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1250 time to fit residues: 73.2889 Evaluate side-chains 306 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 92 optimal weight: 0.0370 chunk 139 optimal weight: 0.0070 chunk 129 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 302 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4158 r_free = 0.4158 target = 0.135924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.102830 restraints weight = 56691.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.105761 restraints weight = 41515.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.108522 restraints weight = 31488.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109507 restraints weight = 25489.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109981 restraints weight = 23397.676| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17761 Z= 0.194 Angle : 0.932 18.797 24344 Z= 0.422 Chirality : 0.056 0.962 3070 Planarity : 0.004 0.058 2860 Dihedral : 9.582 104.714 4728 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.19), residues: 1944 helix: 0.03 (0.26), residues: 424 sheet: -0.03 (0.22), residues: 512 loop : -0.59 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 588 TYR 0.013 0.002 TYR A 61 PHE 0.024 0.002 PHE C 382 TRP 0.034 0.002 TRP B 631 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00411 (17598) covalent geometry : angle 0.80880 (23890) SS BOND : bond 0.00417 ( 35) SS BOND : angle 1.71636 ( 70) hydrogen bonds : bond 0.04287 ( 571) hydrogen bonds : angle 6.26979 ( 1542) link_ALPHA1-2 : bond 0.00287 ( 4) link_ALPHA1-2 : angle 1.67361 ( 12) link_ALPHA1-3 : bond 0.01045 ( 10) link_ALPHA1-3 : angle 1.49645 ( 30) link_ALPHA1-6 : bond 0.00905 ( 8) link_ALPHA1-6 : angle 1.44032 ( 24) link_BETA1-4 : bond 0.00628 ( 49) link_BETA1-4 : angle 2.21562 ( 147) link_NAG-ASN : bond 0.00894 ( 57) link_NAG-ASN : angle 5.08400 ( 171) *********************** 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 368 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.439 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 225 ILE cc_start: 0.7598 (mt) cc_final: 0.7348 (mt) REVERT: A 271 MET cc_start: -0.1047 (ttt) cc_final: -0.1762 (ttt) REVERT: A 298 ARG cc_start: 0.8806 (ptm160) cc_final: 0.8263 (ptm-80) REVERT: A 383 PHE cc_start: 0.9008 (m-80) cc_final: 0.8531 (m-80) REVERT: A 395 TRP cc_start: 0.6107 (t-100) cc_final: 0.5877 (t-100) REVERT: A 423 ILE cc_start: 0.8016 (mm) cc_final: 0.7785 (mm) REVERT: A 435 TYR cc_start: 0.8192 (t80) cc_final: 0.7880 (t80) REVERT: A 480 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7840 (ptp-170) REVERT: C 47 ASP cc_start: 0.8760 (t0) cc_final: 0.8407 (t0) REVERT: C 99 ASN cc_start: 0.7835 (t0) cc_final: 0.7583 (t0) REVERT: C 150 MET cc_start: 0.4684 (tmm) cc_final: 0.4316 (ppp) REVERT: C 180 ASP cc_start: 0.7135 (m-30) cc_final: 0.6451 (m-30) REVERT: C 271 MET cc_start: 0.5838 (tpt) cc_final: 0.5509 (tpt) REVERT: C 298 ARG cc_start: 0.8495 (tmm-80) cc_final: 0.7907 (tmm-80) REVERT: C 423 ILE cc_start: 0.8109 (mt) cc_final: 0.7380 (mt) REVERT: C 490 LYS cc_start: 0.7852 (tptt) cc_final: 0.7595 (tptm) REVERT: D 93 PHE cc_start: 0.8759 (m-10) cc_final: 0.8447 (m-10) REVERT: D 109 ILE cc_start: 0.9424 (pt) cc_final: 0.9046 (pt) REVERT: D 130 GLN cc_start: 0.9487 (mp10) cc_final: 0.9258 (mp10) REVERT: D 176 PHE cc_start: 0.8144 (m-80) cc_final: 0.7757 (m-10) REVERT: D 191 TYR cc_start: 0.8587 (m-10) cc_final: 0.8093 (m-80) REVERT: D 288 PHE cc_start: 0.8316 (m-10) cc_final: 0.8018 (m-10) REVERT: D 342 LEU cc_start: 0.9264 (mp) cc_final: 0.9048 (mp) REVERT: D 391 PHE cc_start: 0.9206 (m-80) cc_final: 0.8389 (m-80) REVERT: D 434 MET cc_start: 0.3667 (ptm) cc_final: 0.2716 (tmm) REVERT: E 581 LEU cc_start: 0.9359 (mm) cc_final: 0.8990 (mm) REVERT: E 635 ILE cc_start: 0.8949 (mm) cc_final: 0.8603 (tp) REVERT: F 530 MET cc_start: 0.7621 (ptm) cc_final: 0.7381 (ptm) REVERT: F 584 GLU cc_start: 0.9240 (pt0) cc_final: 0.8908 (pt0) REVERT: F 601 LYS cc_start: 0.7042 (mppt) cc_final: 0.6342 (pttt) REVERT: F 623 TRP cc_start: 0.8064 (m100) cc_final: 0.7757 (m100) REVERT: F 643 TYR cc_start: 0.9007 (m-80) cc_final: 0.8626 (m-80) REVERT: J 51 MET cc_start: 0.8569 (ttt) cc_final: 0.8164 (ttt) REVERT: J 69 ILE cc_start: 0.7609 (tp) cc_final: 0.6461 (tp) REVERT: J 100 GLU cc_start: 0.7944 (tp30) cc_final: 0.7449 (tp30) REVERT: N 27 HIS cc_start: 0.8981 (t-90) cc_final: 0.8445 (t-90) REVERT: N 39 ARG cc_start: 0.5616 (mmt180) cc_final: 0.4761 (mmt180) REVERT: N 53 HIS cc_start: 0.8601 (t-90) cc_final: 0.8319 (t70) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1303 time to fit residues: 73.0139 Evaluate side-chains 295 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 422 GLN D 103 GLN 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 = 0.4192 r_free = 0.4192 target = 0.138896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.105531 restraints weight = 55784.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.108931 restraints weight = 41644.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.112305 restraints weight = 29818.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.112530 restraints weight = 25598.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.112868 restraints weight = 22846.819| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17761 Z= 0.146 Angle : 0.889 18.385 24344 Z= 0.404 Chirality : 0.053 0.719 3070 Planarity : 0.004 0.056 2860 Dihedral : 9.347 106.669 4728 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.19), residues: 1944 helix: 0.04 (0.26), residues: 423 sheet: -0.06 (0.22), residues: 526 loop : -0.57 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 588 TYR 0.013 0.001 TYR A 484 PHE 0.027 0.002 PHE C 382 TRP 0.059 0.002 TRP B 596 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00312 (17598) covalent geometry : angle 0.76987 (23890) SS BOND : bond 0.00434 ( 35) SS BOND : angle 1.47784 ( 70) hydrogen bonds : bond 0.04160 ( 571) hydrogen bonds : angle 6.12227 ( 1542) link_ALPHA1-2 : bond 0.00325 ( 4) link_ALPHA1-2 : angle 1.60399 ( 12) link_ALPHA1-3 : bond 0.01067 ( 10) link_ALPHA1-3 : angle 1.35816 ( 30) link_ALPHA1-6 : bond 0.00949 ( 8) link_ALPHA1-6 : angle 1.41280 ( 24) link_BETA1-4 : bond 0.00555 ( 49) link_BETA1-4 : angle 2.09046 ( 147) link_NAG-ASN : bond 0.00626 ( 57) link_NAG-ASN : angle 4.93121 ( 171) *********************** 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 : 0.508 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 107 ASP cc_start: 0.8316 (m-30) cc_final: 0.7901 (m-30) REVERT: A 216 HIS cc_start: 0.8763 (m-70) cc_final: 0.8261 (m-70) REVERT: A 225 ILE cc_start: 0.7466 (mt) cc_final: 0.7232 (mp) REVERT: A 271 MET cc_start: -0.1218 (ttt) cc_final: -0.2080 (ttt) REVERT: A 298 ARG cc_start: 0.8816 (ptm160) cc_final: 0.8360 (ptm-80) REVERT: A 383 PHE cc_start: 0.8990 (m-80) cc_final: 0.8523 (m-80) REVERT: A 395 TRP cc_start: 0.6131 (t-100) cc_final: 0.5899 (t-100) REVERT: A 480 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7905 (ptm160) REVERT: B 593 LEU cc_start: 0.9497 (tp) cc_final: 0.9097 (tp) REVERT: B 596 TRP cc_start: 0.8854 (m-90) cc_final: 0.8546 (m-90) REVERT: B 646 LEU cc_start: 0.9185 (mt) cc_final: 0.8947 (mt) REVERT: C 47 ASP cc_start: 0.8723 (t0) cc_final: 0.8267 (t0) REVERT: C 150 MET cc_start: 0.4674 (tmm) cc_final: 0.4326 (ppp) REVERT: C 176 PHE cc_start: 0.8930 (m-80) cc_final: 0.8728 (m-80) REVERT: C 180 ASP cc_start: 0.7184 (m-30) cc_final: 0.6400 (m-30) REVERT: C 271 MET cc_start: 0.6095 (tpt) cc_final: 0.5894 (tpt) REVERT: C 298 ARG cc_start: 0.8623 (tmm-80) cc_final: 0.7781 (tmm-80) REVERT: C 308 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7313 (mmm160) REVERT: C 423 ILE cc_start: 0.8139 (mt) cc_final: 0.7159 (mt) REVERT: C 425 ASN cc_start: 0.8290 (t0) cc_final: 0.7948 (m-40) REVERT: D 109 ILE cc_start: 0.9471 (pt) cc_final: 0.9271 (pt) REVERT: D 111 LEU cc_start: 0.9303 (mt) cc_final: 0.9092 (mt) REVERT: D 130 GLN cc_start: 0.9476 (mp10) cc_final: 0.9243 (mp10) REVERT: D 176 PHE cc_start: 0.8092 (m-80) cc_final: 0.7652 (m-10) REVERT: D 191 TYR cc_start: 0.8612 (m-10) cc_final: 0.8036 (m-80) REVERT: D 216 HIS cc_start: 0.8075 (m-70) cc_final: 0.7780 (m-70) REVERT: D 252 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8504 (tptt) REVERT: D 342 LEU cc_start: 0.9290 (mp) cc_final: 0.9021 (mp) REVERT: D 391 PHE cc_start: 0.9196 (m-80) cc_final: 0.8369 (m-80) REVERT: D 487 LYS cc_start: 0.8985 (pttt) cc_final: 0.8524 (tptt) REVERT: E 635 ILE cc_start: 0.8730 (mm) cc_final: 0.8476 (tp) REVERT: F 584 GLU cc_start: 0.9332 (pt0) cc_final: 0.9019 (pt0) REVERT: F 588 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7571 (mmt180) REVERT: F 623 TRP cc_start: 0.8174 (m100) cc_final: 0.7864 (m100) REVERT: F 643 TYR cc_start: 0.8986 (m-80) cc_final: 0.8601 (m-80) REVERT: J 51 MET cc_start: 0.8522 (ttt) cc_final: 0.8096 (ttt) REVERT: J 69 ILE cc_start: 0.7791 (tp) cc_final: 0.6762 (tp) REVERT: J 100 GLU cc_start: 0.7749 (tp30) cc_final: 0.7267 (tp30) REVERT: N 27 HIS cc_start: 0.8887 (t-90) cc_final: 0.8330 (t-90) REVERT: N 39 ARG cc_start: 0.5681 (mmt180) cc_final: 0.4931 (mmt180) REVERT: N 53 HIS cc_start: 0.8461 (t-90) cc_final: 0.8180 (t70) REVERT: N 87 TYR cc_start: 0.7379 (m-80) cc_final: 0.7044 (m-80) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1309 time to fit residues: 72.6152 Evaluate side-chains 295 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 157 optimal weight: 0.2980 chunk 127 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.137355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104443 restraints weight = 55812.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107752 restraints weight = 41272.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.110766 restraints weight = 30256.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.111180 restraints weight = 25947.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111504 restraints weight = 22922.740| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 17761 Z= 0.170 Angle : 0.928 18.283 24344 Z= 0.422 Chirality : 0.054 0.719 3070 Planarity : 0.004 0.056 2860 Dihedral : 9.317 105.891 4728 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.19), residues: 1944 helix: 0.01 (0.26), residues: 423 sheet: -0.10 (0.22), residues: 517 loop : -0.56 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 588 TYR 0.015 0.001 TYR A 484 PHE 0.026 0.002 PHE C 382 TRP 0.057 0.002 TRP E 571 HIS 0.005 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00372 (17598) covalent geometry : angle 0.80233 (23890) SS BOND : bond 0.00557 ( 35) SS BOND : angle 1.76015 ( 70) hydrogen bonds : bond 0.04315 ( 571) hydrogen bonds : angle 6.25450 ( 1542) link_ALPHA1-2 : bond 0.00301 ( 4) link_ALPHA1-2 : angle 1.61848 ( 12) link_ALPHA1-3 : bond 0.00969 ( 10) link_ALPHA1-3 : angle 1.40393 ( 30) link_ALPHA1-6 : bond 0.00882 ( 8) link_ALPHA1-6 : angle 1.41015 ( 24) link_BETA1-4 : bond 0.00554 ( 49) link_BETA1-4 : angle 2.10631 ( 147) link_NAG-ASN : bond 0.00705 ( 57) link_NAG-ASN : angle 5.17390 ( 171) ********************** 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 362 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.617 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 95 MET cc_start: 0.8982 (tmm) cc_final: 0.8676 (tmm) REVERT: A 107 ASP cc_start: 0.8434 (m-30) cc_final: 0.8070 (m-30) REVERT: A 216 HIS cc_start: 0.8729 (m-70) cc_final: 0.8175 (m-70) REVERT: A 225 ILE cc_start: 0.7496 (mt) cc_final: 0.7293 (mt) REVERT: A 271 MET cc_start: -0.1105 (ttt) cc_final: -0.1982 (ttt) REVERT: A 383 PHE cc_start: 0.8933 (m-80) cc_final: 0.8514 (m-80) REVERT: A 435 TYR cc_start: 0.8036 (t80) cc_final: 0.7683 (t80) REVERT: A 480 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7458 (ptp-170) REVERT: B 545 LEU cc_start: 0.6410 (pp) cc_final: 0.5545 (pp) REVERT: B 586 TYR cc_start: 0.8814 (t80) cc_final: 0.8460 (t80) REVERT: B 646 LEU cc_start: 0.9084 (mt) cc_final: 0.8865 (mt) REVERT: C 47 ASP cc_start: 0.8668 (t0) cc_final: 0.8265 (t0) REVERT: C 59 LYS cc_start: 0.7147 (tptt) cc_final: 0.6844 (tppt) REVERT: C 93 PHE cc_start: 0.6861 (m-80) cc_final: 0.6576 (m-80) REVERT: C 99 ASN cc_start: 0.7807 (t0) cc_final: 0.7294 (t0) REVERT: C 150 MET cc_start: 0.4679 (tmm) cc_final: 0.4342 (ppp) REVERT: C 180 ASP cc_start: 0.6979 (m-30) cc_final: 0.6255 (m-30) REVERT: C 271 MET cc_start: 0.5767 (tpt) cc_final: 0.5507 (tpt) REVERT: C 298 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.7791 (tmm-80) REVERT: C 423 ILE cc_start: 0.8121 (mt) cc_final: 0.7163 (mt) REVERT: C 425 ASN cc_start: 0.8337 (t0) cc_final: 0.7948 (m-40) REVERT: D 130 GLN cc_start: 0.9489 (mp10) cc_final: 0.9214 (pm20) REVERT: D 176 PHE cc_start: 0.8121 (m-80) cc_final: 0.7690 (m-80) REVERT: D 191 TYR cc_start: 0.8480 (m-10) cc_final: 0.7792 (m-80) REVERT: D 216 HIS cc_start: 0.8078 (m-70) cc_final: 0.7792 (m-70) REVERT: D 252 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8557 (mmtm) REVERT: D 302 ASN cc_start: 0.9299 (m-40) cc_final: 0.9096 (m-40) REVERT: D 342 LEU cc_start: 0.9291 (mp) cc_final: 0.9037 (mp) REVERT: D 391 PHE cc_start: 0.9201 (m-80) cc_final: 0.8397 (m-80) REVERT: D 434 MET cc_start: 0.3605 (ptm) cc_final: 0.2765 (ttp) REVERT: D 449 ILE cc_start: 0.8350 (mm) cc_final: 0.7888 (mm) REVERT: E 536 THR cc_start: 0.9415 (p) cc_final: 0.8931 (p) REVERT: E 540 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6770 (mm-40) REVERT: E 635 ILE cc_start: 0.8799 (mm) cc_final: 0.8480 (tp) REVERT: F 584 GLU cc_start: 0.9254 (pt0) cc_final: 0.8957 (pt0) REVERT: F 588 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7806 (mmt180) REVERT: F 601 LYS cc_start: 0.6757 (mppt) cc_final: 0.6148 (pttt) REVERT: F 628 TRP cc_start: 0.6731 (t-100) cc_final: 0.6500 (m100) REVERT: F 643 TYR cc_start: 0.8959 (m-80) cc_final: 0.8596 (m-80) REVERT: J 100 GLU cc_start: 0.7862 (tp30) cc_final: 0.7338 (tp30) REVERT: N 27 HIS cc_start: 0.8908 (t-90) cc_final: 0.8331 (t-90) REVERT: N 39 ARG cc_start: 0.5689 (mmt180) cc_final: 0.4929 (mmt180) REVERT: N 53 HIS cc_start: 0.8528 (t-90) cc_final: 0.8220 (t70) REVERT: N 87 TYR cc_start: 0.7358 (m-80) cc_final: 0.7090 (m-80) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1183 time to fit residues: 65.3360 Evaluate side-chains 288 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 183 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 478 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.138906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105425 restraints weight = 55480.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108543 restraints weight = 40875.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111214 restraints weight = 30734.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.112501 restraints weight = 25160.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.113109 restraints weight = 22361.917| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 17761 Z= 0.143 Angle : 0.894 17.812 24344 Z= 0.405 Chirality : 0.053 0.694 3070 Planarity : 0.005 0.109 2860 Dihedral : 9.025 107.174 4728 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.19), residues: 1944 helix: 0.04 (0.26), residues: 423 sheet: -0.08 (0.22), residues: 517 loop : -0.53 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 588 TYR 0.014 0.001 TYR A 484 PHE 0.023 0.002 PHE C 382 TRP 0.060 0.002 TRP B 596 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00309 (17598) covalent geometry : angle 0.77163 (23890) SS BOND : bond 0.00537 ( 35) SS BOND : angle 1.72447 ( 70) hydrogen bonds : bond 0.04147 ( 571) hydrogen bonds : angle 6.12847 ( 1542) link_ALPHA1-2 : bond 0.00318 ( 4) link_ALPHA1-2 : angle 1.57589 ( 12) link_ALPHA1-3 : bond 0.00997 ( 10) link_ALPHA1-3 : angle 1.37140 ( 30) link_ALPHA1-6 : bond 0.00897 ( 8) link_ALPHA1-6 : angle 1.38470 ( 24) link_BETA1-4 : bond 0.00544 ( 49) link_BETA1-4 : angle 2.06601 ( 147) link_NAG-ASN : bond 0.00643 ( 57) link_NAG-ASN : angle 4.98326 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.39 seconds wall clock time: 46 minutes 15.45 seconds (2775.45 seconds total)