Starting phenix.real_space_refine on Fri Aug 7 11:00:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yid_72986/08_2026/9yid_72986.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yid_72986/08_2026/9yid_72986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yid_72986/08_2026/9yid_72986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yid_72986/08_2026/9yid_72986.map" model { file = "/net/cci-nas-00/data/ceres_data/9yid_72986/08_2026/9yid_72986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yid_72986/08_2026/9yid_72986.cif" } resolution = 4.5 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12924 2.51 5 N 3414 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20652 Number of models: 1 Model: "" Number of chains: 54 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "G" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "H" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 10, 'TRANS': 116} Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 10, 'TRANS': 116} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3482 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 23, 'TRANS': 418} Chain breaks: 3 Chain: "M" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1024 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 10, 'TRANS': 116} Chain: "N" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 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 Chain: "g" 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: "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: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 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: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.26, per 1000 atoms: 0.21 Number of scatterers: 20652 At special positions: 0 Unit cell: (160.95, 159.21, 132.24, 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 120 16.00 O 4194 8.00 N 3414 7.00 C 12924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 5 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA p 3 " - " MAN p 4 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA V 3 " - " MAN V 6 " " BMA d 3 " - " MAN d 5 " " BMA g 3 " - " MAN g 6 " " BMA p 3 " - " MAN p 5 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " 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 u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 618 " " NAG C 702 " - " ASN C 637 " " NAG D 1 " - " ASN B 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 230 " " NAG E 604 " - " ASN E 241 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 344 " " NAG E 608 " - " ASN E 355 " " NAG F 601 " - " ASN F 133 " " NAG F 602 " - " ASN F 197 " " NAG F 603 " - " ASN F 230 " " NAG F 604 " - " ASN F 241 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 344 " " NAG F 608 " - " ASN F 355 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 197 " " NAG G 603 " - " ASN G 230 " " NAG G 604 " - " ASN G 241 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 339 " " NAG G 607 " - " ASN G 344 " " NAG G 608 " - " ASN G 355 " " NAG I 1 " - " ASN C 611 " " NAG O 1 " - " ASN F 88 " " NAG P 1 " - " ASN F 156 " " NAG Q 1 " - " ASN F 160 " " NAG R 1 " - " ASN F 234 " " NAG S 1 " - " ASN F 262 " " NAG T 1 " - " ASN F 276 " " NAG U 1 " - " ASN F 295 " " NAG V 1 " - " ASN F 332 " " NAG W 1 " - " ASN F 386 " " NAG X 1 " - " ASN F 392 " " NAG Y 1 " - " ASN F 448 " " NAG Z 1 " - " ASN G 88 " " NAG a 1 " - " ASN G 156 " " NAG b 1 " - " ASN G 160 " " NAG c 1 " - " ASN G 234 " " NAG d 1 " - " ASN G 262 " " NAG e 1 " - " ASN G 276 " " NAG f 1 " - " ASN G 295 " " NAG g 1 " - " ASN G 332 " " NAG h 1 " - " ASN G 386 " " NAG i 1 " - " ASN G 392 " " NAG j 1 " - " ASN G 448 " " NAG k 1 " - " ASN A 611 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 156 " " NAG n 1 " - " ASN E 160 " " NAG o 1 " - " ASN E 234 " " NAG p 1 " - " ASN E 262 " " NAG q 1 " - " ASN E 276 " " NAG r 1 " - " ASN E 295 " " NAG s 1 " - " ASN E 332 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 818.9 milliseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 49 sheets defined 21.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.532A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.891A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'C' and resid 523 through 527 removed outlier: 4.527A pdb=" N GLY C 527 " --> pdb=" O GLY C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.877A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.990A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 97 removed outlier: 3.516A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 94 through 97' Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.244A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.678A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 474 through 483 removed outlier: 4.115A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 97 removed outlier: 3.511A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.247A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.693A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 483 removed outlier: 4.099A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.599A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.601A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.527A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 3.880A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 650 Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.995A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 removed outlier: 3.512A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 94 through 97' Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.247A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.689A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.097A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.592A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.630A pdb=" N THR B 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL F 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL B 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 603 through 609 removed outlier: 7.654A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.772A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.772A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'F' and resid 157 through 162 Processing sheet with id=AA7, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.356A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 293 through 294 Processing sheet with id=AA9, first strand: chain 'F' and resid 301 through 307 removed outlier: 3.761A pdb=" N THR F 303 " --> pdb=" O ASP F 321A" (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP F 321A" --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LYS F 305 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AB2, first strand: chain 'F' and resid 374 through 378 Processing sheet with id=AB3, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AB4, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.768A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.778A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'G' and resid 157 through 162 Processing sheet with id=AB8, first strand: chain 'G' and resid 259 through 261 Processing sheet with id=AB9, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.374A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 300 through 307 removed outlier: 3.827A pdb=" N THR G 303 " --> pdb=" O ASP G 321A" (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP G 321A" --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 333 through 334 Processing sheet with id=AC3, first strand: chain 'G' and resid 374 through 378 Processing sheet with id=AC4, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.829A pdb=" N VAL H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR H 90 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR H 91 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP H 34 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.830A pdb=" N VAL J 107 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR J 90 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 20 through 21 removed outlier: 3.507A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.413A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP J 34 " --> pdb=" O VAL J 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.776A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.663A pdb=" N THR A 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL E 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.774A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.773A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'E' and resid 157 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AE4, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.376A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 300 through 307 removed outlier: 3.832A pdb=" N THR E 303 " --> pdb=" O ASP E 321A" (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AE7, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AE8, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AE9, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.836A pdb=" N VAL M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR M 90 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR M 91 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE M 37 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP M 34 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 20 through 21 Processing sheet with id=AF3, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AF4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR N 49 " --> pdb=" O ASN N 53 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1515 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: 3.69 Time building geometry restraints manager: 2.29 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: 6403 1.34 - 1.46: 5333 1.46 - 1.58: 9207 1.58 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 21099 Sorted by residual: bond pdb=" C3 MAN g 4 " pdb=" O3 MAN g 4 " ideal model delta sigma weight residual 1.408 1.441 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C3 MAN V 4 " pdb=" O3 MAN V 4 " ideal model delta sigma weight residual 1.408 1.441 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C3 MAN s 4 " pdb=" O3 MAN s 4 " ideal model delta sigma weight residual 1.408 1.440 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 MAN p 4 " pdb=" O5 MAN p 4 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 21094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 27653 1.69 - 3.39: 899 3.39 - 5.08: 112 5.08 - 6.77: 19 6.77 - 8.47: 12 Bond angle restraints: 28695 Sorted by residual: angle pdb=" C TYR F 134 " pdb=" CA TYR F 134 " pdb=" CB TYR F 134 " ideal model delta sigma weight residual 110.42 116.09 -5.67 1.99e+00 2.53e-01 8.11e+00 angle pdb=" C TYR G 134 " pdb=" CA TYR G 134 " pdb=" CB TYR G 134 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.08e+00 angle pdb=" C TYR E 134 " pdb=" CA TYR E 134 " pdb=" CB TYR E 134 " ideal model delta sigma weight residual 110.42 116.06 -5.64 1.99e+00 2.53e-01 8.03e+00 angle pdb=" C1 BMA S 3 " pdb=" O5 BMA S 3 " pdb=" C5 BMA S 3 " ideal model delta sigma weight residual 118.82 110.35 8.47 3.00e+00 1.11e-01 7.97e+00 angle pdb=" C1 BMA p 3 " pdb=" O5 BMA p 3 " pdb=" C5 BMA p 3 " ideal model delta sigma weight residual 118.82 110.38 8.44 3.00e+00 1.11e-01 7.92e+00 ... (remaining 28690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 13269 24.42 - 48.85: 717 48.85 - 73.27: 84 73.27 - 97.69: 51 97.69 - 122.12: 93 Dihedral angle restraints: 14214 sinusoidal: 7272 harmonic: 6942 Sorted by residual: dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.78 -62.78 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.43 -61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.17 -61.17 1 1.00e+01 1.00e-02 4.97e+01 ... (remaining 14211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 3516 1.008 - 2.017: 0 2.017 - 3.025: 0 3.025 - 4.034: 0 4.034 - 5.042: 18 Chirality restraints: 3534 Sorted by residual: chirality pdb=" C4 NAG G 601 " pdb=" C3 NAG G 601 " pdb=" C5 NAG G 601 " pdb=" O4 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.53 2.51 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C4 NAG E 601 " pdb=" C3 NAG E 601 " pdb=" C5 NAG E 601 " pdb=" O4 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.53 2.51 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C4 NAG F 601 " pdb=" C3 NAG F 601 " pdb=" C5 NAG F 601 " pdb=" O4 NAG F 601 " both_signs ideal model delta sigma weight residual False -2.53 2.51 -5.04 2.00e-01 2.50e+01 6.35e+02 ... (remaining 3531 not shown) Planarity restraints: 3570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 13 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO J 14 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO J 14 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 14 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO H 14 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN M 13 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO M 14 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO M 14 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO M 14 " -0.016 5.00e-02 4.00e+02 ... (remaining 3567 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 10503 2.97 - 3.46: 19485 3.46 - 3.94: 32646 3.94 - 4.42: 36013 4.42 - 4.90: 59074 Nonbonded interactions: 157721 Sorted by model distance: nonbonded pdb=" O5 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.493 2.432 nonbonded pdb=" O5 BMA g 3 " pdb=" O6 BMA g 3 " model vdw 2.497 2.432 nonbonded pdb=" O5 BMA s 3 " pdb=" O6 BMA s 3 " model vdw 2.497 2.432 nonbonded pdb=" C4 NAG m 1 " pdb=" O5 NAG m 2 " model vdw 2.509 2.776 nonbonded pdb=" C4 NAG a 1 " pdb=" O5 NAG a 2 " model vdw 2.509 2.776 ... (remaining 157716 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'S' selection = chain 'd' selection = chain 'p' } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 's' } Set up NCS constraints Number of NCS constrained groups: 7 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'S' selection = chain 'd' selection = chain 'p' } pdb_interpretation.ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 's' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.450 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 0.033 21267 Z= 0.247 Angle : 0.702 8.966 29154 Z= 0.298 Chirality : 0.359 5.042 3534 Planarity : 0.003 0.033 3504 Dihedral : 18.223 122.117 9609 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.28 % Allowed : 4.89 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2358 helix: 1.51 (0.27), residues: 414 sheet: -0.19 (0.22), residues: 567 loop : -1.28 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 500 TYR 0.006 0.001 TYR H 91 PHE 0.006 0.001 PHE F 159 TRP 0.010 0.001 TRP E 112 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.25 (21099) covalent geometry : angle 0.67116 / 0.29 (28695) SS BOND : bond 0.00412 / 0.27 ( 45) SS BOND : angle 1.13411 / 0.82 ( 90) hydrogen bonds : bond 0.15509 / 10.25 ( 591) hydrogen bonds : angle 6.31173 / 4.64 ( 1515) link_ALPHA1-3 : bond 0.00380 / 0.21 ( 9) link_ALPHA1-3 : angle 1.48013 / 1.17 ( 27) link_ALPHA1-6 : bond 0.00076 / 0.04 ( 6) link_ALPHA1-6 : angle 0.52017 / 0.31 ( 18) link_BETA1-4 : bond 0.00391 / 0.25 ( 42) link_BETA1-4 : angle 1.26062 / 0.85 ( 126) link_NAG-ASN : bond 0.00481 / 0.31 ( 66) link_NAG-ASN : angle 2.33046 / 1.61 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7990 (tt0) cc_final: 0.7750 (tm-30) REVERT: A 652 GLN cc_start: 0.7708 (mm-40) cc_final: 0.6980 (mm110) REVERT: A 653 GLN cc_start: 0.8734 (mt0) cc_final: 0.8167 (mm-40) REVERT: A 655 LYS cc_start: 0.8861 (tppt) cc_final: 0.7968 (tmtt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0655 time to fit residues: 3.0550 Evaluate side-chains 31 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.038 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 56 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: E 141 ASP cc_start: 0.6243 (p0) cc_final: 0.5850 (p0) REVERT: E 161 MET cc_start: 0.9181 (tpt) cc_final: 0.8961 (tpp) REVERT: E 180 ASP cc_start: 0.8746 (m-30) cc_final: 0.8060 (m-30) REVERT: E 327 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7245 (mmt180) REVERT: E 377 ASN cc_start: 0.9212 (t0) cc_final: 0.8651 (t0) REVERT: E 428 GLN cc_start: 0.8687 (mp10) cc_final: 0.8248 (mp10) REVERT: E 432 GLN cc_start: 0.8653 (mp10) cc_final: 0.8001 (mp10) REVERT: E 434 MET cc_start: 0.8766 (ttp) cc_final: 0.8316 (ttp) REVERT: E 440 GLN cc_start: 0.8397 (tp40) cc_final: 0.8146 (tm-30) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.0828 time to fit residues: 5.5780 Evaluate side-chains 34 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.145 Evaluate side-chains 48 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: H 43 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7846 (mp0) REVERT: H 67 ILE cc_start: 0.8494 (mt) cc_final: 0.7448 (mt) REVERT: H 71 LYS cc_start: 0.8245 (mtmm) cc_final: 0.8033 (ptmm) REVERT: H 98 LEU cc_start: 0.7196 (pp) cc_final: 0.6622 (pp) REVERT: H 100 TYR cc_start: 0.7842 (p90) cc_final: 0.7539 (p90) REVERT: H 103 TRP cc_start: 0.6735 (m100) cc_final: 0.6234 (m-10) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0670 time to fit residues: 3.4669 Evaluate side-chains 29 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.040 Evaluate side-chains 29 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.036 Fit side-chains REVERT: K 21 ILE cc_start: 0.8616 (tp) cc_final: 0.8403 (tp) REVERT: K 70 ASP cc_start: 0.7053 (t0) cc_final: 0.6584 (m-30) REVERT: K 73 LEU cc_start: 0.7865 (tt) cc_final: 0.6336 (tt) REVERT: K 82 ASP cc_start: 0.7791 (m-30) cc_final: 0.7477 (m-30) REVERT: K 96 TRP cc_start: 0.8129 (m-90) cc_final: 0.5564 (p-90) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0658 time to fit residues: 2.0819 Evaluate side-chains 20 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.046 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0050 chunk 235 optimal weight: 7.9990 overall best weight: 1.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 77 GLN K 6 GLN K 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.065565 restraints weight = 3009.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.067120 restraints weight = 2045.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.068250 restraints weight = 1535.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.069052 restraints weight = 1227.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.069451 restraints weight = 1037.084| |-----------------------------------------------------------------------------| r_work (final): 0.2843 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.057407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.057231 restraints weight = 198.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.057344 restraints weight = 13.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.057382 restraints weight = 2.501 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.057394 restraints weight = 0.629 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.057393 restraints weight = 0.166 | |-----------------------------------------------------------------------------| r_work (final): 0.2584 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.080907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.068280 restraints weight = 8374.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.070022 restraints weight = 5430.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.071462 restraints weight = 4020.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.072347 restraints weight = 3199.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.072939 restraints weight = 2719.460| |-----------------------------------------------------------------------------| r_work (final): 0.2776 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111713 restraints weight = 3710.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113674 restraints weight = 2476.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.114891 restraints weight = 1811.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115993 restraints weight = 1476.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116634 restraints weight = 1240.078| |-----------------------------------------------------------------------------| r_work (final): 0.3745 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.087427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078497 restraints weight = 3673.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080172 restraints weight = 2283.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.081364 restraints weight = 1602.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082234 restraints weight = 1207.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082810 restraints weight = 964.547| |-----------------------------------------------------------------------------| r_work (final): 0.3507 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.071184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.066300 restraints weight = 307.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.067256 restraints weight = 165.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.067709 restraints weight = 117.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.068138 restraints weight = 98.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068386 restraints weight = 82.909| |-----------------------------------------------------------------------------| r_work (final): 0.2803 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.076077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074851 restraints weight = 549.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.075082 restraints weight = 317.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075316 restraints weight = 230.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075420 restraints weight = 151.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075571 restraints weight = 121.755| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21267 Z= 0.215 Angle : 0.888 15.745 29154 Z= 0.404 Chirality : 0.066 0.826 3534 Planarity : 0.008 0.197 3504 Dihedral : 10.887 93.149 5124 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.56 % Allowed : 3.39 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -0.73 (0.18), residues: 2358 helix: 1.52 (0.28), residues: 411 sheet: -0.25 (0.21), residues: 636 loop : -1.28 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 99 TYR 0.035 0.003 TYR J 58 PHE 0.026 0.002 PHE N 62 TRP 0.012 0.001 TRP N 94 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (21099) covalent geometry : angle 0.76677 / 0.37 (28695) SS BOND : bond 0.00598 / 0.41 ( 45) SS BOND : angle 2.79330 / 1.67 ( 90) hydrogen bonds : bond 0.04776 / 3.13 ( 591) hydrogen bonds : angle 5.86187 / 4.32 ( 1515) link_ALPHA1-3 : bond 0.00766 / 0.45 ( 9) link_ALPHA1-3 : angle 2.29814 / 1.67 ( 27) link_ALPHA1-6 : bond 0.00203 / 0.10 ( 6) link_ALPHA1-6 : angle 2.44365 / 1.39 ( 18) link_BETA1-4 : bond 0.00494 / 0.32 ( 42) link_BETA1-4 : angle 1.19060 / 0.84 ( 126) link_NAG-ASN : bond 0.01664 / 1.10 ( 66) link_NAG-ASN : angle 5.00733 / 3.47 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.041 Fit side-chains revert: symmetry clash REVERT: A 655 LYS cc_start: 0.8427 (tppt) cc_final: 0.7713 (tmtt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0531 time to fit residues: 1.9369 Evaluate side-chains 28 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.039 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 43 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: F 80 ASN cc_start: 0.7710 (p0) cc_final: 0.7469 (m-40) REVERT: F 95 MET cc_start: 0.9042 (ptm) cc_final: 0.8725 (ppp) REVERT: F 180 ASP cc_start: 0.8614 (m-30) cc_final: 0.8272 (m-30) REVERT: F 213 ILE cc_start: 0.9117 (pt) cc_final: 0.8437 (pt) REVERT: F 327 ARG cc_start: 0.7696 (mtt-85) cc_final: 0.7345 (mmt180) REVERT: F 370 GLU cc_start: 0.8152 (mp0) cc_final: 0.7783 (mt-10) REVERT: F 377 ASN cc_start: 0.9058 (t0) cc_final: 0.8661 (t0) REVERT: F 428 GLN cc_start: 0.8661 (mp10) cc_final: 0.8281 (mp10) REVERT: F 432 GLN cc_start: 0.8671 (mp10) cc_final: 0.8142 (mp10) REVERT: F 440 GLN cc_start: 0.8404 (tp40) cc_final: 0.8187 (tm-30) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.0667 time to fit residues: 3.4965 Evaluate side-chains 31 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.125 Evaluate side-chains 40 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.026 Fit side-chains REVERT: J 13 GLN cc_start: 0.8226 (tt0) cc_final: 0.7901 (tt0) REVERT: J 43 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7854 (mp0) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0399 time to fit residues: 1.7507 Evaluate side-chains 31 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.023 Evaluate side-chains 25 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.041 Fit side-chains revert: symmetry clash REVERT: L 21 ILE cc_start: 0.8291 (tp) cc_final: 0.8049 (pt) REVERT: L 70 ASP cc_start: 0.7081 (t0) cc_final: 0.6691 (m-30) REVERT: L 73 LEU cc_start: 0.7867 (tt) cc_final: 0.5946 (tt) REVERT: L 96 TRP cc_start: 0.8038 (m-90) cc_final: 0.5593 (p-90) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0314 time to fit residues: 0.9223 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.041 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 170 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 113 optimal weight: 20.0000 chunk 188 optimal weight: 0.0050 chunk 185 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 160 ASN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.078448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066973 restraints weight = 2912.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.068514 restraints weight = 1900.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069660 restraints weight = 1408.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.070476 restraints weight = 1123.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.071075 restraints weight = 949.311| |-----------------------------------------------------------------------------| r_work (final): 0.2869 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.073430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.072926 restraints weight = 109.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.073373 restraints weight = 16.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.073390 restraints weight = 3.832 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.073390 restraints weight = 0.571 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.073390 restraints weight = 0.571 | |-----------------------------------------------------------------------------| r_work (final): 0.2689 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.082357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.069855 restraints weight = 8302.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.071962 restraints weight = 5180.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.073412 restraints weight = 3675.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.074438 restraints weight = 2851.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.075156 restraints weight = 2364.265| |-----------------------------------------------------------------------------| r_work (final): 0.2816 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.118887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105045 restraints weight = 3456.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.107842 restraints weight = 2014.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109802 restraints weight = 1347.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110682 restraints weight = 997.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.111778 restraints weight = 830.653| |-----------------------------------------------------------------------------| r_work (final): 0.3739 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.086758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078426 restraints weight = 3813.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080129 restraints weight = 2315.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081439 restraints weight = 1578.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.082427 restraints weight = 1158.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083191 restraints weight = 889.063| |-----------------------------------------------------------------------------| r_work (final): 0.3517 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.068363 restraints weight = 341.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069311 restraints weight = 157.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.069842 restraints weight = 97.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.070216 restraints weight = 70.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.070434 restraints weight = 53.336| |-----------------------------------------------------------------------------| r_work (final): 0.2852 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071340 restraints weight = 468.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.071910 restraints weight = 193.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072349 restraints weight = 115.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.072649 restraints weight = 79.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072782 restraints weight = 58.453| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.406 21267 Z= 0.849 Angle : 1.130 60.924 29154 Z= 0.456 Chirality : 0.100 2.708 3534 Planarity : 0.007 0.180 3504 Dihedral : 9.998 88.001 5124 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.14 % Allowed : 2.54 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2358 helix: 1.36 (0.28), residues: 414 sheet: -0.24 (0.21), residues: 630 loop : -1.34 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 100I TYR 0.018 0.002 TYR M 58 PHE 0.017 0.001 PHE H 100J TRP 0.044 0.002 TRP N 94 HIS 0.006 0.001 HIS N 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (21099) covalent geometry : angle 0.67700 / 0.34 (28695) SS BOND : bond 0.00960 / 0.58 ( 45) SS BOND : angle 1.88216 / 1.39 ( 90) hydrogen bonds : bond 0.03943 / 2.62 ( 591) hydrogen bonds : angle 5.66416 / 4.16 ( 1515) link_ALPHA1-3 : bond 0.00733 / 0.42 ( 9) link_ALPHA1-3 : angle 2.55936 / 1.81 ( 27) link_ALPHA1-6 : bond 0.00340 / 0.18 ( 6) link_ALPHA1-6 : angle 2.21188 / 1.27 ( 18) link_BETA1-4 : bond 0.00434 / 0.29 ( 42) link_BETA1-4 : angle 1.21930 / 0.88 ( 126) link_NAG-ASN : bond 0.29942 / 20.21 ( 66) link_NAG-ASN : angle 10.84925 / 8.13 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 648 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 652 GLN cc_start: 0.7332 (mm110) cc_final: 0.7040 (tt0) REVERT: A 655 LYS cc_start: 0.8435 (tppt) cc_final: 0.7656 (tmtt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0525 time to fit residues: 1.9835 Evaluate side-chains 29 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 44 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.141 Fit side-chains REVERT: F 95 MET cc_start: 0.8950 (ptm) cc_final: 0.8692 (ppp) REVERT: F 161 MET cc_start: 0.9104 (tpt) cc_final: 0.8558 (tpt) REVERT: F 180 ASP cc_start: 0.8656 (m-30) cc_final: 0.8209 (m-30) REVERT: F 213 ILE cc_start: 0.9031 (pt) cc_final: 0.8386 (pt) REVERT: F 327 ARG cc_start: 0.7647 (mtt-85) cc_final: 0.7372 (mmt180) REVERT: F 370 GLU cc_start: 0.8104 (mp0) cc_final: 0.7755 (mt-10) REVERT: F 377 ASN cc_start: 0.9059 (t0) cc_final: 0.8640 (t0) REVERT: F 428 GLN cc_start: 0.8580 (mp10) cc_final: 0.8226 (mp10) REVERT: F 432 GLN cc_start: 0.8785 (mp10) cc_final: 0.8290 (mp10) REVERT: F 440 GLN cc_start: 0.8345 (tp40) cc_final: 0.8127 (tm-30) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0583 time to fit residues: 3.3809 Evaluate side-chains 33 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.144 Evaluate side-chains 39 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.041 Fit side-chains REVERT: J 13 GLN cc_start: 0.8224 (tt0) cc_final: 0.7895 (tt0) REVERT: J 89 VAL cc_start: 0.9004 (t) cc_final: 0.8781 (t) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0390 time to fit residues: 1.7256 Evaluate side-chains 27 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.027 Evaluate side-chains 25 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: L 70 ASP cc_start: 0.7080 (t0) cc_final: 0.6741 (m-30) REVERT: L 73 LEU cc_start: 0.7865 (tt) cc_final: 0.6376 (tt) REVERT: L 96 TRP cc_start: 0.7895 (m-90) cc_final: 0.5614 (p-90) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0341 time to fit residues: 0.9997 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.037 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 15 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 202 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 26 optimal weight: 0.0040 chunk 187 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 214 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.077955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.066287 restraints weight = 2989.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.067980 restraints weight = 1937.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.069195 restraints weight = 1416.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.070083 restraints weight = 1118.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.070565 restraints weight = 930.234| |-----------------------------------------------------------------------------| r_work (final): 0.2856 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.053276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.052920 restraints weight = 144.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.053093 restraints weight = 14.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.053130 restraints weight = 3.510 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.053139 restraints weight = 1.033 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.053139 restraints weight = 0.684 | |-----------------------------------------------------------------------------| r_work (final): 0.2594 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.082931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.070344 restraints weight = 8238.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.072478 restraints weight = 5203.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.073939 restraints weight = 3705.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.074937 restraints weight = 2880.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.075751 restraints weight = 2405.488| |-----------------------------------------------------------------------------| r_work (final): 0.2811 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.120034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106774 restraints weight = 3609.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109621 restraints weight = 2161.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111485 restraints weight = 1449.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.112662 restraints weight = 1061.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113590 restraints weight = 844.505| |-----------------------------------------------------------------------------| r_work (final): 0.3768 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077574 restraints weight = 3812.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079378 restraints weight = 2369.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.080683 restraints weight = 1612.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081768 restraints weight = 1174.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082553 restraints weight = 886.758| |-----------------------------------------------------------------------------| r_work (final): 0.3508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.071153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.068659 restraints weight = 346.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069410 restraints weight = 158.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069832 restraints weight = 98.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.070144 restraints weight = 73.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.070333 restraints weight = 55.299| |-----------------------------------------------------------------------------| r_work (final): 0.2859 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.075033 restraints weight = 536.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.075310 restraints weight = 304.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.075567 restraints weight = 195.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075676 restraints weight = 128.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.075796 restraints weight = 104.605| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21267 Z= 0.152 Angle : 0.774 22.431 29154 Z= 0.348 Chirality : 0.061 0.771 3534 Planarity : 0.006 0.162 3504 Dihedral : 9.352 83.661 5124 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2358 helix: 1.29 (0.28), residues: 417 sheet: -0.18 (0.21), residues: 603 loop : -1.30 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.014 0.002 TYR M 91 PHE 0.017 0.001 PHE E 159 TRP 0.043 0.002 TRP L 94 HIS 0.002 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (21099) covalent geometry : angle 0.62432 / 0.31 (28695) SS BOND : bond 0.01140 / 0.70 ( 45) SS BOND : angle 2.59193 / 1.88 ( 90) hydrogen bonds : bond 0.03653 / 2.43 ( 591) hydrogen bonds : angle 5.68754 / 4.15 ( 1515) link_ALPHA1-3 : bond 0.00789 / 0.46 ( 9) link_ALPHA1-3 : angle 2.52156 / 1.77 ( 27) link_ALPHA1-6 : bond 0.00463 / 0.24 ( 6) link_ALPHA1-6 : angle 2.24148 / 1.30 ( 18) link_BETA1-4 : bond 0.00495 / 0.33 ( 42) link_BETA1-4 : angle 1.23403 / 0.90 ( 126) link_NAG-ASN : bond 0.01166 / 0.76 ( 66) link_NAG-ASN : angle 5.13124 / 3.57 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: A 648 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 655 LYS cc_start: 0.8453 (tppt) cc_final: 0.7736 (tmtt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0432 time to fit residues: 1.6611 Evaluate side-chains 25 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 45 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.083 Fit side-chains REVERT: E 80 ASN cc_start: 0.7663 (p0) cc_final: 0.7416 (m-40) REVERT: E 95 MET cc_start: 0.8973 (ptm) cc_final: 0.8682 (ppp) REVERT: E 161 MET cc_start: 0.9148 (tpt) cc_final: 0.8525 (tpp) REVERT: E 180 ASP cc_start: 0.8750 (m-30) cc_final: 0.8085 (m-30) REVERT: E 213 ILE cc_start: 0.8984 (pt) cc_final: 0.8467 (pt) REVERT: E 327 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7468 (mmt180) REVERT: E 377 ASN cc_start: 0.9036 (t0) cc_final: 0.8580 (t0) REVERT: E 428 GLN cc_start: 0.8674 (mp10) cc_final: 0.8243 (mp10) REVERT: E 432 GLN cc_start: 0.8732 (mp10) cc_final: 0.8006 (mp10) REVERT: E 434 MET cc_start: 0.8994 (ttp) cc_final: 0.8285 (ttp) REVERT: E 440 GLN cc_start: 0.8390 (tp40) cc_final: 0.8092 (tm-30) outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.0615 time to fit residues: 3.5468 Evaluate side-chains 33 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.118 Evaluate side-chains 39 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.026 Fit side-chains REVERT: J 13 GLN cc_start: 0.8167 (tt0) cc_final: 0.7856 (tt0) REVERT: J 39 GLN cc_start: 0.7166 (mm110) cc_final: 0.6911 (mm110) REVERT: J 89 VAL cc_start: 0.9055 (t) cc_final: 0.8823 (t) REVERT: J 99 ARG cc_start: 0.6521 (mmp80) cc_final: 0.5727 (mmt90) REVERT: J 100 ARG cc_start: 0.7468 (ptt90) cc_final: 0.6877 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0516 time to fit residues: 2.2140 Evaluate side-chains 30 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.038 Evaluate side-chains 24 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.034 Fit side-chains REVERT: L 70 ASP cc_start: 0.7034 (t0) cc_final: 0.6684 (m-30) REVERT: L 96 TRP cc_start: 0.7770 (m-90) cc_final: 0.5681 (p-90) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0297 time to fit residues: 0.8453 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 166 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.064723 restraints weight = 3102.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.066407 restraints weight = 2062.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.067565 restraints weight = 1534.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.068381 restraints weight = 1229.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.069023 restraints weight = 1041.924| |-----------------------------------------------------------------------------| r_work (final): 0.2820 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.065161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.064644 restraints weight = 196.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.065006 restraints weight = 22.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.065142 restraints weight = 7.118 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.065207 restraints weight = 2.585 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.065209 restraints weight = 1.045 | |-----------------------------------------------------------------------------| r_work (final): 0.2596 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.082040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.069445 restraints weight = 8400.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.071357 restraints weight = 5380.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.072607 restraints weight = 3894.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.073674 restraints weight = 3100.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.074344 restraints weight = 2595.638| |-----------------------------------------------------------------------------| r_work (final): 0.2835 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.119906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108797 restraints weight = 3564.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.110690 restraints weight = 2355.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112176 restraints weight = 1745.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113001 restraints weight = 1343.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113754 restraints weight = 1129.950| |-----------------------------------------------------------------------------| r_work (final): 0.3735 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.085878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.077714 restraints weight = 3790.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.079536 restraints weight = 2300.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.080849 restraints weight = 1561.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081861 restraints weight = 1126.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.082597 restraints weight = 842.219| |-----------------------------------------------------------------------------| r_work (final): 0.3501 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.068638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.061770 restraints weight = 275.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.062683 restraints weight = 178.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.063052 restraints weight = 139.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.063055 restraints weight = 127.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.063055 restraints weight = 127.254| |-----------------------------------------------------------------------------| r_work (final): 0.2613 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.071211 restraints weight = 553.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071872 restraints weight = 200.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072327 restraints weight = 116.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072585 restraints weight = 80.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072734 restraints weight = 59.926| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21267 Z= 0.156 Angle : 0.754 19.490 29154 Z= 0.343 Chirality : 0.059 0.792 3534 Planarity : 0.006 0.128 3504 Dihedral : 8.978 80.251 5124 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2358 helix: 1.32 (0.28), residues: 417 sheet: -0.15 (0.21), residues: 603 loop : -1.32 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 166 TYR 0.021 0.002 TYR K 49 PHE 0.010 0.001 PHE F 159 TRP 0.031 0.002 TRP N 94 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (21099) covalent geometry : angle 0.62493 / 0.31 (28695) SS BOND : bond 0.00435 / 0.25 ( 45) SS BOND : angle 2.16828 / 1.59 ( 90) hydrogen bonds : bond 0.03499 / 2.33 ( 591) hydrogen bonds : angle 5.62061 / 4.11 ( 1515) link_ALPHA1-3 : bond 0.00783 / 0.45 ( 9) link_ALPHA1-3 : angle 2.40821 / 1.68 ( 27) link_ALPHA1-6 : bond 0.00508 / 0.27 ( 6) link_ALPHA1-6 : angle 2.13308 / 1.25 ( 18) link_BETA1-4 : bond 0.00389 / 0.26 ( 42) link_BETA1-4 : angle 1.25626 / 0.93 ( 126) link_NAG-ASN : bond 0.00800 / 0.51 ( 66) link_NAG-ASN : angle 4.78225 / 3.30 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: A 648 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 652 GLN cc_start: 0.7400 (mm110) cc_final: 0.7127 (tt0) REVERT: A 655 LYS cc_start: 0.8481 (tppt) cc_final: 0.7715 (tmtt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0462 time to fit residues: 1.6549 Evaluate side-chains 25 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.040 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 46 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.083 Fit side-chains REVERT: F 95 MET cc_start: 0.9000 (ptm) cc_final: 0.8756 (ppp) REVERT: F 161 MET cc_start: 0.9112 (tpt) cc_final: 0.8838 (tpt) REVERT: F 180 ASP cc_start: 0.8647 (m-30) cc_final: 0.8267 (m-30) REVERT: F 213 ILE cc_start: 0.9089 (pt) cc_final: 0.8450 (pt) REVERT: F 327 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7303 (mmt180) REVERT: F 370 GLU cc_start: 0.8113 (mp0) cc_final: 0.7734 (mt-10) REVERT: F 377 ASN cc_start: 0.8944 (t0) cc_final: 0.8563 (t0) REVERT: F 428 GLN cc_start: 0.8656 (mp10) cc_final: 0.8228 (mp10) REVERT: F 432 GLN cc_start: 0.8656 (mp10) cc_final: 0.8147 (mp10) REVERT: F 440 GLN cc_start: 0.8367 (tp40) cc_final: 0.8145 (tm-30) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0633 time to fit residues: 3.6788 Evaluate side-chains 33 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.136 Evaluate side-chains 38 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.038 Fit side-chains REVERT: J 13 GLN cc_start: 0.8165 (tt0) cc_final: 0.7818 (tt0) REVERT: J 89 VAL cc_start: 0.9009 (t) cc_final: 0.8681 (t) REVERT: J 98 LEU cc_start: 0.7773 (pp) cc_final: 0.6826 (pp) REVERT: J 99 ARG cc_start: 0.6394 (mmp80) cc_final: 0.5899 (mmt90) REVERT: J 100 ARG cc_start: 0.7633 (ptt90) cc_final: 0.6875 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0535 time to fit residues: 2.2514 Evaluate side-chains 32 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.039 Evaluate side-chains 23 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.032 Fit side-chains REVERT: L 70 ASP cc_start: 0.7108 (t0) cc_final: 0.6773 (m-30) REVERT: L 96 TRP cc_start: 0.7745 (m-90) cc_final: 0.5602 (p-90) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0252 time to fit residues: 0.6745 Evaluate side-chains 20 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 111 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 203 optimal weight: 0.0670 chunk 157 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 163 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.066028 restraints weight = 2974.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.067754 restraints weight = 1948.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.068971 restraints weight = 1454.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.069759 restraints weight = 1162.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.070404 restraints weight = 985.853| |-----------------------------------------------------------------------------| r_work (final): 0.2850 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.068790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.068380 restraints weight = 121.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.068623 restraints weight = 11.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.068680 restraints weight = 1.904 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.068680 restraints weight = 0.362 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.068680 restraints weight = 0.358 | |-----------------------------------------------------------------------------| r_work (final): 0.2639 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.083686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.070408 restraints weight = 8208.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.072603 restraints weight = 5077.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.074196 restraints weight = 3556.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.075258 restraints weight = 2734.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.076020 restraints weight = 2260.227| |-----------------------------------------------------------------------------| r_work (final): 0.2821 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.117849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103316 restraints weight = 3505.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106138 restraints weight = 2113.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108139 restraints weight = 1447.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109390 restraints weight = 1089.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110256 restraints weight = 886.870| |-----------------------------------------------------------------------------| r_work (final): 0.3725 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.086950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.079640 restraints weight = 4308.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.081336 restraints weight = 2638.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.082488 restraints weight = 1749.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.083234 restraints weight = 1251.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083782 restraints weight = 956.147| |-----------------------------------------------------------------------------| r_work (final): 0.3583 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.068253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.060334 restraints weight = 285.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.061681 restraints weight = 159.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.062210 restraints weight = 116.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.062789 restraints weight = 103.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.062789 restraints weight = 89.230| |-----------------------------------------------------------------------------| r_work (final): 0.2650 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.074197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071939 restraints weight = 536.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072555 restraints weight = 209.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073006 restraints weight = 122.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073260 restraints weight = 83.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073415 restraints weight = 60.752| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21267 Z= 0.130 Angle : 0.746 17.209 29154 Z= 0.337 Chirality : 0.059 0.753 3534 Planarity : 0.004 0.075 3504 Dihedral : 10.244 76.708 5124 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.17), residues: 2358 helix: 1.34 (0.28), residues: 417 sheet: -0.18 (0.21), residues: 609 loop : -1.27 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 444 TYR 0.030 0.002 TYR M 58 PHE 0.006 0.001 PHE G 233 TRP 0.052 0.002 TRP N 94 HIS 0.002 0.000 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21099) covalent geometry : angle 0.62081 / 0.31 (28695) SS BOND : bond 0.00987 / 0.63 ( 45) SS BOND : angle 2.34780 / 1.62 ( 90) hydrogen bonds : bond 0.03386 / 2.25 ( 591) hydrogen bonds : angle 5.57693 / 4.07 ( 1515) link_ALPHA1-3 : bond 0.00848 / 0.49 ( 9) link_ALPHA1-3 : angle 2.38745 / 1.69 ( 27) link_ALPHA1-6 : bond 0.00614 / 0.33 ( 6) link_ALPHA1-6 : angle 1.80223 / 1.08 ( 18) link_BETA1-4 : bond 0.00540 / 0.35 ( 42) link_BETA1-4 : angle 1.29044 / 0.95 ( 126) link_NAG-ASN : bond 0.00852 / 0.53 ( 66) link_NAG-ASN : angle 4.63598 / 3.17 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.041 Fit side-chains revert: symmetry clash REVERT: A 652 GLN cc_start: 0.7339 (mm110) cc_final: 0.7129 (tt0) REVERT: A 655 LYS cc_start: 0.8537 (tppt) cc_final: 0.7755 (tmtt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0524 time to fit residues: 1.8516 Evaluate side-chains 28 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.037 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Evaluate side-chains 46 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.139 Fit side-chains REVERT: E 80 ASN cc_start: 0.7831 (p0) cc_final: 0.7420 (m-40) REVERT: E 95 MET cc_start: 0.8958 (ptm) cc_final: 0.8735 (ppp) REVERT: E 166 ARG cc_start: 0.8198 (ptt90) cc_final: 0.7511 (ptt180) REVERT: E 180 ASP cc_start: 0.8794 (m-30) cc_final: 0.8151 (m-30) REVERT: E 213 ILE cc_start: 0.8973 (pt) cc_final: 0.8461 (pt) REVERT: E 300 ASN cc_start: 0.7981 (p0) cc_final: 0.7622 (p0) REVERT: E 327 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7415 (mmt180) REVERT: E 377 ASN cc_start: 0.8985 (t0) cc_final: 0.8612 (t0) REVERT: E 428 GLN cc_start: 0.8681 (mp10) cc_final: 0.8280 (mp10) REVERT: E 432 GLN cc_start: 0.8662 (mp10) cc_final: 0.8073 (mp10) REVERT: E 434 MET cc_start: 0.8848 (ttp) cc_final: 0.8231 (ttp) REVERT: E 440 GLN cc_start: 0.8354 (tp40) cc_final: 0.8051 (tm-30) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0616 time to fit residues: 3.5902 Evaluate side-chains 35 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.132 Evaluate side-chains 37 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.076 Fit side-chains REVERT: J 13 GLN cc_start: 0.8148 (tt0) cc_final: 0.7761 (tt0) REVERT: J 89 VAL cc_start: 0.9077 (t) cc_final: 0.8799 (t) REVERT: J 100 ARG cc_start: 0.7720 (ptt90) cc_final: 0.6843 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0495 time to fit residues: 2.0302 Evaluate side-chains 30 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.036 Evaluate side-chains 26 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.027 Fit side-chains REVERT: N 21 ILE cc_start: 0.8712 (pt) cc_final: 0.8347 (pt) REVERT: N 36 TYR cc_start: 0.7688 (m-80) cc_final: 0.7443 (m-80) REVERT: N 70 ASP cc_start: 0.6887 (t0) cc_final: 0.6476 (m-30) REVERT: N 82 ASP cc_start: 0.7659 (m-30) cc_final: 0.7364 (m-30) REVERT: N 96 TRP cc_start: 0.7650 (m-90) cc_final: 0.5666 (p-90) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0366 time to fit residues: 1.0720 Evaluate side-chains 22 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 0.0670 chunk 49 optimal weight: 0.0170 chunk 74 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 188 optimal weight: 0.0060 chunk 181 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.066841 restraints weight = 2992.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068631 restraints weight = 1944.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069841 restraints weight = 1426.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.070791 restraints weight = 1125.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.071458 restraints weight = 929.303| |-----------------------------------------------------------------------------| r_work (final): 0.2872 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.068719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.068356 restraints weight = 131.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.068578 restraints weight = 8.989 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.068608 restraints weight = 1.084 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.068611 restraints weight = 0.150 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.068605 restraints weight = 0.022 | |-----------------------------------------------------------------------------| r_work (final): 0.2653 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.084406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.071690 restraints weight = 8056.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.073794 restraints weight = 5071.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.075287 restraints weight = 3598.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.076196 restraints weight = 2794.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.077050 restraints weight = 2339.703| |-----------------------------------------------------------------------------| r_work (final): 0.2844 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.123571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111805 restraints weight = 3659.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113847 restraints weight = 2465.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115437 restraints weight = 1821.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.116553 restraints weight = 1430.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.117067 restraints weight = 1137.376| |-----------------------------------------------------------------------------| r_work (final): 0.3787 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.089806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083098 restraints weight = 4168.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084681 restraints weight = 2490.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.085755 restraints weight = 1646.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.086480 restraints weight = 1174.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086867 restraints weight = 888.914| |-----------------------------------------------------------------------------| r_work (final): 0.3623 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.068676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.061489 restraints weight = 271.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.062616 restraints weight = 156.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.063183 restraints weight = 117.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.063651 restraints weight = 101.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.063651 restraints weight = 91.157| |-----------------------------------------------------------------------------| r_work (final): 0.2665 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071910 restraints weight = 497.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072505 restraints weight = 197.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072960 restraints weight = 117.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073135 restraints weight = 77.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073332 restraints weight = 61.531| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21267 Z= 0.134 Angle : 0.746 15.866 29154 Z= 0.342 Chirality : 0.059 0.747 3534 Planarity : 0.005 0.071 3504 Dihedral : 9.154 73.919 5124 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2358 helix: 1.45 (0.28), residues: 414 sheet: -0.09 (0.22), residues: 615 loop : -1.29 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.021 0.002 TYR M 58 PHE 0.020 0.001 PHE L 98 TRP 0.057 0.003 TRP M 47 HIS 0.014 0.001 HIS J 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21099) covalent geometry : angle 0.63000 / 0.31 (28695) SS BOND : bond 0.00687 / 0.39 ( 45) SS BOND : angle 2.04982 / 1.41 ( 90) hydrogen bonds : bond 0.03280 / 2.19 ( 591) hydrogen bonds : angle 5.59585 / 4.09 ( 1515) link_ALPHA1-3 : bond 0.00809 / 0.47 ( 9) link_ALPHA1-3 : angle 2.36946 / 1.69 ( 27) link_ALPHA1-6 : bond 0.00658 / 0.36 ( 6) link_ALPHA1-6 : angle 1.75878 / 1.06 ( 18) link_BETA1-4 : bond 0.00339 / 0.23 ( 42) link_BETA1-4 : angle 1.28675 / 0.95 ( 126) link_NAG-ASN : bond 0.00645 / 0.40 ( 66) link_NAG-ASN : angle 4.52396 / 3.10 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: A 652 GLN cc_start: 0.7367 (mm110) cc_final: 0.7124 (tt0) REVERT: A 655 LYS cc_start: 0.8515 (tppt) cc_final: 0.7735 (tmtt) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0464 time to fit residues: 1.6433 Evaluate side-chains 29 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.039 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 43 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.138 Fit side-chains REVERT: E 80 ASN cc_start: 0.7680 (p0) cc_final: 0.7403 (m-40) REVERT: E 166 ARG cc_start: 0.8181 (ptt90) cc_final: 0.7499 (ptt180) REVERT: E 180 ASP cc_start: 0.8785 (m-30) cc_final: 0.8166 (m-30) REVERT: E 213 ILE cc_start: 0.8969 (pt) cc_final: 0.8454 (pt) REVERT: E 327 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7451 (mmt180) REVERT: E 370 GLU cc_start: 0.7959 (mp0) cc_final: 0.7579 (mt-10) REVERT: E 377 ASN cc_start: 0.8994 (t0) cc_final: 0.8635 (t0) REVERT: E 427 TRP cc_start: 0.7878 (m-10) cc_final: 0.7642 (m-10) REVERT: E 428 GLN cc_start: 0.8697 (mp10) cc_final: 0.8270 (mp10) REVERT: E 432 GLN cc_start: 0.8607 (mp10) cc_final: 0.8048 (mp10) REVERT: E 434 MET cc_start: 0.8847 (ttp) cc_final: 0.8229 (ttt) REVERT: E 440 GLN cc_start: 0.8331 (tp40) cc_final: 0.8037 (tm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0680 time to fit residues: 3.6643 Evaluate side-chains 34 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.113 Evaluate side-chains 38 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: J 13 GLN cc_start: 0.8155 (tt0) cc_final: 0.7776 (tt0) REVERT: J 35 SER cc_start: 0.8558 (m) cc_final: 0.8072 (p) REVERT: J 89 VAL cc_start: 0.9007 (t) cc_final: 0.8694 (t) REVERT: J 100 ARG cc_start: 0.7607 (ptt90) cc_final: 0.6734 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0346 time to fit residues: 1.5050 Evaluate side-chains 32 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.040 Evaluate side-chains 26 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.036 Fit side-chains REVERT: N 21 ILE cc_start: 0.8828 (pt) cc_final: 0.8587 (pt) REVERT: N 70 ASP cc_start: 0.7014 (t0) cc_final: 0.6605 (m-30) REVERT: N 82 ASP cc_start: 0.7634 (m-30) cc_final: 0.7393 (m-30) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0302 time to fit residues: 0.9045 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.035 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 184 optimal weight: 0.0870 chunk 171 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.8350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 50 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.078449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.066776 restraints weight = 2965.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.068492 restraints weight = 1940.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.069703 restraints weight = 1432.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.070634 restraints weight = 1135.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.071294 restraints weight = 943.690| |-----------------------------------------------------------------------------| r_work (final): 0.2870 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.068675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.068340 restraints weight = 157.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.068598 restraints weight = 9.733 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.068636 restraints weight = 1.238 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068645 restraints weight = 0.172 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068641 restraints weight = 0.024 | |-----------------------------------------------------------------------------| r_work (final): 0.2685 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.083917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.071077 restraints weight = 8070.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.073154 restraints weight = 5106.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.074695 restraints weight = 3645.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.075793 restraints weight = 2833.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.076524 restraints weight = 2334.214| |-----------------------------------------------------------------------------| r_work (final): 0.2838 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.118866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.105825 restraints weight = 3493.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108654 restraints weight = 2103.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.110354 restraints weight = 1388.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.111516 restraints weight = 1028.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112343 restraints weight = 833.179| |-----------------------------------------------------------------------------| r_work (final): 0.3780 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.089268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081082 restraints weight = 3794.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.083118 restraints weight = 2345.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084493 restraints weight = 1527.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.085444 restraints weight = 1063.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086097 restraints weight = 782.633| |-----------------------------------------------------------------------------| r_work (final): 0.3535 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.067996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.060560 restraints weight = 325.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.061879 restraints weight = 175.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.062543 restraints weight = 126.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.062924 restraints weight = 105.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.062929 restraints weight = 95.444| |-----------------------------------------------------------------------------| r_work (final): 0.2654 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071883 restraints weight = 553.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072493 restraints weight = 214.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072945 restraints weight = 121.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073234 restraints weight = 79.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073333 restraints weight = 57.553| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21267 Z= 0.132 Angle : 0.713 15.294 29154 Z= 0.323 Chirality : 0.058 0.747 3534 Planarity : 0.004 0.040 3504 Dihedral : 8.064 71.479 5124 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.18), residues: 2358 helix: 1.47 (0.28), residues: 414 sheet: -0.08 (0.22), residues: 615 loop : -1.31 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.011 0.001 TYR B 586 PHE 0.020 0.001 PHE M 100J TRP 0.043 0.002 TRP M 47 HIS 0.006 0.001 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21099) covalent geometry : angle 0.59589 / 0.29 (28695) SS BOND : bond 0.00399 / 0.24 ( 45) SS BOND : angle 1.72234 / 1.21 ( 90) hydrogen bonds : bond 0.03122 / 2.09 ( 591) hydrogen bonds : angle 5.51442 / 4.02 ( 1515) link_ALPHA1-3 : bond 0.00893 / 0.52 ( 9) link_ALPHA1-3 : angle 2.33306 / 1.66 ( 27) link_ALPHA1-6 : bond 0.00580 / 0.32 ( 6) link_ALPHA1-6 : angle 1.84545 / 1.12 ( 18) link_BETA1-4 : bond 0.00401 / 0.27 ( 42) link_BETA1-4 : angle 1.37004 / 1.01 ( 126) link_NAG-ASN : bond 0.00647 / 0.40 ( 66) link_NAG-ASN : angle 4.46060 / 3.06 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: A 652 GLN cc_start: 0.7349 (mm110) cc_final: 0.7109 (tt0) REVERT: A 655 LYS cc_start: 0.8516 (tppt) cc_final: 0.7746 (tmtt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0428 time to fit residues: 1.4820 Evaluate side-chains 29 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 45 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.143 Fit side-chains REVERT: E 80 ASN cc_start: 0.7625 (p0) cc_final: 0.7413 (m-40) REVERT: E 166 ARG cc_start: 0.8193 (ptt90) cc_final: 0.7522 (ptt180) REVERT: E 180 ASP cc_start: 0.8775 (m-30) cc_final: 0.8158 (m-30) REVERT: E 213 ILE cc_start: 0.9014 (pt) cc_final: 0.8480 (pt) REVERT: E 327 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7424 (mmt180) REVERT: E 370 GLU cc_start: 0.7969 (mp0) cc_final: 0.7645 (mt-10) REVERT: E 377 ASN cc_start: 0.9014 (t0) cc_final: 0.8636 (t0) REVERT: E 427 TRP cc_start: 0.7876 (m-10) cc_final: 0.7652 (m-10) REVERT: E 428 GLN cc_start: 0.8687 (mp10) cc_final: 0.8281 (mp10) REVERT: E 432 GLN cc_start: 0.8586 (mp10) cc_final: 0.8044 (mp10) REVERT: E 434 MET cc_start: 0.8853 (ttp) cc_final: 0.8271 (ttt) REVERT: E 440 GLN cc_start: 0.8320 (tp40) cc_final: 0.7954 (tm-30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0614 time to fit residues: 3.5063 Evaluate side-chains 34 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.116 Evaluate side-chains 38 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.037 Fit side-chains REVERT: J 13 GLN cc_start: 0.8162 (tt0) cc_final: 0.7772 (tt0) REVERT: J 100 ARG cc_start: 0.7632 (ptt90) cc_final: 0.6788 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0409 time to fit residues: 1.7627 Evaluate side-chains 32 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.038 Evaluate side-chains 23 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.034 Fit side-chains REVERT: L 49 TYR cc_start: 0.7543 (p90) cc_final: 0.7055 (p90) REVERT: L 70 ASP cc_start: 0.7160 (t0) cc_final: 0.6809 (m-30) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0332 time to fit residues: 0.9011 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 136 optimal weight: 0.0470 chunk 138 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 50 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.078625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.066922 restraints weight = 3020.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.068668 restraints weight = 1968.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.069945 restraints weight = 1447.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.070798 restraints weight = 1136.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.071478 restraints weight = 949.752| |-----------------------------------------------------------------------------| r_work (final): 0.2876 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.069986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.069438 restraints weight = 141.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.069740 restraints weight = 13.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.069820 restraints weight = 1.944 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.069817 restraints weight = 0.312 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.069818 restraints weight = 0.053 | |-----------------------------------------------------------------------------| r_work (final): 0.2704 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.084124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.071223 restraints weight = 8148.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.073335 restraints weight = 5127.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.074691 restraints weight = 3658.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.075901 restraints weight = 2872.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.076616 restraints weight = 2354.492| |-----------------------------------------------------------------------------| r_work (final): 0.2839 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.118360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103823 restraints weight = 3579.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106628 restraints weight = 2108.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108602 restraints weight = 1423.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109964 restraints weight = 1057.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110846 restraints weight = 849.130| |-----------------------------------------------------------------------------| r_work (final): 0.3707 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.089600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081626 restraints weight = 3549.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083679 restraints weight = 2183.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.085103 restraints weight = 1411.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.085993 restraints weight = 966.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086684 restraints weight = 697.344| |-----------------------------------------------------------------------------| r_work (final): 0.3546 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.068603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.060478 restraints weight = 310.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.061839 restraints weight = 160.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.062530 restraints weight = 114.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.063003 restraints weight = 95.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.063003 restraints weight = 85.235| |-----------------------------------------------------------------------------| r_work (final): 0.2662 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.073944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.071933 restraints weight = 498.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072532 restraints weight = 195.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072932 restraints weight = 112.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073113 restraints weight = 75.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073250 restraints weight = 58.853| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21267 Z= 0.121 Angle : 0.706 14.556 29154 Z= 0.320 Chirality : 0.057 0.757 3534 Planarity : 0.004 0.041 3504 Dihedral : 7.739 68.186 5124 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2358 helix: 1.44 (0.28), residues: 414 sheet: -0.06 (0.23), residues: 567 loop : -1.32 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 45 TYR 0.018 0.002 TYR H 58 PHE 0.014 0.001 PHE J 100J TRP 0.036 0.002 TRP N 94 HIS 0.021 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21099) covalent geometry : angle 0.59156 / 0.29 (28695) SS BOND : bond 0.00387 / 0.24 ( 45) SS BOND : angle 1.60500 / 1.13 ( 90) hydrogen bonds : bond 0.03179 / 2.12 ( 591) hydrogen bonds : angle 5.49825 / 3.99 ( 1515) link_ALPHA1-3 : bond 0.00874 / 0.51 ( 9) link_ALPHA1-3 : angle 2.32902 / 1.66 ( 27) link_ALPHA1-6 : bond 0.00600 / 0.34 ( 6) link_ALPHA1-6 : angle 1.85265 / 1.12 ( 18) link_BETA1-4 : bond 0.00482 / 0.31 ( 42) link_BETA1-4 : angle 1.31261 / 0.97 ( 126) link_NAG-ASN : bond 0.00617 / 0.38 ( 66) link_NAG-ASN : angle 4.38941 / 3.00 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: A 652 GLN cc_start: 0.7319 (mm110) cc_final: 0.7115 (tt0) REVERT: A 655 LYS cc_start: 0.8515 (tppt) cc_final: 0.7731 (tmtt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0476 time to fit residues: 1.6321 Evaluate side-chains 29 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.041 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Evaluate side-chains 43 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.138 Fit side-chains REVERT: E 166 ARG cc_start: 0.8194 (ptt90) cc_final: 0.7499 (ptt-90) REVERT: E 180 ASP cc_start: 0.8765 (m-30) cc_final: 0.8158 (m-30) REVERT: E 211 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8218 (tp30) REVERT: E 213 ILE cc_start: 0.8969 (pt) cc_final: 0.8494 (pt) REVERT: E 327 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7438 (mmt180) REVERT: E 370 GLU cc_start: 0.7992 (mp0) cc_final: 0.7659 (mt-10) REVERT: E 377 ASN cc_start: 0.8953 (t0) cc_final: 0.8633 (t0) REVERT: E 427 TRP cc_start: 0.7882 (m-10) cc_final: 0.7661 (m-10) REVERT: E 428 GLN cc_start: 0.8686 (mp10) cc_final: 0.8287 (mp10) REVERT: E 432 GLN cc_start: 0.8561 (mp10) cc_final: 0.8030 (mp10) REVERT: E 434 MET cc_start: 0.8845 (ttp) cc_final: 0.8268 (ttt) REVERT: E 440 GLN cc_start: 0.8230 (tp40) cc_final: 0.7920 (tm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0650 time to fit residues: 3.5552 Evaluate side-chains 36 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.121 Evaluate side-chains 37 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.038 Fit side-chains REVERT: J 13 GLN cc_start: 0.8124 (tt0) cc_final: 0.7749 (tt0) REVERT: J 35 SER cc_start: 0.8441 (m) cc_final: 0.7769 (p) REVERT: J 39 GLN cc_start: 0.7027 (tp40) cc_final: 0.6738 (tp40) REVERT: J 89 VAL cc_start: 0.9043 (t) cc_final: 0.8693 (t) REVERT: J 100 ARG cc_start: 0.7731 (ptt90) cc_final: 0.6832 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0393 time to fit residues: 1.6522 Evaluate side-chains 31 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.039 Evaluate side-chains 23 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.036 Fit side-chains REVERT: L 49 TYR cc_start: 0.7574 (p90) cc_final: 0.7054 (p90) REVERT: L 70 ASP cc_start: 0.7104 (t0) cc_final: 0.6788 (m-30) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0321 time to fit residues: 0.8751 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 232 optimal weight: 0.0370 chunk 150 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 139 optimal weight: 0.0050 chunk 27 optimal weight: 9.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.078827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.067462 restraints weight = 2946.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.069177 restraints weight = 1953.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.070310 restraints weight = 1444.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071173 restraints weight = 1147.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.071865 restraints weight = 955.788| |-----------------------------------------------------------------------------| r_work (final): 0.2882 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.068981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.068643 restraints weight = 139.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068843 restraints weight = 8.744 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068876 restraints weight = 0.673 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068870 restraints weight = 0.079 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068870 restraints weight = 0.009 | |-----------------------------------------------------------------------------| r_work (final): 0.2681 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.071791 restraints weight = 8004.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.073913 restraints weight = 5062.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.075339 restraints weight = 3620.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.076352 restraints weight = 2836.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.077191 restraints weight = 2364.292| |-----------------------------------------------------------------------------| r_work (final): 0.2849 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.119564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105451 restraints weight = 3558.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.108061 restraints weight = 2194.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109974 restraints weight = 1522.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111113 restraints weight = 1165.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.111900 restraints weight = 965.944| |-----------------------------------------------------------------------------| r_work (final): 0.3729 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.090975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082435 restraints weight = 3671.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084484 restraints weight = 2291.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.085973 restraints weight = 1537.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087000 restraints weight = 1079.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.087703 restraints weight = 793.452| |-----------------------------------------------------------------------------| r_work (final): 0.3565 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.068577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.059270 restraints weight = 206.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.060210 restraints weight = 148.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.060826 restraints weight = 123.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.061068 restraints weight = 108.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.061319 restraints weight = 103.783| |-----------------------------------------------------------------------------| r_work (final): 0.2479 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072123 restraints weight = 512.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072690 restraints weight = 200.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073071 restraints weight = 114.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073239 restraints weight = 77.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073379 restraints weight = 62.217| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21267 Z= 0.111 Angle : 0.693 14.390 29154 Z= 0.312 Chirality : 0.057 0.757 3534 Planarity : 0.004 0.039 3504 Dihedral : 7.592 64.836 5124 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2358 helix: 1.45 (0.28), residues: 414 sheet: 0.07 (0.23), residues: 552 loop : -1.32 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 45 TYR 0.023 0.001 TYR M 58 PHE 0.009 0.001 PHE J 100J TRP 0.064 0.002 TRP M 103 HIS 0.017 0.001 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (21099) covalent geometry : angle 0.57856 / 0.29 (28695) SS BOND : bond 0.00360 / 0.23 ( 45) SS BOND : angle 1.52528 / 1.08 ( 90) hydrogen bonds : bond 0.03035 / 2.04 ( 591) hydrogen bonds : angle 5.50636 / 3.99 ( 1515) link_ALPHA1-3 : bond 0.00921 / 0.54 ( 9) link_ALPHA1-3 : angle 2.34781 / 1.67 ( 27) link_ALPHA1-6 : bond 0.00582 / 0.33 ( 6) link_ALPHA1-6 : angle 1.84424 / 1.12 ( 18) link_BETA1-4 : bond 0.00453 / 0.29 ( 42) link_BETA1-4 : angle 1.32668 / 0.98 ( 126) link_NAG-ASN : bond 0.00641 / 0.40 ( 66) link_NAG-ASN : angle 4.34764 / 2.97 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.038 Fit side-chains REVERT: A 655 LYS cc_start: 0.8471 (tppt) cc_final: 0.7715 (tmtt) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0538 time to fit residues: 1.9608 Evaluate side-chains 29 residues out of total 104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.036 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 43 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.146 Fit side-chains REVERT: E 166 ARG cc_start: 0.8196 (ptt90) cc_final: 0.7498 (ptt-90) REVERT: E 180 ASP cc_start: 0.8760 (m-30) cc_final: 0.8161 (m-30) REVERT: E 211 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8197 (tp30) REVERT: E 213 ILE cc_start: 0.8936 (pt) cc_final: 0.8457 (pt) REVERT: E 327 ARG cc_start: 0.7710 (mtt-85) cc_final: 0.7444 (mmt180) REVERT: E 370 GLU cc_start: 0.8032 (mp0) cc_final: 0.7702 (mt-10) REVERT: E 377 ASN cc_start: 0.8934 (t0) cc_final: 0.8624 (t0) REVERT: E 427 TRP cc_start: 0.7902 (m-10) cc_final: 0.7645 (m-10) REVERT: E 428 GLN cc_start: 0.8683 (mp10) cc_final: 0.8287 (mp10) REVERT: E 432 GLN cc_start: 0.8501 (mp10) cc_final: 0.7992 (mp10) REVERT: E 434 MET cc_start: 0.8861 (ttp) cc_final: 0.8312 (ttt) REVERT: E 440 GLN cc_start: 0.8212 (tp40) cc_final: 0.7909 (tm-30) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0580 time to fit residues: 3.1530 Evaluate side-chains 35 residues out of total 398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.085 Evaluate side-chains 36 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.024 Fit side-chains REVERT: J 13 GLN cc_start: 0.8146 (tt0) cc_final: 0.7756 (tt0) REVERT: J 35 SER cc_start: 0.8476 (m) cc_final: 0.7964 (p) REVERT: J 89 VAL cc_start: 0.9066 (t) cc_final: 0.8710 (t) REVERT: J 100 ARG cc_start: 0.7697 (ptt90) cc_final: 0.6819 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0282 time to fit residues: 1.1667 Evaluate side-chains 31 residues out of total 110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.039 Evaluate side-chains 23 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.026 Fit side-chains REVERT: L 49 TYR cc_start: 0.7587 (p90) cc_final: 0.7056 (p90) REVERT: L 70 ASP cc_start: 0.7091 (t0) cc_final: 0.6772 (m-30) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0279 time to fit residues: 0.7656 Evaluate side-chains 21 residues out of total 97 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 162 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 86 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 50 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.068457 restraints weight = 3032.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.070011 restraints weight = 2029.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.071226 restraints weight = 1517.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.072080 restraints weight = 1202.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072698 restraints weight = 1000.787| |-----------------------------------------------------------------------------| r_work (final): 0.2900 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.068660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.068381 restraints weight = 131.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.068531 restraints weight = 8.382 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068550 restraints weight = 0.795 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068554 restraints weight = 0.084 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.068550 restraints weight = 0.009 | |-----------------------------------------------------------------------------| r_work (final): 0.2677 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.072271 restraints weight = 7968.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.074280 restraints weight = 5081.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.075745 restraints weight = 3626.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.076646 restraints weight = 2835.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.077437 restraints weight = 2369.154| |-----------------------------------------------------------------------------| r_work (final): 0.2860 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.117704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103012 restraints weight = 3538.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.106094 restraints weight = 2089.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108287 restraints weight = 1401.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109539 restraints weight = 1023.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110564 restraints weight = 821.208| |-----------------------------------------------------------------------------| r_work (final): 0.3710 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.090538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082330 restraints weight = 3624.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.084297 restraints weight = 2260.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.085686 restraints weight = 1507.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086681 restraints weight = 1063.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087336 restraints weight = 781.205| |-----------------------------------------------------------------------------| r_work (final): 0.3556 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.070671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.063781 restraints weight = 228.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.064738 restraints weight = 160.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.065168 restraints weight = 130.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.065512 restraints weight = 115.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.065710 restraints weight = 105.817| |-----------------------------------------------------------------------------| r_work (final): 0.2518 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.074254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.072289 restraints weight = 511.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072868 restraints weight = 199.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.073249 restraints weight = 113.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073454 restraints weight = 75.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073624 restraints weight = 53.877| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21267 Z= 0.114 Angle : 0.690 14.384 29154 Z= 0.311 Chirality : 0.057 0.757 3534 Planarity : 0.004 0.039 3504 Dihedral : 7.445 60.463 5124 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2358 helix: 1.42 (0.28), residues: 414 sheet: 0.08 (0.23), residues: 552 loop : -1.31 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 178 TYR 0.015 0.001 TYR M 58 PHE 0.007 0.001 PHE J 100J TRP 0.060 0.003 TRP H 103 HIS 0.023 0.002 HIS J 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21099) covalent geometry : angle 0.57729 / 0.28 (28695) SS BOND : bond 0.00355 / 0.22 ( 45) SS BOND : angle 1.47012 / 1.04 ( 90) hydrogen bonds : bond 0.03079 / 2.05 ( 591) hydrogen bonds : angle 5.53175 / 4.00 ( 1515) link_ALPHA1-3 : bond 0.00935 / 0.54 ( 9) link_ALPHA1-3 : angle 2.35696 / 1.68 ( 27) link_ALPHA1-6 : bond 0.00540 / 0.31 ( 6) link_ALPHA1-6 : angle 1.83599 / 1.11 ( 18) link_BETA1-4 : bond 0.00406 / 0.27 ( 42) link_BETA1-4 : angle 1.30666 / 0.97 ( 126) link_NAG-ASN : bond 0.00623 / 0.39 ( 66) link_NAG-ASN : angle 4.32684 / 2.95 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.40 seconds wall clock time: 37 minutes 25.67 seconds (2245.67 seconds total)