Starting phenix.real_space_refine on Mon Aug 25 09:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6u_29783/08_2025/8g6u_29783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6u_29783/08_2025/8g6u_29783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g6u_29783/08_2025/8g6u_29783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6u_29783/08_2025/8g6u_29783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g6u_29783/08_2025/8g6u_29783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6u_29783/08_2025/8g6u_29783.map" } resolution = 3.16 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= -0.014 sd= 0.602 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 138 5.16 5 C 16788 2.51 5 N 4377 2.21 5 O 5568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "I" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3510 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Chain: "J" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "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: 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: "Z" 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: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "b" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: "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: "g" 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: "h" 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: "i" 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: "j" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "k" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 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: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.56, per 1000 atoms: 0.21 Number of scatterers: 26871 At special positions: 0 Unit cell: (169.32, 156.04, 147.74, 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 138 16.00 O 5568 8.00 N 4377 7.00 C 16788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 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 218 " - pdb=" SG CYS E 247 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN S 10 " - " MAN S 11 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN Y 4 " - " MAN Y 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN a 10 " - " MAN a 11 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " " MAN h 4 " - " MAN h 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN j 10 " - " MAN j 11 " " MAN k 4 " - " MAN k 5 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 10 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " MAN d 7 " - " MAN d 10 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 10 " " BMA T 3 " - " MAN T 6 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 8 " " BMA Y 3 " - " MAN Y 6 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 7 " " MAN d 7 " - " MAN d 8 " " BMA h 3 " - " MAN h 6 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 10 " " BMA k 3 " - " MAN k 6 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA r 3 " - " MAN r 6 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " 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 h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " 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 r 2 " - " BMA r 3 " " 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 w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN A 448 " " NAG 1 1 " - " ASN E 448 " " NAG 2 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 187 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 411 " " NAG A 608 " - " ASN A 465 " " NAG A 609 " - " ASN A 392 " " NAG B 700 " - " ASN B 611 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 187 " " NAG E 604 " - " ASN E 295 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 355 " " NAG E 607 " - " ASN E 411 " " NAG E 608 " - " ASN E 465 " " NAG E 609 " - " ASN E 392 " " NAG F 700 " - " ASN F 611 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 625 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 603 " - " ASN I 187 " " NAG I 604 " - " ASN I 295 " " NAG I 605 " - " ASN I 301 " " NAG I 606 " - " ASN I 355 " " NAG I 607 " - " ASN I 411 " " NAG I 608 " - " ASN I 465 " " NAG I 609 " - " ASN I 392 " " NAG J 700 " - " ASN J 611 " " NAG J 701 " - " ASN J 616 " " NAG J 702 " - " ASN J 625 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN E 234 " " NAG b 1 " - " ASN E 276 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN A 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN F 637 " " NAG j 1 " - " ASN I 234 " " NAG k 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 289 " " NAG n 1 " - " ASN I 332 " " NAG o 1 " - " ASN I 386 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " " NAG t 1 " - " ASN A 130 " " NAG u 1 " - " ASN E 130 " " NAG v 1 " - " ASN A 289 " " NAG w 1 " - " ASN E 289 " " NAG x 1 " - " ASN A 241 " " NAG y 1 " - " ASN E 241 " " NAG z 1 " - " ASN I 241 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 888.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5718 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 57 sheets defined 15.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.640A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.937A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.796A pdb=" N ILE B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.902A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100D through 100H Processing helix chain 'N' and resid 79 through 84 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.641A pdb=" N MET E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.936A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.795A pdb=" N ILE F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.902A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100D through 100H Processing helix chain 'P' and resid 79 through 84 Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.860A pdb=" N GLU I 351 " --> pdb=" O ASN I 347 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.640A pdb=" N MET I 373 " --> pdb=" O PRO I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.936A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 537 Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 removed outlier: 3.796A pdb=" N ILE J 622 " --> pdb=" O THR J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 661 Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.903A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.666A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'Q' and resid 100D through 100H Processing helix chain 'R' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.093A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.545A pdb=" N ILE A 271 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS A 331 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.862A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 35 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TYR C 33 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.722A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.617A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.578A pdb=" N GLN M 5 " --> pdb=" O SER M 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA M 93 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M 35 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG M 100 " --> pdb=" O PHE M 100K" (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE M 100K" --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.559A pdb=" N HIS N 89 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.092A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 155 through 162 Processing sheet with id=AC6, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.544A pdb=" N ILE E 271 " --> pdb=" O HIS E 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS E 331 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD1, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.863A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN G 50 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL G 35 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP G 52 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N TYR G 33 " --> pdb=" O TRP G 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.721A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.617A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR H 72 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.579A pdb=" N GLN O 5 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR O 90 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR O 35 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 11 through 12 removed outlier: 4.253A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR O 90 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA O 88 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG O 100 " --> pdb=" O PHE O 100K" (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.559A pdb=" N HIS P 89 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR P 36 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 494 through 499 Processing sheet with id=AE4, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.092A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 92 through 94 Processing sheet with id=AE6, first strand: chain 'I' and resid 155 through 162 Processing sheet with id=AE7, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE8, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.544A pdb=" N ILE I 271 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 414 through 417 removed outlier: 3.592A pdb=" N CYS I 331 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 296 " --> pdb=" O CYS I 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF2, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.863A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.990A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N TYR K 33 " --> pdb=" O TRP K 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.722A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.616A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.577A pdb=" N GLN Q 5 " --> pdb=" O SER Q 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.254A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR Q 90 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 93 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR Q 35 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.254A pdb=" N THR Q 107 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR Q 90 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG Q 100 " --> pdb=" O PHE Q 100K" (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE Q 100K" --> pdb=" O ARG Q 100 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.560A pdb=" N HIS R 89 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR R 36 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 1836 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: 4.59 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7692 1.34 - 1.46: 5853 1.46 - 1.58: 13698 1.58 - 1.70: 6 1.70 - 1.82: 186 Bond restraints: 27435 Sorted by residual: bond pdb=" N LEU F 544 " pdb=" CA LEU F 544 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" N LEU B 544 " pdb=" CA LEU B 544 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" N LEU J 544 " pdb=" CA LEU J 544 " ideal model delta sigma weight residual 1.457 1.507 -0.049 1.29e-02 6.01e+03 1.45e+01 bond pdb=" C1 NAG E 603 " pdb=" O5 NAG E 603 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 27430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 36195 2.62 - 5.24: 849 5.24 - 7.86: 177 7.86 - 10.48: 30 10.48 - 13.10: 12 Bond angle restraints: 37263 Sorted by residual: angle pdb=" C PRO O 41 " pdb=" CA PRO O 41 " pdb=" CB PRO O 41 " ideal model delta sigma weight residual 111.56 124.66 -13.10 1.65e+00 3.67e-01 6.30e+01 angle pdb=" C PRO Q 41 " pdb=" CA PRO Q 41 " pdb=" CB PRO Q 41 " ideal model delta sigma weight residual 111.56 124.65 -13.09 1.65e+00 3.67e-01 6.29e+01 angle pdb=" C PRO M 41 " pdb=" CA PRO M 41 " pdb=" CB PRO M 41 " ideal model delta sigma weight residual 111.56 124.64 -13.08 1.65e+00 3.67e-01 6.28e+01 angle pdb=" N ARG F 542 " pdb=" CA ARG F 542 " pdb=" C ARG F 542 " ideal model delta sigma weight residual 107.49 119.28 -11.79 1.74e+00 3.30e-01 4.59e+01 angle pdb=" N ARG B 542 " pdb=" CA ARG B 542 " pdb=" C ARG B 542 " ideal model delta sigma weight residual 107.49 119.27 -11.78 1.74e+00 3.30e-01 4.58e+01 ... (remaining 37258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 17235 24.58 - 49.15: 980 49.15 - 73.73: 248 73.73 - 98.31: 140 98.31 - 122.88: 108 Dihedral angle restraints: 18711 sinusoidal: 9786 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 88 " pdb=" CB CYS R 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.23 -82.77 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.28 -82.72 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.28 -82.72 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 18708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4641 0.168 - 0.337: 45 0.337 - 0.505: 6 0.505 - 0.674: 3 0.674 - 0.842: 12 Chirality restraints: 4707 Sorted by residual: chirality pdb=" C1 NAG 2 1 " pdb=" ND2 ASN I 448 " pdb=" C2 NAG 2 1 " pdb=" O5 NAG 2 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" C1 NAG 0 1 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG 0 1 " pdb=" O5 NAG 0 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" C1 NAG 1 1 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG 1 1 " pdb=" O5 NAG 1 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4704 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " 0.011 2.00e-02 2.50e+03 6.99e-02 6.10e+01 pdb=" CG ASN A 386 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " 0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 386 " -0.011 2.00e-02 2.50e+03 6.96e-02 6.05e+01 pdb=" CG ASN E 386 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN E 386 " -0.078 2.00e-02 2.50e+03 pdb=" ND2 ASN E 386 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 386 " -0.011 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" CG ASN I 386 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN I 386 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN I 386 " 0.084 2.00e-02 2.50e+03 pdb=" C1 NAG o 1 " -0.069 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 278 2.54 - 3.13: 20837 3.13 - 3.72: 38379 3.72 - 4.31: 55133 4.31 - 4.90: 92275 Nonbonded interactions: 206902 Sorted by model distance: nonbonded pdb=" O GLN F 543 " pdb=" O LEU F 544 " model vdw 1.945 3.040 nonbonded pdb=" O GLN B 543 " pdb=" O LEU B 544 " model vdw 1.945 3.040 nonbonded pdb=" O GLN J 543 " pdb=" O LEU J 544 " model vdw 1.946 3.040 nonbonded pdb=" N GLU B 620 " pdb=" OE1 GLU B 620 " model vdw 2.056 3.120 nonbonded pdb=" N GLU J 620 " pdb=" OE1 GLU J 620 " model vdw 2.056 3.120 ... (remaining 206897 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: 0.04 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 2 or resid 5 through 11)) selection = (chain 'U' and (resid 1 or resid 4 through 10)) selection = (chain 'a' and (resid 2 or resid 5 through 11)) selection = (chain 'd' and (resid 1 or resid 4 through 10)) selection = (chain 'j' and (resid 2 or resid 5 through 11)) selection = (chain 'n' and (resid 1 or resid 4 through 10)) } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'b' selection = chain 'h' selection = chain 'k' selection = chain 'r' } ncs_group { reference = chain 'Z' selection = chain 'i' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.480 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.330 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.006 0.074 27672 Z= 0.295 Angle : 1.129 23.078 37929 Z= 0.527 Chirality : 0.070 0.842 4707 Planarity : 0.007 0.097 4446 Dihedral : 19.478 122.885 12858 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.56 % Favored : 91.45 % Rotamer: Outliers : 3.79 % Allowed : 1.93 % Favored : 94.28 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.15), residues: 3054 helix: 1.65 (0.27), residues: 381 sheet: -0.19 (0.19), residues: 795 loop : -2.04 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 45 TYR 0.019 0.001 TYR R 49 PHE 0.013 0.001 PHE E 288 TRP 0.019 0.001 TRP I 69 HIS 0.003 0.001 HIS I 287 Details of bonding type rmsd covalent geometry : bond 0.00567 (27435) covalent geometry : angle 0.99315 (37263) SS BOND : bond 0.00470 ( 45) SS BOND : angle 1.54818 ( 90) hydrogen bonds : bond 0.22036 ( 708) hydrogen bonds : angle 8.41360 ( 1836) link_ALPHA1-2 : bond 0.00476 ( 27) link_ALPHA1-2 : angle 1.59671 ( 81) link_ALPHA1-3 : bond 0.00352 ( 21) link_ALPHA1-3 : angle 1.98881 ( 63) link_ALPHA1-6 : bond 0.00367 ( 21) link_ALPHA1-6 : angle 1.85561 ( 63) link_BETA1-4 : bond 0.00711 ( 51) link_BETA1-4 : angle 2.16681 ( 153) link_NAG-ASN : bond 0.00879 ( 72) link_NAG-ASN : angle 6.80255 ( 216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 612 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 545 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4601 (tp) REVERT: C 66 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8032 (ttt-90) REVERT: G 13 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8380 (mmmt) REVERT: H 4 MET cc_start: 0.7499 (ttm) cc_final: 0.7054 (ttm) REVERT: H 88 CYS cc_start: 0.5394 (p) cc_final: 0.5050 (p) REVERT: O 100 MET cc_start: 0.8126 (mpp) cc_final: 0.7355 (mpp) REVERT: I 103 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: I 107 ASP cc_start: 0.8100 (m-30) cc_final: 0.7884 (m-30) REVERT: L 24 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7642 (ttm110) REVERT: Q 100 TYR cc_start: 0.7833 (m-10) cc_final: 0.7221 (m-10) outliers start: 102 outliers final: 31 residues processed: 662 average time/residue: 0.1560 time to fit residues: 165.9736 Evaluate side-chains 511 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 476 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 474 ASP Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 503 ARG Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 650 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain P residue 95 SER Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 474 ASP Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 650 GLN Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 229 ASN B 540 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 6 GLN M 64 ASN E 229 ASN F 540 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 64 ASN I 229 ASN J 540 GLN ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 641 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 64 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119534 restraints weight = 42293.905| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.28 r_work: 0.3394 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 27672 Z= 0.232 Angle : 0.940 21.056 37929 Z= 0.427 Chirality : 0.056 0.543 4707 Planarity : 0.006 0.145 4446 Dihedral : 16.271 106.194 7309 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.86 % Favored : 91.36 % Rotamer: Outliers : 3.34 % Allowed : 11.85 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.15), residues: 3054 helix: 1.32 (0.26), residues: 411 sheet: -0.41 (0.17), residues: 873 loop : -1.92 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 542 TYR 0.016 0.002 TYR E 39 PHE 0.020 0.002 PHE I 288 TRP 0.017 0.002 TRP R 91 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00546 (27435) covalent geometry : angle 0.82422 (37263) SS BOND : bond 0.00902 ( 45) SS BOND : angle 1.45112 ( 90) hydrogen bonds : bond 0.04546 ( 708) hydrogen bonds : angle 6.25189 ( 1836) link_ALPHA1-2 : bond 0.00817 ( 27) link_ALPHA1-2 : angle 1.96851 ( 81) link_ALPHA1-3 : bond 0.00815 ( 21) link_ALPHA1-3 : angle 2.37052 ( 63) link_ALPHA1-6 : bond 0.00529 ( 21) link_ALPHA1-6 : angle 1.88588 ( 63) link_BETA1-4 : bond 0.00548 ( 51) link_BETA1-4 : angle 2.59526 ( 153) link_NAG-ASN : bond 0.00671 ( 72) link_NAG-ASN : angle 5.31209 ( 216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 517 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLN cc_start: 0.7779 (tp40) cc_final: 0.7573 (tp40) REVERT: D 24 ARG cc_start: 0.8544 (ttm110) cc_final: 0.7901 (ttm110) REVERT: E 368 ASP cc_start: 0.7607 (m-30) cc_final: 0.7290 (m-30) REVERT: E 377 ASN cc_start: 0.8557 (p0) cc_final: 0.8301 (p0) REVERT: F 652 GLN cc_start: 0.8020 (tp40) cc_final: 0.7786 (tp40) REVERT: G 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8785 (m-30) REVERT: I 103 GLN cc_start: 0.8507 (mm110) cc_final: 0.8028 (mm-40) REVERT: I 104 MET cc_start: 0.9112 (ttt) cc_final: 0.8831 (ttt) REVERT: I 107 ASP cc_start: 0.8679 (m-30) cc_final: 0.8465 (m-30) REVERT: I 377 ASN cc_start: 0.8328 (p0) cc_final: 0.8116 (p0) REVERT: J 640 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8557 (m) REVERT: K 66 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8215 (ttt90) REVERT: L 24 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8111 (ttm110) REVERT: L 81 GLU cc_start: 0.8574 (pm20) cc_final: 0.8365 (pm20) REVERT: L 90 GLN cc_start: 0.9376 (pp30) cc_final: 0.9026 (pp30) REVERT: Q 74 SER cc_start: 0.7537 (p) cc_final: 0.7173 (m) outliers start: 90 outliers final: 54 residues processed: 581 average time/residue: 0.1559 time to fit residues: 145.8980 Evaluate side-chains 509 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 454 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 640 SER Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 146 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 296 optimal weight: 0.0030 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN R 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118837 restraints weight = 42270.171| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.26 r_work: 0.3376 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27672 Z= 0.163 Angle : 0.805 15.647 37929 Z= 0.366 Chirality : 0.050 0.469 4707 Planarity : 0.006 0.151 4446 Dihedral : 14.846 103.297 7239 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.53 % Favored : 91.88 % Rotamer: Outliers : 3.20 % Allowed : 16.28 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.15), residues: 3054 helix: 1.53 (0.26), residues: 417 sheet: -0.55 (0.17), residues: 894 loop : -1.94 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 100 TYR 0.022 0.001 TYR A 39 PHE 0.011 0.001 PHE N 95B TRP 0.014 0.001 TRP A 427 HIS 0.004 0.001 HIS I 287 Details of bonding type rmsd covalent geometry : bond 0.00361 (27435) covalent geometry : angle 0.71241 (37263) SS BOND : bond 0.00451 ( 45) SS BOND : angle 1.23137 ( 90) hydrogen bonds : bond 0.04538 ( 708) hydrogen bonds : angle 5.77498 ( 1836) link_ALPHA1-2 : bond 0.00942 ( 27) link_ALPHA1-2 : angle 1.78140 ( 81) link_ALPHA1-3 : bond 0.01021 ( 21) link_ALPHA1-3 : angle 2.06778 ( 63) link_ALPHA1-6 : bond 0.00627 ( 21) link_ALPHA1-6 : angle 1.84088 ( 63) link_BETA1-4 : bond 0.00485 ( 51) link_BETA1-4 : angle 1.99423 ( 153) link_NAG-ASN : bond 0.00631 ( 72) link_NAG-ASN : angle 4.41541 ( 216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 489 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8305 (tp40) REVERT: A 107 ASP cc_start: 0.8753 (m-30) cc_final: 0.8245 (m-30) REVERT: A 125 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 368 ASP cc_start: 0.7530 (m-30) cc_final: 0.7188 (m-30) REVERT: B 545 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4745 (tp) REVERT: C 100 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7625 (ttt180) REVERT: D 24 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8220 (ttm110) REVERT: M 97 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7857 (ttp80) REVERT: N 35 TRP cc_start: 0.7413 (m100) cc_final: 0.6716 (m100) REVERT: N 47 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8140 (mm) REVERT: N 49 TYR cc_start: 0.7852 (p90) cc_final: 0.7542 (p90) REVERT: E 168 LYS cc_start: 0.9338 (mmmt) cc_final: 0.9047 (mmtp) REVERT: E 368 ASP cc_start: 0.7592 (m-30) cc_final: 0.7315 (m-30) REVERT: E 377 ASN cc_start: 0.8617 (p0) cc_final: 0.8376 (p0) REVERT: F 652 GLN cc_start: 0.8146 (tp40) cc_final: 0.7833 (tp40) REVERT: G 86 ASP cc_start: 0.9012 (m-30) cc_final: 0.8786 (m-30) REVERT: O 100 MET cc_start: 0.8270 (mpp) cc_final: 0.7537 (mpp) REVERT: I 103 GLN cc_start: 0.8542 (mm110) cc_final: 0.7897 (mm-40) REVERT: I 104 MET cc_start: 0.9109 (ttt) cc_final: 0.8836 (ttt) REVERT: I 368 ASP cc_start: 0.7504 (m-30) cc_final: 0.6995 (m-30) REVERT: K 100 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7514 (ttt180) REVERT: L 24 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8091 (ttm110) REVERT: Q 74 SER cc_start: 0.7584 (p) cc_final: 0.7238 (m) REVERT: R 97 SER cc_start: 0.9318 (t) cc_final: 0.9039 (t) outliers start: 86 outliers final: 49 residues processed: 544 average time/residue: 0.1478 time to fit residues: 130.6725 Evaluate side-chains 518 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 466 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 227 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 290 optimal weight: 0.0670 chunk 284 optimal weight: 30.0000 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN N 52 GLN E 302 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 302 ASN I 377 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.169142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124517 restraints weight = 42188.992| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.29 r_work: 0.3464 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27672 Z= 0.135 Angle : 0.768 15.213 37929 Z= 0.346 Chirality : 0.050 0.442 4707 Planarity : 0.005 0.149 4446 Dihedral : 13.590 100.303 7233 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.66 % Favored : 91.78 % Rotamer: Outliers : 3.79 % Allowed : 17.61 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.15), residues: 3054 helix: 1.66 (0.26), residues: 417 sheet: -0.57 (0.17), residues: 888 loop : -1.78 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.014 0.001 TYR E 330 PHE 0.010 0.001 PHE P 67 TRP 0.022 0.001 TRP P 35 HIS 0.002 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00293 (27435) covalent geometry : angle 0.68564 (37263) SS BOND : bond 0.00577 ( 45) SS BOND : angle 1.23206 ( 90) hydrogen bonds : bond 0.03898 ( 708) hydrogen bonds : angle 5.34770 ( 1836) link_ALPHA1-2 : bond 0.00946 ( 27) link_ALPHA1-2 : angle 1.78561 ( 81) link_ALPHA1-3 : bond 0.01090 ( 21) link_ALPHA1-3 : angle 2.04970 ( 63) link_ALPHA1-6 : bond 0.00689 ( 21) link_ALPHA1-6 : angle 1.82982 ( 63) link_BETA1-4 : bond 0.00446 ( 51) link_BETA1-4 : angle 1.78370 ( 153) link_NAG-ASN : bond 0.00573 ( 72) link_NAG-ASN : angle 4.01247 ( 216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 517 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8086 (mm-40) REVERT: A 107 ASP cc_start: 0.8792 (m-30) cc_final: 0.8288 (m-30) REVERT: A 368 ASP cc_start: 0.7513 (m-30) cc_final: 0.7086 (m-30) REVERT: A 373 MET cc_start: 0.8446 (mmt) cc_final: 0.8045 (mmt) REVERT: B 545 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4852 (tp) REVERT: C 10 GLU cc_start: 0.8356 (pm20) cc_final: 0.8105 (pm20) REVERT: C 100 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7695 (ttt180) REVERT: D 24 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8388 (ttm110) REVERT: N 35 TRP cc_start: 0.7467 (m100) cc_final: 0.6823 (m100) REVERT: N 47 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8307 (mm) REVERT: N 49 TYR cc_start: 0.7865 (p90) cc_final: 0.7551 (p90) REVERT: E 103 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8489 (mm-40) REVERT: E 168 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9090 (mmtp) REVERT: E 368 ASP cc_start: 0.7625 (m-30) cc_final: 0.7210 (m-30) REVERT: E 377 ASN cc_start: 0.8544 (p0) cc_final: 0.8338 (p0) REVERT: F 652 GLN cc_start: 0.8266 (tp40) cc_final: 0.7966 (tp40) REVERT: G 10 GLU cc_start: 0.8281 (pm20) cc_final: 0.8068 (pm20) REVERT: G 100 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7512 (ttt90) REVERT: H 4 MET cc_start: 0.8233 (ttt) cc_final: 0.7951 (ttt) REVERT: H 20 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.7946 (mmt-90) REVERT: H 77 ASN cc_start: 0.8399 (t0) cc_final: 0.8192 (t0) REVERT: I 102 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8562 (mm-30) REVERT: I 103 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8072 (mm-40) REVERT: I 107 ASP cc_start: 0.8709 (m-30) cc_final: 0.8338 (m-30) REVERT: J 588 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8413 (tp-100) REVERT: K 100 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7561 (ttt180) REVERT: L 24 ARG cc_start: 0.8394 (ttm110) cc_final: 0.8003 (ttm110) REVERT: Q 97 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7197 (ttp80) REVERT: R 97 SER cc_start: 0.9389 (t) cc_final: 0.9113 (t) outliers start: 102 outliers final: 66 residues processed: 577 average time/residue: 0.1463 time to fit residues: 137.4022 Evaluate side-chains 547 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 477 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain M residue 41 PRO Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 371 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 295 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 50 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 302 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN K 43 GLN R 26 GLN R 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116910 restraints weight = 41879.268| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.22 r_work: 0.3325 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27672 Z= 0.215 Angle : 0.839 16.897 37929 Z= 0.382 Chirality : 0.053 0.504 4707 Planarity : 0.006 0.153 4446 Dihedral : 13.101 106.037 7233 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.19 % Favored : 91.32 % Rotamer: Outliers : 4.50 % Allowed : 18.73 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.15), residues: 3054 helix: 1.28 (0.26), residues: 435 sheet: -0.70 (0.17), residues: 924 loop : -1.64 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 166 TYR 0.021 0.002 TYR O 32 PHE 0.016 0.002 PHE F 592 TRP 0.016 0.001 TRP E 427 HIS 0.004 0.001 HIS P 89 Details of bonding type rmsd covalent geometry : bond 0.00497 (27435) covalent geometry : angle 0.75051 (37263) SS BOND : bond 0.00567 ( 45) SS BOND : angle 1.33514 ( 90) hydrogen bonds : bond 0.04568 ( 708) hydrogen bonds : angle 5.51584 ( 1836) link_ALPHA1-2 : bond 0.00885 ( 27) link_ALPHA1-2 : angle 2.07021 ( 81) link_ALPHA1-3 : bond 0.00947 ( 21) link_ALPHA1-3 : angle 2.14877 ( 63) link_ALPHA1-6 : bond 0.00561 ( 21) link_ALPHA1-6 : angle 1.83170 ( 63) link_BETA1-4 : bond 0.00402 ( 51) link_BETA1-4 : angle 2.03298 ( 153) link_NAG-ASN : bond 0.00628 ( 72) link_NAG-ASN : angle 4.33653 ( 216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 489 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: A 107 ASP cc_start: 0.8794 (m-30) cc_final: 0.8252 (m-30) REVERT: A 199 SER cc_start: 0.9187 (p) cc_final: 0.8878 (t) REVERT: C 100 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7781 (ttt180) REVERT: D 77 ASN cc_start: 0.8308 (t0) cc_final: 0.8101 (t0) REVERT: M 97 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8110 (ttp80) REVERT: N 35 TRP cc_start: 0.7748 (m100) cc_final: 0.7293 (m100) REVERT: N 47 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8098 (mm) REVERT: E 168 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9165 (mmtp) REVERT: E 234 ASN cc_start: 0.8368 (m-40) cc_final: 0.8148 (t0) REVERT: G 100 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7748 (ttt90) REVERT: H 77 ASN cc_start: 0.8663 (t0) cc_final: 0.8448 (t0) REVERT: O 100 MET cc_start: 0.8363 (mpp) cc_final: 0.7515 (mpp) REVERT: P 51 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: I 103 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8015 (mm-40) REVERT: I 107 ASP cc_start: 0.8706 (m-30) cc_final: 0.8275 (m-30) REVERT: I 381 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7681 (mt-10) REVERT: J 588 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8519 (tp-100) REVERT: K 100 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7655 (ttt180) REVERT: L 20 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8106 (mmt-90) REVERT: L 79 GLN cc_start: 0.7842 (tp40) cc_final: 0.7612 (tp40) REVERT: R 97 SER cc_start: 0.9518 (t) cc_final: 0.9259 (t) outliers start: 121 outliers final: 89 residues processed: 568 average time/residue: 0.1450 time to fit residues: 133.8824 Evaluate side-chains 555 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 463 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 41 PRO Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 428 GLN Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain Q residue 41 PRO Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 222 optimal weight: 0.0980 chunk 26 optimal weight: 0.0870 chunk 113 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 213 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS C 50 GLN E 92 ASN E 258 GLN I 302 ASN R 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.166375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122032 restraints weight = 41770.706| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.26 r_work: 0.3407 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27672 Z= 0.125 Angle : 0.757 14.989 37929 Z= 0.341 Chirality : 0.049 0.415 4707 Planarity : 0.005 0.157 4446 Dihedral : 12.383 108.570 7229 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.20 % Favored : 92.31 % Rotamer: Outliers : 3.31 % Allowed : 21.03 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.15), residues: 3054 helix: 1.31 (0.25), residues: 450 sheet: -0.52 (0.18), residues: 852 loop : -1.67 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 66 TYR 0.016 0.001 TYR I 39 PHE 0.009 0.001 PHE M 100K TRP 0.015 0.001 TRP P 35 HIS 0.002 0.001 HIS K 100F Details of bonding type rmsd covalent geometry : bond 0.00261 (27435) covalent geometry : angle 0.68030 (37263) SS BOND : bond 0.00430 ( 45) SS BOND : angle 1.04509 ( 90) hydrogen bonds : bond 0.03828 ( 708) hydrogen bonds : angle 5.21476 ( 1836) link_ALPHA1-2 : bond 0.00988 ( 27) link_ALPHA1-2 : angle 1.80196 ( 81) link_ALPHA1-3 : bond 0.01132 ( 21) link_ALPHA1-3 : angle 1.99527 ( 63) link_ALPHA1-6 : bond 0.00715 ( 21) link_ALPHA1-6 : angle 1.80207 ( 63) link_BETA1-4 : bond 0.00501 ( 51) link_BETA1-4 : angle 1.67990 ( 153) link_NAG-ASN : bond 0.00559 ( 72) link_NAG-ASN : angle 3.86883 ( 216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 527 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8032 (mm-40) REVERT: A 107 ASP cc_start: 0.8808 (m-30) cc_final: 0.8352 (m-30) REVERT: A 199 SER cc_start: 0.9107 (p) cc_final: 0.8858 (t) REVERT: A 475 MET cc_start: 0.7769 (ttp) cc_final: 0.7551 (ttp) REVERT: C 100 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7699 (ttt180) REVERT: D 42 LYS cc_start: 0.7852 (pttp) cc_final: 0.7622 (ptpt) REVERT: D 77 ASN cc_start: 0.8410 (t0) cc_final: 0.8199 (t0) REVERT: M 97 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8045 (ttp80) REVERT: N 35 TRP cc_start: 0.7568 (m100) cc_final: 0.7339 (m100) REVERT: N 47 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8172 (mm) REVERT: E 168 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9164 (mmtp) REVERT: E 377 ASN cc_start: 0.8733 (p0) cc_final: 0.8515 (p0) REVERT: F 586 TYR cc_start: 0.8932 (t80) cc_final: 0.8612 (t80) REVERT: G 100 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7640 (ttt90) REVERT: H 55 LEU cc_start: 0.8499 (tt) cc_final: 0.8182 (tt) REVERT: H 77 ASN cc_start: 0.8705 (t0) cc_final: 0.8472 (t0) REVERT: I 103 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8080 (mm-40) REVERT: I 107 ASP cc_start: 0.8711 (m-30) cc_final: 0.8260 (m-30) REVERT: I 201 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8292 (mp) REVERT: J 617 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8813 (ptpp) REVERT: K 100 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7646 (ttt180) REVERT: Q 29 MET cc_start: 0.5482 (tpt) cc_final: 0.5176 (tpt) REVERT: R 97 SER cc_start: 0.9491 (t) cc_final: 0.9229 (t) outliers start: 89 outliers final: 59 residues processed: 583 average time/residue: 0.1581 time to fit residues: 149.2745 Evaluate side-chains 554 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 491 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 428 GLN Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 138 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 280 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 258 GLN A 428 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN G 3 HIS I 92 ASN I 258 GLN I 302 ASN K 3 HIS R 26 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115626 restraints weight = 41516.731| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.21 r_work: 0.3310 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27672 Z= 0.213 Angle : 0.823 16.702 37929 Z= 0.372 Chirality : 0.052 0.474 4707 Planarity : 0.005 0.163 4446 Dihedral : 12.267 108.073 7227 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.22 % Favored : 91.29 % Rotamer: Outliers : 3.72 % Allowed : 22.07 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.15), residues: 3054 helix: 1.18 (0.25), residues: 453 sheet: -0.45 (0.18), residues: 813 loop : -1.67 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 24 TYR 0.017 0.001 TYR A 384 PHE 0.013 0.002 PHE I 317 TRP 0.019 0.001 TRP I 112 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00500 (27435) covalent geometry : angle 0.73575 (37263) SS BOND : bond 0.00538 ( 45) SS BOND : angle 1.44529 ( 90) hydrogen bonds : bond 0.04378 ( 708) hydrogen bonds : angle 5.41592 ( 1836) link_ALPHA1-2 : bond 0.00938 ( 27) link_ALPHA1-2 : angle 1.97937 ( 81) link_ALPHA1-3 : bond 0.00908 ( 21) link_ALPHA1-3 : angle 2.11056 ( 63) link_ALPHA1-6 : bond 0.00513 ( 21) link_ALPHA1-6 : angle 1.82202 ( 63) link_BETA1-4 : bond 0.00402 ( 51) link_BETA1-4 : angle 2.03160 ( 153) link_NAG-ASN : bond 0.00603 ( 72) link_NAG-ASN : angle 4.24259 ( 216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 484 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8697 (tp40) cc_final: 0.7983 (mm-40) REVERT: A 107 ASP cc_start: 0.8807 (m-30) cc_final: 0.8293 (m-30) REVERT: A 199 SER cc_start: 0.9170 (p) cc_final: 0.8923 (t) REVERT: A 475 MET cc_start: 0.8048 (ttp) cc_final: 0.7836 (ttp) REVERT: C 100 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7755 (ttt180) REVERT: D 77 ASN cc_start: 0.8534 (t0) cc_final: 0.8306 (t0) REVERT: N 47 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8430 (mm) REVERT: E 168 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9207 (mmtp) REVERT: E 377 ASN cc_start: 0.8932 (p0) cc_final: 0.8640 (p0) REVERT: G 100 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7664 (ttt90) REVERT: H 77 ASN cc_start: 0.8729 (t0) cc_final: 0.8476 (t0) REVERT: O 100 MET cc_start: 0.8394 (mpp) cc_final: 0.7352 (mpp) REVERT: I 103 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8075 (mm-40) REVERT: I 107 ASP cc_start: 0.8769 (m-30) cc_final: 0.8419 (m-30) REVERT: I 164 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8024 (mm-30) REVERT: K 100 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7740 (ttt180) REVERT: R 35 TRP cc_start: 0.7515 (m100) cc_final: 0.7110 (m100) REVERT: R 97 SER cc_start: 0.9566 (t) cc_final: 0.9317 (t) outliers start: 100 outliers final: 86 residues processed: 552 average time/residue: 0.1467 time to fit residues: 132.1413 Evaluate side-chains 563 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 476 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 244 SER Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 428 GLN Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 264 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 428 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN E 92 ASN E 258 GLN F 590 GLN I 92 ASN I 302 ASN R 26 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.160512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116520 restraints weight = 41857.092| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.19 r_work: 0.3321 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27672 Z= 0.174 Angle : 0.809 16.626 37929 Z= 0.363 Chirality : 0.050 0.448 4707 Planarity : 0.006 0.165 4446 Dihedral : 11.958 104.951 7227 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.20 % Favored : 92.31 % Rotamer: Outliers : 3.64 % Allowed : 22.59 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.15), residues: 3054 helix: 1.22 (0.26), residues: 453 sheet: -0.50 (0.18), residues: 819 loop : -1.64 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 24 TYR 0.016 0.001 TYR N 49 PHE 0.017 0.001 PHE A 233 TRP 0.029 0.001 TRP N 35 HIS 0.003 0.001 HIS K 100F Details of bonding type rmsd covalent geometry : bond 0.00397 (27435) covalent geometry : angle 0.72115 (37263) SS BOND : bond 0.00489 ( 45) SS BOND : angle 1.27496 ( 90) hydrogen bonds : bond 0.04174 ( 708) hydrogen bonds : angle 5.36153 ( 1836) link_ALPHA1-2 : bond 0.00882 ( 27) link_ALPHA1-2 : angle 1.89298 ( 81) link_ALPHA1-3 : bond 0.00888 ( 21) link_ALPHA1-3 : angle 2.00539 ( 63) link_ALPHA1-6 : bond 0.00544 ( 21) link_ALPHA1-6 : angle 1.76296 ( 63) link_BETA1-4 : bond 0.00444 ( 51) link_BETA1-4 : angle 1.97887 ( 153) link_NAG-ASN : bond 0.00618 ( 72) link_NAG-ASN : angle 4.28226 ( 216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 477 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8722 (tp40) cc_final: 0.7990 (mm-40) REVERT: A 107 ASP cc_start: 0.8807 (m-30) cc_final: 0.8334 (m-30) REVERT: A 181 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 199 SER cc_start: 0.9170 (p) cc_final: 0.8902 (t) REVERT: A 475 MET cc_start: 0.8006 (ttp) cc_final: 0.7803 (ttp) REVERT: C 100 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7762 (ttt180) REVERT: D 77 ASN cc_start: 0.8586 (t0) cc_final: 0.8362 (t0) REVERT: M 97 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8190 (ttp80) REVERT: N 47 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8449 (mm) REVERT: E 377 ASN cc_start: 0.8955 (p0) cc_final: 0.8688 (p0) REVERT: G 100 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7683 (ttt90) REVERT: H 77 ASN cc_start: 0.8720 (t0) cc_final: 0.8469 (t0) REVERT: O 100 MET cc_start: 0.8412 (mpp) cc_final: 0.7406 (mpp) REVERT: I 103 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8036 (mm-40) REVERT: I 107 ASP cc_start: 0.8779 (m-30) cc_final: 0.8412 (m-30) REVERT: K 100 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7764 (ttt90) REVERT: Q 29 MET cc_start: 0.5464 (tpt) cc_final: 0.5075 (tpt) REVERT: Q 32 TYR cc_start: 0.7265 (p90) cc_final: 0.6778 (p90) REVERT: R 97 SER cc_start: 0.9553 (t) cc_final: 0.9320 (t) outliers start: 98 outliers final: 84 residues processed: 544 average time/residue: 0.1479 time to fit residues: 130.7603 Evaluate side-chains 547 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 461 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 97 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 290 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN I 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.159462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115415 restraints weight = 41865.466| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.17 r_work: 0.3303 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27672 Z= 0.181 Angle : 0.815 16.027 37929 Z= 0.368 Chirality : 0.050 0.452 4707 Planarity : 0.005 0.150 4446 Dihedral : 11.514 96.604 7227 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.42 % Favored : 91.16 % Rotamer: Outliers : 3.72 % Allowed : 22.71 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.15), residues: 3054 helix: 1.40 (0.26), residues: 435 sheet: -0.63 (0.17), residues: 900 loop : -1.54 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 24 TYR 0.015 0.001 TYR L 91 PHE 0.010 0.001 PHE J 592 TRP 0.030 0.002 TRP N 96 HIS 0.006 0.001 HIS N 38 Details of bonding type rmsd covalent geometry : bond 0.00419 (27435) covalent geometry : angle 0.72449 (37263) SS BOND : bond 0.00515 ( 45) SS BOND : angle 1.18098 ( 90) hydrogen bonds : bond 0.04258 ( 708) hydrogen bonds : angle 5.43913 ( 1836) link_ALPHA1-2 : bond 0.00900 ( 27) link_ALPHA1-2 : angle 1.96643 ( 81) link_ALPHA1-3 : bond 0.00765 ( 21) link_ALPHA1-3 : angle 1.97294 ( 63) link_ALPHA1-6 : bond 0.00517 ( 21) link_ALPHA1-6 : angle 1.82934 ( 63) link_BETA1-4 : bond 0.00426 ( 51) link_BETA1-4 : angle 1.98232 ( 153) link_NAG-ASN : bond 0.00630 ( 72) link_NAG-ASN : angle 4.37119 ( 216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 478 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8751 (tp40) cc_final: 0.8448 (mm-40) REVERT: A 199 SER cc_start: 0.9234 (p) cc_final: 0.8969 (t) REVERT: B 588 GLN cc_start: 0.8763 (tp40) cc_final: 0.8464 (tt0) REVERT: C 100 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7792 (ttt180) REVERT: N 47 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mm) REVERT: E 161 MET cc_start: 0.8924 (tpp) cc_final: 0.8622 (tpt) REVERT: E 377 ASN cc_start: 0.8975 (p0) cc_final: 0.8702 (p0) REVERT: F 588 GLN cc_start: 0.8801 (tp40) cc_final: 0.8361 (tt0) REVERT: G 100 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7671 (ttt90) REVERT: H 77 ASN cc_start: 0.8783 (t0) cc_final: 0.8542 (t0) REVERT: O 100 MET cc_start: 0.8463 (mpp) cc_final: 0.7449 (mpp) REVERT: I 103 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8047 (mm-40) REVERT: I 107 ASP cc_start: 0.8792 (m-30) cc_final: 0.8439 (m-30) REVERT: I 164 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7976 (mm-30) REVERT: K 100 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7804 (ttt90) REVERT: Q 32 TYR cc_start: 0.7247 (p90) cc_final: 0.6737 (p90) REVERT: R 97 SER cc_start: 0.9557 (t) cc_final: 0.9348 (t) outliers start: 100 outliers final: 91 residues processed: 543 average time/residue: 0.1453 time to fit residues: 128.6583 Evaluate side-chains 559 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 467 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 103 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 48 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN E 92 ASN I 92 ASN I 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097441 restraints weight = 39923.230| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.71 r_work: 0.2963 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 27672 Z= 0.238 Angle : 0.866 18.110 37929 Z= 0.393 Chirality : 0.052 0.475 4707 Planarity : 0.006 0.168 4446 Dihedral : 11.602 91.805 7227 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.42 % Favored : 91.22 % Rotamer: Outliers : 3.79 % Allowed : 22.63 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.15), residues: 3054 helix: 1.25 (0.26), residues: 435 sheet: -0.63 (0.17), residues: 888 loop : -1.57 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 166 TYR 0.018 0.002 TYR A 39 PHE 0.014 0.002 PHE F 592 TRP 0.029 0.002 TRP P 35 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00560 (27435) covalent geometry : angle 0.77305 (37263) SS BOND : bond 0.00613 ( 45) SS BOND : angle 1.67926 ( 90) hydrogen bonds : bond 0.04601 ( 708) hydrogen bonds : angle 5.60469 ( 1836) link_ALPHA1-2 : bond 0.00916 ( 27) link_ALPHA1-2 : angle 2.03960 ( 81) link_ALPHA1-3 : bond 0.00683 ( 21) link_ALPHA1-3 : angle 1.99628 ( 63) link_ALPHA1-6 : bond 0.00469 ( 21) link_ALPHA1-6 : angle 1.79640 ( 63) link_BETA1-4 : bond 0.00433 ( 51) link_BETA1-4 : angle 2.12368 ( 153) link_NAG-ASN : bond 0.00625 ( 72) link_NAG-ASN : angle 4.53531 ( 216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 451 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8702 (tpp) cc_final: 0.8431 (tpt) REVERT: A 103 GLN cc_start: 0.8926 (tp40) cc_final: 0.8712 (mm-40) REVERT: A 161 MET cc_start: 0.9053 (tpt) cc_final: 0.8737 (tpt) REVERT: A 199 SER cc_start: 0.9301 (p) cc_final: 0.9033 (t) REVERT: B 523 LEU cc_start: 0.9095 (mm) cc_final: 0.8845 (mt) REVERT: C 100 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8024 (ttt180) REVERT: D 92 ASP cc_start: 0.8778 (p0) cc_final: 0.7984 (t0) REVERT: E 161 MET cc_start: 0.9061 (tpp) cc_final: 0.8805 (tpt) REVERT: F 588 GLN cc_start: 0.8989 (tp40) cc_final: 0.8636 (tt0) REVERT: G 100 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7853 (ttt90) REVERT: H 77 ASN cc_start: 0.8883 (t0) cc_final: 0.8666 (t0) REVERT: H 92 ASP cc_start: 0.8819 (p0) cc_final: 0.7954 (t0) REVERT: I 107 ASP cc_start: 0.8933 (m-30) cc_final: 0.8615 (m-30) REVERT: I 164 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8343 (mm-30) REVERT: K 100 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.7960 (ttt90) REVERT: Q 32 TYR cc_start: 0.7370 (p90) cc_final: 0.6880 (p90) REVERT: R 20 ARG cc_start: 0.7689 (ptp-170) cc_final: 0.7339 (ptp-170) REVERT: R 49 TYR cc_start: 0.8016 (p90) cc_final: 0.7559 (p90) REVERT: R 60 GLU cc_start: 0.8584 (pp20) cc_final: 0.7792 (pp20) outliers start: 102 outliers final: 96 residues processed: 522 average time/residue: 0.1439 time to fit residues: 122.5152 Evaluate side-chains 531 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 435 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 56 LYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 539 VAL Chi-restraints excluded: chain J residue 617 LYS Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain R residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 280 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 189 optimal weight: 30.0000 chunk 282 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN D 3 GLN N 37 GLN E 92 ASN I 92 ASN I 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.100509 restraints weight = 39654.285| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.70 r_work: 0.3013 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27672 Z= 0.149 Angle : 0.800 15.646 37929 Z= 0.361 Chirality : 0.050 0.435 4707 Planarity : 0.005 0.156 4446 Dihedral : 11.250 86.390 7227 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.12 % Favored : 91.45 % Rotamer: Outliers : 3.38 % Allowed : 23.52 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 3054 helix: 1.35 (0.26), residues: 435 sheet: -0.58 (0.17), residues: 873 loop : -1.58 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 476 TYR 0.015 0.001 TYR N 49 PHE 0.008 0.001 PHE J 592 TRP 0.025 0.001 TRP P 35 HIS 0.003 0.001 HIS K 100F Details of bonding type rmsd covalent geometry : bond 0.00338 (27435) covalent geometry : angle 0.71185 (37263) SS BOND : bond 0.00479 ( 45) SS BOND : angle 1.34709 ( 90) hydrogen bonds : bond 0.04174 ( 708) hydrogen bonds : angle 5.42760 ( 1836) link_ALPHA1-2 : bond 0.00952 ( 27) link_ALPHA1-2 : angle 1.85449 ( 81) link_ALPHA1-3 : bond 0.00794 ( 21) link_ALPHA1-3 : angle 1.87235 ( 63) link_ALPHA1-6 : bond 0.00522 ( 21) link_ALPHA1-6 : angle 1.74785 ( 63) link_BETA1-4 : bond 0.00468 ( 51) link_BETA1-4 : angle 1.88136 ( 153) link_NAG-ASN : bond 0.00596 ( 72) link_NAG-ASN : angle 4.28536 ( 216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6148.61 seconds wall clock time: 106 minutes 32.93 seconds (6392.93 seconds total)