Starting phenix.real_space_refine on Thu Feb 5 20:16:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pnu_71772/02_2026/9pnu_71772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pnu_71772/02_2026/9pnu_71772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pnu_71772/02_2026/9pnu_71772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pnu_71772/02_2026/9pnu_71772.map" model { file = "/net/cci-nas-00/data/ceres_data/9pnu_71772/02_2026/9pnu_71772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pnu_71772/02_2026/9pnu_71772.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 126 5.16 5 C 12111 2.51 5 N 3090 2.21 5 O 4095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19422 Number of models: 1 Model: "" Number of chains: 57 Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1798 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 223} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1704 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "A" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1005 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3591 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 23, 'TRANS': 429} Chain breaks: 2 Chain: "B" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "G" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3584 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1028 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3591 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 23, 'TRANS': 429} Chain breaks: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "G" 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.47, per 1000 atoms: 0.23 Number of scatterers: 19422 At special positions: 0 Unit cell: (130.35, 130.35, 176.55, 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 126 16.00 O 4095 8.00 N 3090 7.00 C 12111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 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 M 4 " - " MAN M 5 " " MAN T 4 " - " MAN T 5 " " MAN b 4 " - " MAN b 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA b 3 " - " MAN b 4 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA T 3 " - " MAN T 6 " " BMA b 3 " - " MAN b 6 " " BMA j 3 " - " MAN j 5 " " BMA q 3 " - " MAN q 6 " " BMA u 3 " - " MAN u 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " 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 m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " 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 w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 616 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 637 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 135 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 392 " " NAG D 1 " - " ASN C 156 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 616 " " NAG F 703 " - " ASN F 625 " " NAG F 704 " - " ASN F 637 " " NAG G 601 " - " ASN G 156 " " NAG G 602 " - " ASN G 355 " " NAG G 603 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 301 " " NAG I 603 " - " ASN I 355 " " NAG I 604 " - " ASN I 442 " " NAG I 605 " - " ASN I 392 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 241 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 276 " " NAG O 1 " - " ASN C 289 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 442 " " NAG S 1 " - " ASN C 448 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 230 " " NAG V 1 " - " ASN C 339 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN G 88 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 241 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 276 " " NAG d 1 " - " ASN G 289 " " NAG e 1 " - " ASN G 301 " " NAG f 1 " - " ASN G 332 " " NAG g 1 " - " ASN G 386 " " NAG h 1 " - " ASN G 442 " " NAG i 1 " - " ASN G 448 " " NAG j 1 " - " ASN G 160 " " NAG k 1 " - " ASN G 230 " " NAG l 1 " - " ASN G 339 " " NAG m 1 " - " ASN I 156 " " NAG n 1 " - " ASN I 197 " " NAG o 1 " - " ASN I 234 " " NAG p 1 " - " ASN I 241 " " NAG q 1 " - " ASN I 262 " " NAG r 1 " - " ASN I 276 " " NAG s 1 " - " ASN I 289 " " NAG t 1 " - " ASN I 332 " " NAG u 1 " - " ASN I 386 " " NAG v 1 " - " ASN I 448 " " NAG w 1 " - " ASN I 160 " " NAG x 1 " - " ASN I 230 " " NAG y 1 " - " ASN I 339 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 779.2 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 31 sheets defined 22.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.542A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.700A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 544 removed outlier: 4.209A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.610A pdb=" N ILE A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 664 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 101 through 116 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.069A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.292A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.109A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.812A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.606A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.856A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.184A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 101 through 117 Processing helix chain 'I' and resid 136 through 141 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 427 through 429 No H-bonds generated for 'chain 'I' and resid 427 through 429' Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.627A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100P through 103 Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 100A Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 120 through 124 current: chain 'H' and resid 135 through 145 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 135 through 145 current: chain 'H' and resid 176 through 185 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.361A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.574A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AB1, first strand: chain 'A' and resid 603 through 609 removed outlier: 8.333A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.303A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 7.068A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.589A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.908A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.458A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 removed outlier: 4.317A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 413 through 421 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.907A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR C 303 " --> pdb=" O ASN C 321 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.951A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.576A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'G' and resid 202 through 203 Processing sheet with id=AC5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 298 removed outlier: 7.428A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 334 current: chain 'G' and resid 381 through 385 removed outlier: 4.394A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 413 through 421 current: chain 'G' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'G' and resid 301 through 312 removed outlier: 7.028A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR G 303 " --> pdb=" O ASN G 321 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 603 through 609 removed outlier: 7.549A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.216A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD1, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.593A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.486A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 261 current: chain 'I' and resid 284 through 312 removed outlier: 6.668A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR I 303 " --> pdb=" O ASN I 321 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 315 through 323 current: chain 'I' and resid 381 through 385 removed outlier: 4.503A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 413 through 421 current: chain 'I' and resid 465 through 470 558 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5762 1.34 - 1.47: 5262 1.47 - 1.59: 8614 1.59 - 1.71: 1 1.71 - 1.84: 167 Bond restraints: 19806 Sorted by residual: bond pdb=" CB GLN G 428 " pdb=" CG GLN G 428 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CB LYS L 183 " pdb=" CG LYS L 183 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB GLN G 82 " pdb=" CG GLN G 82 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CB GLN G 246 " pdb=" CG GLN G 246 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CB GLN I 428 " pdb=" CG GLN I 428 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 ... (remaining 19801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 26407 1.95 - 3.91: 411 3.91 - 5.86: 75 5.86 - 7.81: 15 7.81 - 9.77: 9 Bond angle restraints: 26917 Sorted by residual: angle pdb=" CA GLN G 428 " pdb=" CB GLN G 428 " pdb=" CG GLN G 428 " ideal model delta sigma weight residual 114.10 122.62 -8.52 2.00e+00 2.50e-01 1.82e+01 angle pdb=" CB LYS A 574 " pdb=" CG LYS A 574 " pdb=" CD LYS A 574 " ideal model delta sigma weight residual 111.30 121.07 -9.77 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CB LYS C 207 " pdb=" CG LYS C 207 " pdb=" CD LYS C 207 " ideal model delta sigma weight residual 111.30 120.66 -9.36 2.30e+00 1.89e-01 1.66e+01 angle pdb=" CB GLN G 246 " pdb=" CG GLN G 246 " pdb=" CD GLN G 246 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CA GLN G 246 " pdb=" CB GLN G 246 " pdb=" CG GLN G 246 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 ... (remaining 26912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 13067 25.76 - 51.52: 749 51.52 - 77.29: 124 77.29 - 103.05: 28 103.05 - 128.81: 5 Dihedral angle restraints: 13973 sinusoidal: 7607 harmonic: 6366 Sorted by residual: dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.96 62.96 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 30.98 62.02 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS I 201 " pdb=" SG CYS I 201 " pdb=" SG CYS I 433 " pdb=" CB CYS I 433 " ideal model delta sinusoidal sigma weight residual -86.00 -145.22 59.22 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 13970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2850 0.049 - 0.099: 470 0.099 - 0.148: 187 0.148 - 0.198: 6 0.198 - 0.247: 5 Chirality restraints: 3518 Sorted by residual: chirality pdb=" C2 NAG v 1 " pdb=" C1 NAG v 1 " pdb=" C3 NAG v 1 " pdb=" N2 NAG v 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C2 NAG S 1 " pdb=" C1 NAG S 1 " pdb=" C3 NAG S 1 " pdb=" N2 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.25 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN G 442 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3515 not shown) Planarity restraints: 3249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 647 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" CD GLU F 647 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU F 647 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU F 647 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 631 " -0.014 2.00e-02 2.50e+03 1.37e-02 4.66e+00 pdb=" CG TRP F 631 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP F 631 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP F 631 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 631 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 631 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 631 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 631 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 631 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 631 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 644 " -0.137 9.50e-02 1.11e+02 6.18e-02 2.87e+00 pdb=" NE ARG B 644 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 644 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 644 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 644 " -0.001 2.00e-02 2.50e+03 ... (remaining 3246 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 7926 2.89 - 3.39: 17408 3.39 - 3.90: 32412 3.90 - 4.40: 35867 4.40 - 4.90: 60767 Nonbonded interactions: 154380 Sorted by model distance: nonbonded pdb=" O2 BMA Q 3 " pdb=" O3 BMA Q 3 " model vdw 2.388 2.432 nonbonded pdb=" O5 BMA b 3 " pdb=" O6 BMA b 3 " model vdw 2.439 2.432 nonbonded pdb=" O2 BMA T 3 " pdb=" O3 BMA T 3 " model vdw 2.445 2.432 nonbonded pdb=" O5 MAN j 4 " pdb=" O6 MAN j 4 " model vdw 2.449 2.432 nonbonded pdb=" O5 MAN b 5 " pdb=" O6 MAN b 5 " model vdw 2.460 2.432 ... (remaining 154375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 520 through 546 or resid 567 through 703)) selection = (chain 'B' and (resid 520 through 546 or resid 567 through 703)) selection = (chain 'F' and (resid 520 through 546 or resid 567 through 703)) } ncs_group { reference = (chain 'C' and (resid 32 through 139 or resid 150 through 603)) selection = (chain 'G' and (resid 32 through 139 or resid 150 through 603)) selection = (chain 'I' and (resid 32 through 139 or resid 150 through 603)) } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'g' selection = chain 'm' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'M' selection = chain 'T' selection = chain 'b' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'e' selection = chain 'h' selection = chain 'l' selection = chain 's' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'j' selection = chain 'u' } 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.110 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.004 0.048 20008 Z= 0.162 Angle : 0.664 9.767 27482 Z= 0.307 Chirality : 0.044 0.247 3518 Planarity : 0.004 0.062 3182 Dihedral : 15.006 128.811 9734 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.02 % Allowed : 22.70 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 2160 helix: 1.52 (0.26), residues: 461 sheet: 0.27 (0.21), residues: 594 loop : -0.08 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 644 TYR 0.021 0.001 TYR L 140 PHE 0.011 0.001 PHE G 159 TRP 0.036 0.001 TRP F 631 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00373 (19806) covalent geometry : angle 0.63210 (26917) SS BOND : bond 0.00282 ( 41) SS BOND : angle 0.87470 ( 82) hydrogen bonds : bond 0.14570 ( 558) hydrogen bonds : angle 6.92514 ( 1548) link_ALPHA1-2 : bond 0.00470 ( 4) link_ALPHA1-2 : angle 1.77699 ( 12) link_ALPHA1-3 : bond 0.00545 ( 10) link_ALPHA1-3 : angle 1.72229 ( 30) link_ALPHA1-6 : bond 0.00682 ( 6) link_ALPHA1-6 : angle 1.59005 ( 18) link_BETA1-4 : bond 0.00598 ( 74) link_BETA1-4 : angle 1.67103 ( 222) link_NAG-ASN : bond 0.00306 ( 67) link_NAG-ASN : angle 1.61211 ( 201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8198 (tp30) cc_final: 0.7927 (tp30) REVERT: H 16 GLU cc_start: 0.8439 (mp0) cc_final: 0.8150 (mp0) REVERT: H 43 MET cc_start: 0.8422 (mpp) cc_final: 0.7984 (mpp) REVERT: L 24 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7349 (ttm110) REVERT: L 158 ASN cc_start: 0.8658 (m110) cc_final: 0.8237 (t0) REVERT: C 51 THR cc_start: 0.8966 (m) cc_final: 0.8581 (p) REVERT: C 178 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8755 (ttmt) REVERT: G 66 HIS cc_start: 0.7646 (p-80) cc_final: 0.7348 (p-80) REVERT: G 107 ASP cc_start: 0.8720 (m-30) cc_final: 0.8512 (m-30) REVERT: G 166 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8378 (ptm-80) REVERT: G 178 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8786 (ttpt) REVERT: G 217 TYR cc_start: 0.8752 (m-80) cc_final: 0.8273 (m-80) REVERT: F 530 MET cc_start: 0.8958 (mtt) cc_final: 0.8652 (mtt) REVERT: F 626 MET cc_start: 0.8225 (ttm) cc_final: 0.8005 (ttm) REVERT: I 103 GLN cc_start: 0.8501 (tp40) cc_final: 0.8150 (tm-30) REVERT: I 130 GLU cc_start: 0.8712 (tt0) cc_final: 0.8113 (tm-30) REVERT: I 154 MET cc_start: 0.8717 (mtm) cc_final: 0.8333 (mtm) REVERT: I 446 THR cc_start: 0.9182 (p) cc_final: 0.8793 (p) outliers start: 20 outliers final: 15 residues processed: 211 average time/residue: 0.1675 time to fit residues: 50.8208 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 445 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN C 425 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS I 187 ASN I 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.100988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068077 restraints weight = 40876.905| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.79 r_work: 0.2855 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20008 Z= 0.186 Angle : 0.622 9.399 27482 Z= 0.285 Chirality : 0.044 0.245 3518 Planarity : 0.003 0.041 3182 Dihedral : 8.834 110.870 5644 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.67 % Allowed : 19.49 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 2160 helix: 1.61 (0.26), residues: 463 sheet: 0.28 (0.20), residues: 616 loop : -0.07 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 633 TYR 0.015 0.001 TYR L 91 PHE 0.014 0.001 PHE H 78 TRP 0.013 0.001 TRP I 338 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00427 (19806) covalent geometry : angle 0.58503 (26917) SS BOND : bond 0.00308 ( 41) SS BOND : angle 0.78630 ( 82) hydrogen bonds : bond 0.04301 ( 558) hydrogen bonds : angle 5.37547 ( 1548) link_ALPHA1-2 : bond 0.00428 ( 4) link_ALPHA1-2 : angle 1.89434 ( 12) link_ALPHA1-3 : bond 0.00720 ( 10) link_ALPHA1-3 : angle 1.97175 ( 30) link_ALPHA1-6 : bond 0.00909 ( 6) link_ALPHA1-6 : angle 1.80453 ( 18) link_BETA1-4 : bond 0.00593 ( 74) link_BETA1-4 : angle 1.65491 ( 222) link_NAG-ASN : bond 0.00350 ( 67) link_NAG-ASN : angle 1.61992 ( 201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 191 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8230 (tp30) cc_final: 0.7966 (tp30) REVERT: H 16 GLU cc_start: 0.8481 (mp0) cc_final: 0.8155 (mp0) REVERT: H 43 MET cc_start: 0.8449 (mpp) cc_final: 0.8042 (mpp) REVERT: H 105 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: L 24 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7534 (ttm110) REVERT: L 47 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9244 (mp) REVERT: L 158 ASN cc_start: 0.8603 (m110) cc_final: 0.8280 (t0) REVERT: A 633 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8751 (mtm110) REVERT: C 49 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.8954 (mtpp) REVERT: C 51 THR cc_start: 0.8967 (m) cc_final: 0.8569 (p) REVERT: C 168 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: C 178 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8805 (ttmt) REVERT: B 617 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8799 (mtmt) REVERT: B 633 ARG cc_start: 0.9077 (ttm-80) cc_final: 0.8856 (mtm110) REVERT: G 69 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7107 (m100) REVERT: G 91 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: G 107 ASP cc_start: 0.8740 (m-30) cc_final: 0.8491 (m-30) REVERT: G 166 ARG cc_start: 0.8766 (ptm-80) cc_final: 0.8494 (ptm-80) REVERT: G 178 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8822 (ttpt) REVERT: G 217 TYR cc_start: 0.8812 (m-80) cc_final: 0.8342 (m-80) REVERT: G 423 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9306 (mp) REVERT: F 530 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8794 (mtt) REVERT: F 626 MET cc_start: 0.8459 (ttm) cc_final: 0.7929 (ttm) REVERT: I 49 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8945 (mtpp) REVERT: I 103 GLN cc_start: 0.8532 (tp40) cc_final: 0.8190 (tm-30) REVERT: I 130 GLU cc_start: 0.8566 (tt0) cc_final: 0.8111 (tm-30) REVERT: I 154 MET cc_start: 0.8785 (mtm) cc_final: 0.8415 (mtm) REVERT: I 446 THR cc_start: 0.9195 (p) cc_final: 0.8819 (p) outliers start: 72 outliers final: 29 residues processed: 247 average time/residue: 0.1810 time to fit residues: 64.9242 Evaluate side-chains 223 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 152 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 147 GLN L 210 ASN C 425 ASN C 428 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067823 restraints weight = 41664.026| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.96 r_work: 0.2855 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20008 Z= 0.157 Angle : 0.604 9.387 27482 Z= 0.276 Chirality : 0.043 0.243 3518 Planarity : 0.003 0.040 3182 Dihedral : 8.394 103.350 5637 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.03 % Allowed : 19.23 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2160 helix: 1.69 (0.25), residues: 464 sheet: 0.27 (0.20), residues: 620 loop : -0.06 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 633 TYR 0.015 0.001 TYR L 91 PHE 0.014 0.001 PHE H 78 TRP 0.013 0.001 TRP I 338 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00358 (19806) covalent geometry : angle 0.56713 (26917) SS BOND : bond 0.00375 ( 41) SS BOND : angle 0.91557 ( 82) hydrogen bonds : bond 0.03606 ( 558) hydrogen bonds : angle 4.92013 ( 1548) link_ALPHA1-2 : bond 0.00427 ( 4) link_ALPHA1-2 : angle 1.91524 ( 12) link_ALPHA1-3 : bond 0.00796 ( 10) link_ALPHA1-3 : angle 2.04911 ( 30) link_ALPHA1-6 : bond 0.00952 ( 6) link_ALPHA1-6 : angle 1.84773 ( 18) link_BETA1-4 : bond 0.00582 ( 74) link_BETA1-4 : angle 1.63384 ( 222) link_NAG-ASN : bond 0.00294 ( 67) link_NAG-ASN : angle 1.56003 ( 201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 198 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8205 (tp30) cc_final: 0.7896 (tp30) REVERT: H 16 GLU cc_start: 0.8484 (mp0) cc_final: 0.8112 (mp0) REVERT: H 43 MET cc_start: 0.8429 (mpp) cc_final: 0.7991 (mpp) REVERT: H 105 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: H 117 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: L 47 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9241 (mp) REVERT: L 142 ARG cc_start: 0.8929 (ptm160) cc_final: 0.8715 (ptm-80) REVERT: L 158 ASN cc_start: 0.8659 (m110) cc_final: 0.8252 (t0) REVERT: A 585 ARG cc_start: 0.8609 (mtp85) cc_final: 0.8085 (mtp85) REVERT: A 633 ARG cc_start: 0.9151 (ptm160) cc_final: 0.8751 (mtm110) REVERT: C 49 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8964 (mtpp) REVERT: C 51 THR cc_start: 0.8904 (m) cc_final: 0.8558 (p) REVERT: C 129 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9076 (mt) REVERT: C 168 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8410 (mmmt) REVERT: C 178 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8790 (ttmt) REVERT: B 617 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8861 (mtmt) REVERT: B 652 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8422 (tp40) REVERT: G 52 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9127 (mt) REVERT: G 66 HIS cc_start: 0.7673 (p-80) cc_final: 0.7313 (p-80) REVERT: G 69 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7129 (m100) REVERT: G 91 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: G 107 ASP cc_start: 0.8748 (m-30) cc_final: 0.8467 (m-30) REVERT: G 166 ARG cc_start: 0.8739 (ptm-80) cc_final: 0.8443 (ptm-80) REVERT: G 217 TYR cc_start: 0.8798 (m-80) cc_final: 0.8334 (m-80) REVERT: G 315 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8643 (mt0) REVERT: G 423 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9255 (mp) REVERT: F 530 MET cc_start: 0.8986 (mtt) cc_final: 0.8749 (mtt) REVERT: F 588 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8376 (tm-30) REVERT: F 601 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8243 (mtmm) REVERT: F 617 LYS cc_start: 0.8691 (mtpm) cc_final: 0.8407 (mmmt) REVERT: F 626 MET cc_start: 0.8542 (ttm) cc_final: 0.8104 (ttm) REVERT: I 49 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8957 (mtpp) REVERT: I 66 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.6772 (p90) REVERT: I 103 GLN cc_start: 0.8542 (tp40) cc_final: 0.8071 (tm-30) REVERT: I 130 GLU cc_start: 0.8560 (tt0) cc_final: 0.8061 (tm-30) REVERT: I 154 MET cc_start: 0.8753 (mtm) cc_final: 0.8381 (mtm) REVERT: I 446 THR cc_start: 0.9193 (p) cc_final: 0.8840 (p) outliers start: 79 outliers final: 37 residues processed: 257 average time/residue: 0.1733 time to fit residues: 65.0128 Evaluate side-chains 239 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN A 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.100359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065502 restraints weight = 41824.573| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.00 r_work: 0.2807 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20008 Z= 0.232 Angle : 0.645 9.372 27482 Z= 0.294 Chirality : 0.044 0.245 3518 Planarity : 0.003 0.040 3182 Dihedral : 8.266 103.227 5630 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.08 % Allowed : 19.95 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 2160 helix: 1.72 (0.26), residues: 463 sheet: 0.19 (0.20), residues: 621 loop : -0.11 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 166 TYR 0.015 0.001 TYR L 91 PHE 0.016 0.001 PHE H 78 TRP 0.014 0.001 TRP I 338 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00540 (19806) covalent geometry : angle 0.60625 (26917) SS BOND : bond 0.00397 ( 41) SS BOND : angle 1.11007 ( 82) hydrogen bonds : bond 0.03743 ( 558) hydrogen bonds : angle 4.94145 ( 1548) link_ALPHA1-2 : bond 0.00409 ( 4) link_ALPHA1-2 : angle 1.93834 ( 12) link_ALPHA1-3 : bond 0.00778 ( 10) link_ALPHA1-3 : angle 2.14274 ( 30) link_ALPHA1-6 : bond 0.00917 ( 6) link_ALPHA1-6 : angle 1.86270 ( 18) link_BETA1-4 : bond 0.00584 ( 74) link_BETA1-4 : angle 1.66518 ( 222) link_NAG-ASN : bond 0.00421 ( 67) link_NAG-ASN : angle 1.69431 ( 201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8257 (tp30) cc_final: 0.7958 (tp30) REVERT: H 43 MET cc_start: 0.8456 (mpp) cc_final: 0.8019 (mpp) REVERT: H 105 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: H 117 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8278 (ttpp) REVERT: L 24 ARG cc_start: 0.8635 (mtp-110) cc_final: 0.7861 (ttm110) REVERT: L 142 ARG cc_start: 0.8978 (ptm160) cc_final: 0.8763 (ptm-80) REVERT: L 158 ASN cc_start: 0.8664 (m110) cc_final: 0.8212 (t0) REVERT: A 585 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8124 (mtp85) REVERT: A 633 ARG cc_start: 0.9167 (ptm160) cc_final: 0.8772 (mtm110) REVERT: C 49 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8974 (mtpp) REVERT: C 51 THR cc_start: 0.8931 (m) cc_final: 0.8609 (p) REVERT: C 97 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9156 (mmmm) REVERT: C 129 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9226 (mt) REVERT: C 168 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8498 (mmmt) REVERT: C 178 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8838 (ttmt) REVERT: C 265 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8931 (mp) REVERT: B 588 GLU cc_start: 0.8524 (tp30) cc_final: 0.8244 (mt-10) REVERT: B 617 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8892 (mtmt) REVERT: B 657 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: G 52 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9106 (mt) REVERT: G 69 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7226 (m100) REVERT: G 91 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: G 166 ARG cc_start: 0.8797 (ptm-80) cc_final: 0.8513 (ptm-80) REVERT: G 217 TYR cc_start: 0.8861 (m-80) cc_final: 0.8311 (m-80) REVERT: G 315 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8643 (mt0) REVERT: G 370 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: G 423 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9329 (mp) REVERT: F 530 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8799 (mtt) REVERT: F 588 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8400 (tm-30) REVERT: F 601 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8317 (mtmm) REVERT: F 631 TRP cc_start: 0.8920 (t-100) cc_final: 0.8496 (t-100) REVERT: I 66 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.6832 (p90) REVERT: I 103 GLN cc_start: 0.8625 (tp40) cc_final: 0.8136 (tm-30) REVERT: I 121 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8965 (mmtt) REVERT: I 130 GLU cc_start: 0.8612 (tt0) cc_final: 0.8106 (tm-30) REVERT: I 154 MET cc_start: 0.8837 (mtm) cc_final: 0.8440 (mtm) REVERT: I 446 THR cc_start: 0.9235 (p) cc_final: 0.8904 (p) outliers start: 80 outliers final: 49 residues processed: 252 average time/residue: 0.1672 time to fit residues: 61.3761 Evaluate side-chains 249 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 75 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN B 652 GLN I 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.100388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065527 restraints weight = 41817.647| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.01 r_work: 0.2808 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20008 Z= 0.206 Angle : 0.634 9.332 27482 Z= 0.289 Chirality : 0.044 0.243 3518 Planarity : 0.003 0.040 3182 Dihedral : 8.122 102.844 5630 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.59 % Allowed : 20.00 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2160 helix: 1.75 (0.26), residues: 463 sheet: 0.18 (0.20), residues: 621 loop : -0.16 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 166 TYR 0.016 0.001 TYR L 91 PHE 0.015 0.001 PHE H 78 TRP 0.015 0.001 TRP I 338 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00476 (19806) covalent geometry : angle 0.59678 (26917) SS BOND : bond 0.00327 ( 41) SS BOND : angle 0.89576 ( 82) hydrogen bonds : bond 0.03657 ( 558) hydrogen bonds : angle 4.85722 ( 1548) link_ALPHA1-2 : bond 0.00413 ( 4) link_ALPHA1-2 : angle 1.95628 ( 12) link_ALPHA1-3 : bond 0.00828 ( 10) link_ALPHA1-3 : angle 2.18446 ( 30) link_ALPHA1-6 : bond 0.00951 ( 6) link_ALPHA1-6 : angle 1.87986 ( 18) link_BETA1-4 : bond 0.00576 ( 74) link_BETA1-4 : angle 1.64771 ( 222) link_NAG-ASN : bond 0.00380 ( 67) link_NAG-ASN : angle 1.66242 ( 201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 186 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8259 (tp30) cc_final: 0.7945 (tp30) REVERT: H 43 MET cc_start: 0.8458 (mpp) cc_final: 0.8018 (mpp) REVERT: H 105 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: H 117 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8270 (ttpp) REVERT: L 24 ARG cc_start: 0.8644 (mtp-110) cc_final: 0.7888 (ttm110) REVERT: L 142 ARG cc_start: 0.8990 (ptm160) cc_final: 0.8778 (ptm-80) REVERT: L 158 ASN cc_start: 0.8647 (m110) cc_final: 0.8164 (t0) REVERT: A 585 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8116 (mtp85) REVERT: A 601 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8294 (mtpt) REVERT: A 633 ARG cc_start: 0.9153 (ptm160) cc_final: 0.8772 (mtm110) REVERT: C 49 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.8973 (mtpp) REVERT: C 51 THR cc_start: 0.8928 (m) cc_final: 0.8612 (p) REVERT: C 97 LYS cc_start: 0.9364 (mmmm) cc_final: 0.9140 (mmmm) REVERT: C 129 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9196 (mt) REVERT: C 168 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8491 (mmmt) REVERT: C 178 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8836 (ttmt) REVERT: C 205 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7209 (m) REVERT: C 265 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8926 (mp) REVERT: B 588 GLU cc_start: 0.8482 (tp30) cc_final: 0.8224 (mt-10) REVERT: B 617 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8887 (mtmt) REVERT: B 633 ARG cc_start: 0.9140 (ttp-110) cc_final: 0.8886 (mtm110) REVERT: B 652 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8109 (mm-40) REVERT: B 657 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8060 (tp30) REVERT: G 52 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9053 (mt) REVERT: G 69 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7287 (m100) REVERT: G 91 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: G 107 ASP cc_start: 0.8744 (m-30) cc_final: 0.8531 (m-30) REVERT: G 166 ARG cc_start: 0.8753 (ptm-80) cc_final: 0.8474 (ptm-80) REVERT: G 217 TYR cc_start: 0.8847 (m-80) cc_final: 0.8310 (m-80) REVERT: G 315 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: G 370 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: G 423 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9321 (mp) REVERT: F 530 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8809 (mtt) REVERT: F 588 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8389 (tm-30) REVERT: F 601 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8350 (mtmm) REVERT: F 631 TRP cc_start: 0.8909 (t-100) cc_final: 0.8513 (t-100) REVERT: I 46 ARG cc_start: 0.8431 (ttm170) cc_final: 0.8185 (ttm170) REVERT: I 66 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.6843 (p90) REVERT: I 103 GLN cc_start: 0.8641 (tp40) cc_final: 0.8148 (tm-30) REVERT: I 121 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8941 (mmtt) REVERT: I 130 GLU cc_start: 0.8599 (tt0) cc_final: 0.8079 (tm-30) REVERT: I 154 MET cc_start: 0.8831 (mtm) cc_final: 0.8434 (mtm) REVERT: I 446 THR cc_start: 0.9240 (p) cc_final: 0.8914 (p) outliers start: 90 outliers final: 54 residues processed: 256 average time/residue: 0.1715 time to fit residues: 64.2909 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 202 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 210 ASN A 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065738 restraints weight = 41667.488| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.98 r_work: 0.2811 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20008 Z= 0.193 Angle : 0.634 9.342 27482 Z= 0.287 Chirality : 0.044 0.242 3518 Planarity : 0.003 0.040 3182 Dihedral : 7.972 102.575 5630 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.49 % Allowed : 20.31 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 2160 helix: 1.79 (0.25), residues: 457 sheet: 0.05 (0.20), residues: 641 loop : -0.13 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 166 TYR 0.015 0.001 TYR L 91 PHE 0.014 0.001 PHE H 78 TRP 0.014 0.001 TRP I 338 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00445 (19806) covalent geometry : angle 0.59625 (26917) SS BOND : bond 0.00356 ( 41) SS BOND : angle 0.94215 ( 82) hydrogen bonds : bond 0.03599 ( 558) hydrogen bonds : angle 4.80478 ( 1548) link_ALPHA1-2 : bond 0.00434 ( 4) link_ALPHA1-2 : angle 1.95496 ( 12) link_ALPHA1-3 : bond 0.00885 ( 10) link_ALPHA1-3 : angle 2.22224 ( 30) link_ALPHA1-6 : bond 0.00986 ( 6) link_ALPHA1-6 : angle 1.90183 ( 18) link_BETA1-4 : bond 0.00568 ( 74) link_BETA1-4 : angle 1.64156 ( 222) link_NAG-ASN : bond 0.00356 ( 67) link_NAG-ASN : angle 1.63355 ( 201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 187 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8250 (tp30) cc_final: 0.7932 (tp30) REVERT: H 43 MET cc_start: 0.8460 (mpp) cc_final: 0.8017 (mpp) REVERT: H 105 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: H 117 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8279 (ttpp) REVERT: L 24 ARG cc_start: 0.8655 (mtp-110) cc_final: 0.7913 (ttm110) REVERT: L 142 ARG cc_start: 0.8988 (ptm160) cc_final: 0.8774 (ptm-80) REVERT: L 158 ASN cc_start: 0.8654 (m110) cc_final: 0.8154 (t0) REVERT: A 585 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8111 (mtp85) REVERT: A 601 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: A 633 ARG cc_start: 0.9150 (ptm160) cc_final: 0.8769 (mtm110) REVERT: C 49 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8980 (mtpp) REVERT: C 51 THR cc_start: 0.8928 (m) cc_final: 0.8591 (p) REVERT: C 97 LYS cc_start: 0.9369 (mmmm) cc_final: 0.9141 (mmmm) REVERT: C 129 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9186 (mt) REVERT: C 168 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8490 (mmmt) REVERT: C 178 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8833 (ttmt) REVERT: C 265 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8921 (mp) REVERT: B 588 GLU cc_start: 0.8474 (tp30) cc_final: 0.8206 (mt-10) REVERT: B 617 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8852 (mtmt) REVERT: B 633 ARG cc_start: 0.9153 (ttp-110) cc_final: 0.8903 (mtm110) REVERT: B 657 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: G 52 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9059 (mt) REVERT: G 69 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7274 (m100) REVERT: G 91 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: G 166 ARG cc_start: 0.8790 (ptm-80) cc_final: 0.8507 (ptm-80) REVERT: G 217 TYR cc_start: 0.8844 (m-80) cc_final: 0.8312 (m-80) REVERT: G 315 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8640 (mt0) REVERT: G 370 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: G 423 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9323 (mp) REVERT: F 530 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8799 (mtt) REVERT: F 588 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8358 (tm-30) REVERT: F 601 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8254 (mtmm) REVERT: F 617 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8740 (mmmt) REVERT: F 631 TRP cc_start: 0.8935 (t-100) cc_final: 0.8493 (t-100) REVERT: I 66 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.6828 (p90) REVERT: I 103 GLN cc_start: 0.8638 (tp40) cc_final: 0.8139 (tm-30) REVERT: I 121 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8933 (mmtt) REVERT: I 130 GLU cc_start: 0.8595 (tt0) cc_final: 0.8076 (tm-30) REVERT: I 154 MET cc_start: 0.8830 (mtm) cc_final: 0.8448 (mtm) REVERT: I 446 THR cc_start: 0.9236 (p) cc_final: 0.8915 (p) outliers start: 88 outliers final: 56 residues processed: 251 average time/residue: 0.1648 time to fit residues: 60.4565 Evaluate side-chains 258 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 184 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 4 optimal weight: 0.0470 chunk 211 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN C 66 HIS B 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.101228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.066571 restraints weight = 41749.093| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.99 r_work: 0.2844 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20008 Z= 0.140 Angle : 0.614 9.363 27482 Z= 0.278 Chirality : 0.043 0.283 3518 Planarity : 0.003 0.040 3182 Dihedral : 7.683 102.069 5630 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.13 % Allowed : 20.51 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 2160 helix: 1.76 (0.26), residues: 463 sheet: 0.10 (0.20), residues: 641 loop : -0.08 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 166 TYR 0.015 0.001 TYR L 91 PHE 0.012 0.001 PHE H 78 TRP 0.014 0.001 TRP I 338 HIS 0.002 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00317 (19806) covalent geometry : angle 0.57785 (26917) SS BOND : bond 0.00265 ( 41) SS BOND : angle 0.82398 ( 82) hydrogen bonds : bond 0.03397 ( 558) hydrogen bonds : angle 4.68986 ( 1548) link_ALPHA1-2 : bond 0.00431 ( 4) link_ALPHA1-2 : angle 1.95137 ( 12) link_ALPHA1-3 : bond 0.01002 ( 10) link_ALPHA1-3 : angle 2.22093 ( 30) link_ALPHA1-6 : bond 0.01073 ( 6) link_ALPHA1-6 : angle 1.92825 ( 18) link_BETA1-4 : bond 0.00564 ( 74) link_BETA1-4 : angle 1.61402 ( 222) link_NAG-ASN : bond 0.00306 ( 67) link_NAG-ASN : angle 1.53064 ( 201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 197 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 MET cc_start: 0.8428 (mpp) cc_final: 0.7981 (mpp) REVERT: H 105 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: L 24 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.7890 (ttm110) REVERT: L 142 ARG cc_start: 0.8980 (ptm160) cc_final: 0.8759 (ptm-80) REVERT: L 158 ASN cc_start: 0.8671 (m110) cc_final: 0.8128 (t0) REVERT: A 585 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8084 (mtp85) REVERT: A 601 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8182 (mtpt) REVERT: A 633 ARG cc_start: 0.9142 (ptm160) cc_final: 0.8736 (mtm110) REVERT: C 49 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8967 (mtpp) REVERT: C 51 THR cc_start: 0.8905 (m) cc_final: 0.8556 (p) REVERT: C 97 LYS cc_start: 0.9372 (mmmm) cc_final: 0.9133 (mmmm) REVERT: C 129 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9057 (mt) REVERT: C 168 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8436 (mmmt) REVERT: C 178 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8812 (ttmt) REVERT: B 588 GLU cc_start: 0.8421 (tp30) cc_final: 0.8146 (mt-10) REVERT: B 617 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8822 (mtmt) REVERT: B 633 ARG cc_start: 0.9155 (ttp-110) cc_final: 0.8891 (mtm110) REVERT: B 652 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8178 (mm-40) REVERT: G 52 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9044 (mt) REVERT: G 66 HIS cc_start: 0.7702 (p-80) cc_final: 0.7217 (p-80) REVERT: G 69 TRP cc_start: 0.8331 (OUTLIER) cc_final: 0.7201 (m100) REVERT: G 91 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: G 107 ASP cc_start: 0.8702 (m-30) cc_final: 0.8479 (m-30) REVERT: G 166 ARG cc_start: 0.8742 (ptm-80) cc_final: 0.8410 (ptm-80) REVERT: G 217 TYR cc_start: 0.8809 (m-80) cc_final: 0.8275 (m-80) REVERT: G 315 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8584 (mt0) REVERT: G 370 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: F 530 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (mtt) REVERT: F 588 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8350 (tm-30) REVERT: F 601 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8189 (mtmm) REVERT: F 617 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8721 (mmmt) REVERT: F 631 TRP cc_start: 0.8913 (t-100) cc_final: 0.8490 (t-100) REVERT: I 46 ARG cc_start: 0.8424 (ttm170) cc_final: 0.8147 (ttm170) REVERT: I 66 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6807 (p90) REVERT: I 103 GLN cc_start: 0.8589 (tp40) cc_final: 0.8100 (tm-30) REVERT: I 117 LYS cc_start: 0.9329 (tppt) cc_final: 0.9127 (ttpp) REVERT: I 121 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8916 (mmtt) REVERT: I 130 GLU cc_start: 0.8584 (tt0) cc_final: 0.8049 (tm-30) REVERT: I 426 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6611 (mpp) REVERT: I 446 THR cc_start: 0.9206 (p) cc_final: 0.8878 (p) outliers start: 81 outliers final: 50 residues processed: 259 average time/residue: 0.1567 time to fit residues: 59.7545 Evaluate side-chains 256 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 426 MET Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 181 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN B 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.101937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067687 restraints weight = 41518.146| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.97 r_work: 0.2849 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20008 Z= 0.148 Angle : 0.620 9.581 27482 Z= 0.281 Chirality : 0.044 0.261 3518 Planarity : 0.003 0.041 3182 Dihedral : 7.518 101.838 5630 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.78 % Allowed : 20.92 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 2160 helix: 1.79 (0.26), residues: 463 sheet: 0.13 (0.20), residues: 641 loop : -0.09 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 166 TYR 0.015 0.001 TYR L 91 PHE 0.012 0.001 PHE H 78 TRP 0.013 0.001 TRP G 338 HIS 0.002 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00335 (19806) covalent geometry : angle 0.58378 (26917) SS BOND : bond 0.00278 ( 41) SS BOND : angle 0.82625 ( 82) hydrogen bonds : bond 0.03370 ( 558) hydrogen bonds : angle 4.67095 ( 1548) link_ALPHA1-2 : bond 0.00432 ( 4) link_ALPHA1-2 : angle 1.93333 ( 12) link_ALPHA1-3 : bond 0.01050 ( 10) link_ALPHA1-3 : angle 2.25434 ( 30) link_ALPHA1-6 : bond 0.01126 ( 6) link_ALPHA1-6 : angle 1.95411 ( 18) link_BETA1-4 : bond 0.00564 ( 74) link_BETA1-4 : angle 1.61383 ( 222) link_NAG-ASN : bond 0.00358 ( 67) link_NAG-ASN : angle 1.55383 ( 201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 189 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 MET cc_start: 0.8422 (mpp) cc_final: 0.7977 (mpp) REVERT: H 105 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: L 24 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.7917 (ttm110) REVERT: L 142 ARG cc_start: 0.8992 (ptm160) cc_final: 0.8773 (ptm-80) REVERT: L 158 ASN cc_start: 0.8680 (m110) cc_final: 0.8136 (t0) REVERT: A 585 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8086 (mtp85) REVERT: A 601 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (mtpt) REVERT: A 633 ARG cc_start: 0.9150 (ptm160) cc_final: 0.8754 (mtm110) REVERT: C 49 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8966 (mtpp) REVERT: C 51 THR cc_start: 0.8900 (m) cc_final: 0.8549 (p) REVERT: C 97 LYS cc_start: 0.9368 (mmmm) cc_final: 0.9129 (mmmm) REVERT: C 129 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9021 (mt) REVERT: C 178 LYS cc_start: 0.9078 (mtpt) cc_final: 0.8811 (ttmt) REVERT: B 588 GLU cc_start: 0.8410 (tp30) cc_final: 0.8145 (mt-10) REVERT: B 617 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8834 (mtmt) REVERT: B 633 ARG cc_start: 0.9159 (ttp-110) cc_final: 0.8905 (mtm110) REVERT: G 52 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9027 (mt) REVERT: G 66 HIS cc_start: 0.7673 (p-80) cc_final: 0.7201 (p-80) REVERT: G 69 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7233 (m100) REVERT: G 91 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: G 166 ARG cc_start: 0.8767 (ptm-80) cc_final: 0.8448 (ptm-80) REVERT: G 217 TYR cc_start: 0.8810 (m-80) cc_final: 0.8283 (m-80) REVERT: G 315 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: G 370 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: F 530 MET cc_start: 0.9022 (mtt) cc_final: 0.8775 (mtt) REVERT: F 588 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 601 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8200 (mtmm) REVERT: F 617 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8704 (mmmt) REVERT: F 631 TRP cc_start: 0.8922 (t-100) cc_final: 0.8488 (t-100) REVERT: I 66 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6801 (p90) REVERT: I 103 GLN cc_start: 0.8586 (tp40) cc_final: 0.8095 (tm-30) REVERT: I 121 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8902 (mmtt) REVERT: I 130 GLU cc_start: 0.8583 (tt0) cc_final: 0.8052 (tm-30) REVERT: I 446 THR cc_start: 0.9199 (p) cc_final: 0.8875 (p) outliers start: 74 outliers final: 53 residues processed: 247 average time/residue: 0.1574 time to fit residues: 56.8349 Evaluate side-chains 253 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 370 GLU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 150 optimal weight: 0.0870 chunk 179 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN B 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.067267 restraints weight = 41382.081| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.95 r_work: 0.2838 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20008 Z= 0.173 Angle : 0.629 9.993 27482 Z= 0.286 Chirality : 0.044 0.251 3518 Planarity : 0.003 0.041 3182 Dihedral : 7.352 101.361 5630 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.83 % Allowed : 20.61 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2160 helix: 1.77 (0.26), residues: 463 sheet: 0.10 (0.20), residues: 641 loop : -0.11 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 166 TYR 0.015 0.001 TYR L 91 PHE 0.013 0.001 PHE H 78 TRP 0.013 0.001 TRP I 338 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00400 (19806) covalent geometry : angle 0.59111 (26917) SS BOND : bond 0.00300 ( 41) SS BOND : angle 0.86820 ( 82) hydrogen bonds : bond 0.03488 ( 558) hydrogen bonds : angle 4.68456 ( 1548) link_ALPHA1-2 : bond 0.00423 ( 4) link_ALPHA1-2 : angle 1.92228 ( 12) link_ALPHA1-3 : bond 0.00979 ( 10) link_ALPHA1-3 : angle 2.43160 ( 30) link_ALPHA1-6 : bond 0.01215 ( 6) link_ALPHA1-6 : angle 2.00476 ( 18) link_BETA1-4 : bond 0.00566 ( 74) link_BETA1-4 : angle 1.63261 ( 222) link_NAG-ASN : bond 0.00347 ( 67) link_NAG-ASN : angle 1.58603 ( 201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 MET cc_start: 0.8431 (mpp) cc_final: 0.7985 (mpp) REVERT: H 105 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: H 117 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8272 (ttpp) REVERT: L 24 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.7923 (ttm110) REVERT: L 142 ARG cc_start: 0.9003 (ptm160) cc_final: 0.8769 (ptm-80) REVERT: A 585 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8102 (mtp85) REVERT: A 601 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8238 (mtpt) REVERT: A 633 ARG cc_start: 0.9150 (ptm160) cc_final: 0.8761 (mtm110) REVERT: A 634 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8770 (mt-10) REVERT: C 49 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.8975 (mtpp) REVERT: C 51 THR cc_start: 0.8900 (m) cc_final: 0.8582 (p) REVERT: C 97 LYS cc_start: 0.9372 (mmmm) cc_final: 0.9136 (mmmm) REVERT: C 129 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9074 (mt) REVERT: C 168 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8432 (mmmt) REVERT: C 178 LYS cc_start: 0.9078 (mtpt) cc_final: 0.8814 (ttmt) REVERT: C 265 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 588 GLU cc_start: 0.8447 (tp30) cc_final: 0.8214 (mt-10) REVERT: B 617 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8867 (mtmt) REVERT: B 633 ARG cc_start: 0.9161 (ttp-110) cc_final: 0.8909 (mtm110) REVERT: B 652 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8115 (mm-40) REVERT: G 52 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9023 (mt) REVERT: G 66 HIS cc_start: 0.7705 (p-80) cc_final: 0.7231 (p-80) REVERT: G 69 TRP cc_start: 0.8337 (OUTLIER) cc_final: 0.7268 (m100) REVERT: G 91 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: G 107 ASP cc_start: 0.8703 (m-30) cc_final: 0.8471 (m-30) REVERT: G 166 ARG cc_start: 0.8741 (ptm-80) cc_final: 0.8472 (ptm-80) REVERT: G 217 TYR cc_start: 0.8817 (m-80) cc_final: 0.8296 (m-80) REVERT: G 315 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: F 588 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8351 (tm-30) REVERT: F 601 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8279 (mtmm) REVERT: F 617 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8620 (mmmt) REVERT: F 633 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8792 (tpp80) REVERT: I 66 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.6805 (p90) REVERT: I 103 GLN cc_start: 0.8617 (tp40) cc_final: 0.8122 (tm-30) REVERT: I 121 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8914 (mmtt) REVERT: I 130 GLU cc_start: 0.8595 (tt0) cc_final: 0.8038 (tm-30) REVERT: I 446 THR cc_start: 0.9214 (p) cc_final: 0.8900 (p) outliers start: 75 outliers final: 51 residues processed: 247 average time/residue: 0.1603 time to fit residues: 57.7084 Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 186 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.064692 restraints weight = 42083.640| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.07 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20008 Z= 0.266 Angle : 0.677 10.047 27482 Z= 0.309 Chirality : 0.045 0.246 3518 Planarity : 0.003 0.041 3182 Dihedral : 7.443 101.285 5628 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.62 % Allowed : 20.87 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2160 helix: 1.74 (0.25), residues: 463 sheet: 0.03 (0.20), residues: 641 loop : -0.20 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 166 TYR 0.015 0.002 TYR L 91 PHE 0.023 0.002 PHE B 651 TRP 0.012 0.001 TRP I 338 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00622 (19806) covalent geometry : angle 0.63948 (26917) SS BOND : bond 0.00398 ( 41) SS BOND : angle 0.96817 ( 82) hydrogen bonds : bond 0.03742 ( 558) hydrogen bonds : angle 4.82664 ( 1548) link_ALPHA1-2 : bond 0.00407 ( 4) link_ALPHA1-2 : angle 1.93922 ( 12) link_ALPHA1-3 : bond 0.00833 ( 10) link_ALPHA1-3 : angle 2.31046 ( 30) link_ALPHA1-6 : bond 0.01222 ( 6) link_ALPHA1-6 : angle 2.03481 ( 18) link_BETA1-4 : bond 0.00570 ( 74) link_BETA1-4 : angle 1.66432 ( 222) link_NAG-ASN : bond 0.00476 ( 67) link_NAG-ASN : angle 1.73046 ( 201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 185 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 MET cc_start: 0.8473 (mpp) cc_final: 0.8028 (mpp) REVERT: H 105 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8334 (pm20) REVERT: H 117 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8277 (ttpp) REVERT: L 24 ARG cc_start: 0.8668 (mtp-110) cc_final: 0.7985 (ttm110) REVERT: L 142 ARG cc_start: 0.8981 (ptm160) cc_final: 0.8755 (ptm-80) REVERT: A 585 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8137 (mtp85) REVERT: A 601 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (mtpt) REVERT: A 633 ARG cc_start: 0.9160 (ptm160) cc_final: 0.8775 (mtm110) REVERT: C 49 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.8982 (mtpp) REVERT: C 51 THR cc_start: 0.8958 (m) cc_final: 0.8642 (p) REVERT: C 97 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9149 (mmmm) REVERT: C 129 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9238 (mt) REVERT: C 168 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8466 (mmmt) REVERT: C 178 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8875 (ttmt) REVERT: C 265 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8946 (mp) REVERT: B 588 GLU cc_start: 0.8512 (tp30) cc_final: 0.8276 (mt-10) REVERT: B 617 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8932 (mtmt) REVERT: B 633 ARG cc_start: 0.9166 (ttp-110) cc_final: 0.8916 (mtm110) REVERT: B 652 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: G 52 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9053 (mt) REVERT: G 66 HIS cc_start: 0.7778 (p-80) cc_final: 0.7300 (p-80) REVERT: G 69 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7280 (m100) REVERT: G 91 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: G 166 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8530 (ptm-80) REVERT: G 217 TYR cc_start: 0.8867 (m-80) cc_final: 0.8334 (m-80) REVERT: G 315 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8639 (mt0) REVERT: G 502 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8048 (tttp) REVERT: F 588 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8603 (tm-30) REVERT: F 601 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8333 (mtmm) REVERT: F 617 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8655 (mmmt) REVERT: F 631 TRP cc_start: 0.8930 (t-100) cc_final: 0.8518 (t-100) REVERT: I 66 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.6829 (p90) REVERT: I 103 GLN cc_start: 0.8703 (tp40) cc_final: 0.8196 (tm-30) REVERT: I 121 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8951 (mmtt) REVERT: I 130 GLU cc_start: 0.8653 (tt0) cc_final: 0.8080 (tm-30) REVERT: I 446 THR cc_start: 0.9262 (p) cc_final: 0.8965 (p) outliers start: 71 outliers final: 52 residues processed: 243 average time/residue: 0.1484 time to fit residues: 52.2649 Evaluate side-chains 251 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 315 GLN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 496 ILE Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain G residue 502 LYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 361 PHE Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 496 ILE Chi-restraints excluded: chain I residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065145 restraints weight = 41850.939| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.01 r_work: 0.2800 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 20008 Z= 0.219 Angle : 0.816 59.102 27482 Z= 0.420 Chirality : 0.044 0.314 3518 Planarity : 0.003 0.041 3182 Dihedral : 7.438 101.250 5628 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.72 % Allowed : 20.61 % Favored : 75.66 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2160 helix: 1.77 (0.26), residues: 463 sheet: 0.01 (0.20), residues: 641 loop : -0.20 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 644 TYR 0.015 0.001 TYR L 91 PHE 0.021 0.001 PHE B 651 TRP 0.013 0.001 TRP I 338 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00493 (19806) covalent geometry : angle 0.78863 (26917) SS BOND : bond 0.00349 ( 41) SS BOND : angle 0.95919 ( 82) hydrogen bonds : bond 0.03715 ( 558) hydrogen bonds : angle 4.82583 ( 1548) link_ALPHA1-2 : bond 0.00433 ( 4) link_ALPHA1-2 : angle 1.96464 ( 12) link_ALPHA1-3 : bond 0.00845 ( 10) link_ALPHA1-3 : angle 2.32563 ( 30) link_ALPHA1-6 : bond 0.01168 ( 6) link_ALPHA1-6 : angle 2.03334 ( 18) link_BETA1-4 : bond 0.00555 ( 74) link_BETA1-4 : angle 1.65652 ( 222) link_NAG-ASN : bond 0.00466 ( 67) link_NAG-ASN : angle 1.74417 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4980.17 seconds wall clock time: 86 minutes 12.81 seconds (5172.81 seconds total)