Starting phenix.real_space_refine on Thu Mar 5 11:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6opp_20152/03_2026/6opp_20152.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opp_20152/03_2026/6opp_20152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6opp_20152/03_2026/6opp_20152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opp_20152/03_2026/6opp_20152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6opp_20152/03_2026/6opp_20152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opp_20152/03_2026/6opp_20152.map" } resolution = 3.7 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= -0.002 sd= 0.074 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 115 5.16 5 C 13657 2.51 5 N 3604 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21852 Number of models: 1 Model: "" Number of chains: 54 Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1071 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3051 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3051 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 21, 'TRANS': 367} Chain breaks: 3 Chain: "E" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1101 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain breaks: 1 Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "K" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1046 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "J" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2998 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 3 Chain: "M" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: "o" 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "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: 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: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Unusual residues: {'LMT': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "D" 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: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'LMT': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 9 Chain: "K" 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: "J" 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 Time building chain proxies: 5.31, per 1000 atoms: 0.24 Number of scatterers: 21852 At special positions: 0 Unit cell: (161.13, 158.51, 145.41, 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 115 16.00 O 4476 8.00 N 3604 7.00 C 13657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 A 501 " distance=2.12 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.08 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.12 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.12 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.06 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 605 " - pdb=" SG CYS J 501 " distance=2.08 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.07 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.02 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 84 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.02 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 R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA c 3 " - " MAN c 4 " " BMA g 3 " - " MAN g 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA R 3 " - " MAN R 7 " " BMA c 3 " - " MAN c 7 " " BMA n 3 " - " MAN n 6 " " BMA o 3 " - " MAN o 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG 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 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 621 " - " ASN A 339 " " NAG A 622 " - " ASN A 355 " " NAG A 632 " - " ASN A 397 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 616 " " NAG B 704 " - " ASN B 625 " " NAG B 705 " - " ASN B 637 " " NAG D 601 " - " ASN D 88 " " NAG D 620 " - " ASN D 339 " " NAG D 621 " - " ASN D 355 " " NAG D 631 " - " ASN D 397 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 616 " " NAG E 703 " - " ASN E 625 " " NAG E 704 " - " ASN E 637 " " NAG J 601 " - " ASN J 88 " " NAG J 620 " - " ASN J 339 " " NAG J 621 " - " ASN J 355 " " NAG J 632 " - " ASN J 397 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 616 " " NAG K 703 " - " ASN K 625 " " NAG K 704 " - " ASN K 637 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 241 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 362 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 392 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN D 234 " " NAG b 1 " - " ASN D 241 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 276 " " NAG e 1 " - " ASN D 295 " " NAG f 1 " - " ASN D 332 " " NAG g 1 " - " ASN D 362 " " NAG h 1 " - " ASN D 386 " " NAG i 1 " - " ASN D 392 " " NAG j 1 " - " ASN D 413 " " NAG k 1 " - " ASN D 448 " " NAG l 1 " - " ASN J 234 " " NAG m 1 " - " ASN J 241 " " NAG n 1 " - " ASN J 262 " " NAG o 1 " - " ASN J 276 " " NAG p 1 " - " ASN J 295 " " NAG q 1 " - " ASN J 332 " " NAG r 1 " - " ASN J 362 " " NAG s 1 " - " ASN J 386 " " NAG t 1 " - " ASN J 392 " " NAG u 1 " - " ASN J 413 " " NAG v 1 " - " ASN J 448 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 22.1% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 568 through 593 Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.033A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 4.025A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.610A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.623A pdb=" N ASN A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.072A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.711A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 114 removed outlier: 4.230A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 350 removed outlier: 3.557A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.692A pdb=" N ASN D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 547 Processing helix chain 'E' and resid 567 through 593 Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 100C Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'K' and resid 529 through 547 Processing helix chain 'K' and resid 566 through 593 removed outlier: 4.249A pdb=" N VAL K 570 " --> pdb=" O LEU K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 597 Processing helix chain 'K' and resid 618 through 626 Processing helix chain 'K' and resid 627 through 635 removed outlier: 3.888A pdb=" N LYS K 633 " --> pdb=" O MET K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 661 Processing helix chain 'J' and resid 64 through 74 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 98 through 114 removed outlier: 4.211A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 353 removed outlier: 3.836A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 476 through 484 removed outlier: 4.444A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 64 removed outlier: 4.163A pdb=" N ASP M 63 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 99 through 100C Processing helix chain 'F' and resid 58 through 64 removed outlier: 4.408A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.015A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA8, first strand: chain 'A' and resid 196 through 202 Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.805A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.329A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.329A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.801A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.524A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU C 96 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 4 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE C 26 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY C 38 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP C 28 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.557A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.557A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.663A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.239A pdb=" N VAL E 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N TYR D 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N CYS E 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AC6, first strand: chain 'D' and resid 259 through 260 removed outlier: 6.537A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.184A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.640A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.184A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.799A pdb=" N SER G 33 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AD2, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 10 through 12 removed outlier: 7.079A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N CYS O 88 " --> pdb=" O GLY O 99 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY O 101 " --> pdb=" O TYR O 86 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR O 86 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 603 through 609 removed outlier: 7.296A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 removed outlier: 5.356A pdb=" N ILE J 215 " --> pdb=" O GLY J 250 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY J 250 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR J 217 " --> pdb=" O THR J 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=AD8, first strand: chain 'J' and resid 197 through 202 Processing sheet with id=AD9, first strand: chain 'J' and resid 259 through 261 removed outlier: 3.749A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY J 451 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N GLU J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU J 453 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N LEU J 288 " --> pdb=" O LEU J 453 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N ASP J 457 " --> pdb=" O ILE J 284 " (cutoff:3.500A) removed outlier: 12.349A pdb=" N ILE J 284 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER J 334 " --> pdb=" O GLU J 293 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 271 through 273 removed outlier: 12.349A pdb=" N ILE J 284 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 11.150A pdb=" N ASP J 457 " --> pdb=" O ILE J 284 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N VAL J 286 " --> pdb=" O THR J 455 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR J 455 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 12.034A pdb=" N LEU J 288 " --> pdb=" O LEU J 453 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU J 453 " --> pdb=" O LEU J 288 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N GLU J 290 " --> pdb=" O GLY J 451 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY J 451 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR J 357 " --> pdb=" O GLU J 466 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE J 468 " --> pdb=" O THR J 357 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE J 359 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 2 through 5 removed outlier: 6.598A pdb=" N LYS M 2 " --> pdb=" O GLN M 94 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU M 96 " --> pdb=" O LYS M 2 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL M 4 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP M 28 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 12 through 17 Processing sheet with id=AE4, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AE5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.446A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.446A pdb=" N GLU N 10 " --> pdb=" O THR N 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.345A pdb=" N LYS F 2 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU F 96 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL F 4 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE F 26 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY F 38 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP F 28 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 12 through 17 879 hydrogen bonds defined for protein. 2253 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: 3.57 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4013 1.31 - 1.45: 6630 1.45 - 1.58: 11450 1.58 - 1.71: 23 1.71 - 1.85: 144 Bond restraints: 22260 Sorted by residual: bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.385 0.112 1.40e-02 5.10e+03 6.42e+01 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 ... (remaining 22255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 25081 2.26 - 4.51: 4249 4.51 - 6.77: 735 6.77 - 9.02: 125 9.02 - 11.28: 11 Bond angle restraints: 30201 Sorted by residual: angle pdb=" C PRO J 437 " pdb=" N PRO J 438 " pdb=" CA PRO J 438 " ideal model delta sigma weight residual 120.03 128.37 -8.34 9.90e-01 1.02e+00 7.10e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.92 128.85 -8.93 1.07e+00 8.73e-01 6.96e+01 angle pdb=" N ARG A 440 " pdb=" CA ARG A 440 " pdb=" C ARG A 440 " ideal model delta sigma weight residual 111.28 120.31 -9.03 1.09e+00 8.42e-01 6.86e+01 angle pdb=" C ALA H 60 " pdb=" N PRO H 61 " pdb=" CA PRO H 61 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.02e+00 9.61e-01 6.03e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 120.38 128.28 -7.90 1.03e+00 9.43e-01 5.89e+01 ... (remaining 30196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.47: 14345 26.47 - 52.93: 416 52.93 - 79.40: 108 79.40 - 105.87: 118 105.87 - 132.33: 50 Dihedral angle restraints: 15037 sinusoidal: 7662 harmonic: 7375 Sorted by residual: dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual 93.00 154.83 -61.83 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 150.63 -57.63 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual 93.00 149.72 -56.72 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 15034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2900 0.115 - 0.230: 738 0.230 - 0.345: 96 0.345 - 0.460: 21 0.460 - 0.575: 15 Chirality restraints: 3770 Sorted by residual: chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 BMA i 3 " pdb=" O4 NAG i 2 " pdb=" C2 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.73e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.55e+01 ... (remaining 3767 not shown) Planarity restraints: 3729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.093 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" CG ASN D 234 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.162 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 234 " -0.063 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN J 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN J 234 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN J 234 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG q 1 " 0.082 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" C7 NAG q 1 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG q 1 " 0.062 2.00e-02 2.50e+03 pdb=" N2 NAG q 1 " -0.108 2.00e-02 2.50e+03 pdb=" O7 NAG q 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 3726 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5839 2.80 - 3.32: 19524 3.32 - 3.85: 37510 3.85 - 4.37: 43807 4.37 - 4.90: 71531 Nonbonded interactions: 178211 Sorted by model distance: nonbonded pdb=" N ASN A 88 " pdb=" OD1 ASN A 88 " model vdw 2.271 3.120 nonbonded pdb=" O4 NAG q 2 " pdb=" O6 NAG q 2 " model vdw 2.346 3.040 nonbonded pdb=" OG1 THR D 37 " pdb=" OG1 THR D 499 " model vdw 2.385 3.040 nonbonded pdb=" N ASP N 100A" pdb=" OD1 ASP N 100A" model vdw 2.398 3.120 nonbonded pdb=" O5 NAG W 1 " pdb=" O6 NAG W 1 " model vdw 2.404 2.432 ... (remaining 178206 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 32 through 127 or resid 196 through 632)) selection = (chain 'D' and (resid 32 through 127 or resid 196 through 631)) selection = chain 'J' } ncs_group { reference = (chain 'B' and (resid 518 through 547 or resid 567 through 664 or resid 702 thro \ ugh 704)) selection = (chain 'E' and (resid 518 through 547 or resid 563 or resid 568 through 664 or r \ esid 702 through 704)) selection = (chain 'K' and (resid 518 through 547 or resid 567 through 664 or resid 702 thro \ ugh 704)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'X' selection = chain 'Y' selection = chain 'd' selection = chain 'i' selection = chain 'j' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'R' and (resid 2 or resid 5 through 7)) selection = (chain 'c' and (resid 2 or resid 5 through 7)) selection = (chain 'n' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 'o' selection = chain 'r' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.660 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.023 0.144 22421 Z= 1.203 Angle : 1.825 11.280 30645 Z= 1.140 Chirality : 0.107 0.575 3770 Planarity : 0.009 0.068 3672 Dihedral : 17.095 132.332 10158 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 0.58 % Allowed : 0.49 % Favored : 98.92 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2511 helix: 0.78 (0.23), residues: 429 sheet: 0.69 (0.18), residues: 752 loop : 0.47 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 542 TYR 0.083 0.009 TYR E 638 PHE 0.044 0.007 PHE H 29 TRP 0.065 0.010 TRP J 479 HIS 0.016 0.002 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.02272 (22260) covalent geometry : angle 1.79494 (30201) SS BOND : bond 0.03156 ( 39) SS BOND : angle 2.67591 ( 78) hydrogen bonds : bond 0.15514 ( 836) hydrogen bonds : angle 7.58285 ( 2253) link_ALPHA1-2 : bond 0.03977 ( 5) link_ALPHA1-2 : angle 3.24932 ( 15) link_ALPHA1-3 : bond 0.03191 ( 6) link_ALPHA1-3 : angle 2.41868 ( 18) link_ALPHA1-6 : bond 0.02905 ( 4) link_ALPHA1-6 : angle 2.81623 ( 12) link_BETA1-4 : bond 0.03231 ( 50) link_BETA1-4 : angle 3.66395 ( 150) link_NAG-ASN : bond 0.03151 ( 57) link_NAG-ASN : angle 3.27993 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 601 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 652 GLN cc_start: 0.8861 (tp40) cc_final: 0.8338 (tm-30) REVERT: A 368 ASP cc_start: 0.7830 (m-30) cc_final: 0.7448 (m-30) REVERT: H 100 TYR cc_start: 0.7061 (t80) cc_final: 0.6533 (t80) REVERT: I 79 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7542 (mp10) REVERT: E 530 MET cc_start: 0.9031 (mtm) cc_final: 0.8743 (mtp) REVERT: E 662 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7820 (mt-10) REVERT: O 33 LEU cc_start: 0.7624 (tp) cc_final: 0.7183 (tp) REVERT: O 36 TYR cc_start: 0.6914 (m-80) cc_final: 0.6489 (m-80) REVERT: O 38 GLN cc_start: 0.5532 (tt0) cc_final: 0.4954 (tm-30) REVERT: O 42 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7799 (mm110) REVERT: K 629 MET cc_start: 0.8349 (mtm) cc_final: 0.7508 (ttm) REVERT: K 635 ILE cc_start: 0.9300 (pt) cc_final: 0.9100 (pt) REVERT: J 61 TYR cc_start: 0.8237 (p90) cc_final: 0.7521 (p90) REVERT: J 95 MET cc_start: 0.8239 (ptm) cc_final: 0.8023 (ptm) REVERT: J 100 MET cc_start: 0.8986 (mtp) cc_final: 0.8653 (mtm) REVERT: J 215 ILE cc_start: 0.9489 (mm) cc_final: 0.9129 (pt) REVERT: J 435 TYR cc_start: 0.8267 (m-80) cc_final: 0.8023 (m-80) REVERT: J 486 TYR cc_start: 0.8973 (m-80) cc_final: 0.8476 (m-10) REVERT: M 85 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7507 (tm-30) REVERT: N 6 GLU cc_start: 0.6063 (pm20) cc_final: 0.5644 (pm20) REVERT: N 23 LYS cc_start: 0.7260 (tptt) cc_final: 0.7006 (tptt) REVERT: N 32 TYR cc_start: 0.7844 (p90) cc_final: 0.7320 (p90) REVERT: N 62 HIS cc_start: 0.8410 (p-80) cc_final: 0.8207 (p90) REVERT: N 63 LEU cc_start: 0.9062 (mt) cc_final: 0.8794 (mt) REVERT: N 81 GLU cc_start: 0.8976 (tt0) cc_final: 0.8757 (tm-30) REVERT: N 82 ASN cc_start: 0.8974 (m-40) cc_final: 0.8548 (m-40) REVERT: F 39 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: F 78 ASP cc_start: 0.7629 (m-30) cc_final: 0.7323 (m-30) REVERT: F 97 VAL cc_start: 0.4379 (t) cc_final: 0.3088 (t) outliers start: 13 outliers final: 9 residues processed: 612 average time/residue: 0.1762 time to fit residues: 158.1909 Evaluate side-chains 279 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain K residue 611 ASN Chi-restraints excluded: chain K residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 GLN H 39 GLN H 102 HIS O 93 ASN K 652 GLN J 302 ASN J 308 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.101319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081141 restraints weight = 64750.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084041 restraints weight = 33094.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.085931 restraints weight = 22393.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.087127 restraints weight = 17486.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087892 restraints weight = 14930.338| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22421 Z= 0.189 Angle : 0.850 14.046 30645 Z= 0.422 Chirality : 0.050 0.251 3770 Planarity : 0.005 0.045 3672 Dihedral : 13.592 112.990 5398 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 8.39 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.45 (0.16), residues: 2511 helix: 2.01 (0.25), residues: 420 sheet: 0.34 (0.18), residues: 762 loop : -0.22 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 24 TYR 0.026 0.002 TYR N 32 PHE 0.030 0.003 PHE O 98 TRP 0.033 0.002 TRP J 96 HIS 0.007 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00419 (22260) covalent geometry : angle 0.79664 (30201) SS BOND : bond 0.00372 ( 39) SS BOND : angle 1.68748 ( 78) hydrogen bonds : bond 0.05606 ( 836) hydrogen bonds : angle 6.18046 ( 2253) link_ALPHA1-2 : bond 0.00341 ( 5) link_ALPHA1-2 : angle 1.73463 ( 15) link_ALPHA1-3 : bond 0.00891 ( 6) link_ALPHA1-3 : angle 1.89355 ( 18) link_ALPHA1-6 : bond 0.00676 ( 4) link_ALPHA1-6 : angle 1.65914 ( 12) link_BETA1-4 : bond 0.00632 ( 50) link_BETA1-4 : angle 2.66625 ( 150) link_NAG-ASN : bond 0.00512 ( 57) link_NAG-ASN : angle 3.00084 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.6601 (ttt180) cc_final: 0.6306 (ttt90) REVERT: A 426 MET cc_start: 0.8651 (mtp) cc_final: 0.8398 (mtm) REVERT: A 434 MET cc_start: 0.8078 (ttt) cc_final: 0.7400 (ttt) REVERT: A 475 MET cc_start: 0.8357 (mmp) cc_final: 0.7727 (mmt) REVERT: A 479 TRP cc_start: 0.7772 (m-10) cc_final: 0.7363 (m-90) REVERT: C 56 ASP cc_start: 0.8413 (t70) cc_final: 0.8135 (m-30) REVERT: C 70 ILE cc_start: 0.8956 (mp) cc_final: 0.8734 (mt) REVERT: C 80 ASP cc_start: 0.8072 (m-30) cc_final: 0.7046 (m-30) REVERT: C 88 ASP cc_start: 0.8514 (p0) cc_final: 0.8229 (p0) REVERT: C 89 GLN cc_start: 0.8123 (mp10) cc_final: 0.7864 (tm-30) REVERT: H 100 TYR cc_start: 0.7273 (t80) cc_final: 0.6258 (t80) REVERT: H 100 PHE cc_start: 0.5453 (m-80) cc_final: 0.5110 (m-80) REVERT: D 368 ASP cc_start: 0.7039 (m-30) cc_final: 0.6830 (m-30) REVERT: E 633 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8601 (mtmm) REVERT: E 638 TYR cc_start: 0.8052 (m-80) cc_final: 0.7786 (m-10) REVERT: G 12 LYS cc_start: 0.8292 (mmmm) cc_final: 0.7926 (mmmt) REVERT: G 101 LYS cc_start: 0.8728 (tptt) cc_final: 0.8356 (tptp) REVERT: O 36 TYR cc_start: 0.6932 (m-80) cc_final: 0.6511 (m-80) REVERT: O 37 GLN cc_start: 0.5182 (OUTLIER) cc_final: 0.4738 (tm-30) REVERT: O 38 GLN cc_start: 0.6662 (tt0) cc_final: 0.5656 (tm-30) REVERT: K 629 MET cc_start: 0.8161 (mtm) cc_final: 0.6859 (mtp) REVERT: J 95 MET cc_start: 0.8184 (ptm) cc_final: 0.7959 (ptt) REVERT: J 100 MET cc_start: 0.8737 (mtp) cc_final: 0.8504 (mtm) REVERT: J 333 ILE cc_start: 0.8631 (mt) cc_final: 0.8370 (tt) REVERT: J 475 MET cc_start: 0.7950 (mmt) cc_final: 0.7498 (mmt) REVERT: M 85 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7335 (tm-30) REVERT: N 19 LYS cc_start: 0.9030 (tttt) cc_final: 0.8291 (tptp) REVERT: N 63 LEU cc_start: 0.8745 (mt) cc_final: 0.8478 (mt) REVERT: F 73 ASN cc_start: 0.7925 (t0) cc_final: 0.7651 (p0) outliers start: 49 outliers final: 25 residues processed: 393 average time/residue: 0.1575 time to fit residues: 94.7085 Evaluate side-chains 301 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 3 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 189 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 201 optimal weight: 0.2980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS K 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.100569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.080301 restraints weight = 64668.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083302 restraints weight = 31928.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.085186 restraints weight = 21233.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.086380 restraints weight = 16538.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.087092 restraints weight = 14081.421| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22421 Z= 0.152 Angle : 0.759 13.164 30645 Z= 0.369 Chirality : 0.048 0.517 3770 Planarity : 0.004 0.062 3672 Dihedral : 10.176 98.255 5383 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 10.19 % Favored : 87.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.94 % 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: 0.25 (0.16), residues: 2511 helix: 1.81 (0.25), residues: 452 sheet: 0.36 (0.19), residues: 699 loop : -0.47 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.024 0.002 TYR H 32 PHE 0.043 0.002 PHE H 29 TRP 0.044 0.002 TRP J 96 HIS 0.005 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00331 (22260) covalent geometry : angle 0.71522 (30201) SS BOND : bond 0.00259 ( 39) SS BOND : angle 1.00312 ( 78) hydrogen bonds : bond 0.04584 ( 836) hydrogen bonds : angle 5.79374 ( 2253) link_ALPHA1-2 : bond 0.00164 ( 5) link_ALPHA1-2 : angle 1.74159 ( 15) link_ALPHA1-3 : bond 0.01196 ( 6) link_ALPHA1-3 : angle 1.22997 ( 18) link_ALPHA1-6 : bond 0.00758 ( 4) link_ALPHA1-6 : angle 1.66197 ( 12) link_BETA1-4 : bond 0.00633 ( 50) link_BETA1-4 : angle 2.19132 ( 150) link_NAG-ASN : bond 0.00898 ( 57) link_NAG-ASN : angle 2.74205 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8124 (mp0) cc_final: 0.7837 (mp0) REVERT: B 629 MET cc_start: 0.8027 (mtp) cc_final: 0.7823 (mtp) REVERT: B 647 GLU cc_start: 0.7971 (tt0) cc_final: 0.7609 (tt0) REVERT: A 426 MET cc_start: 0.8728 (mtp) cc_final: 0.8499 (mtm) REVERT: A 475 MET cc_start: 0.8276 (mmp) cc_final: 0.7514 (mmt) REVERT: A 479 TRP cc_start: 0.7920 (m-10) cc_final: 0.7551 (m-90) REVERT: C 88 ASP cc_start: 0.8547 (p0) cc_final: 0.8275 (p0) REVERT: H 13 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8211 (tppt) REVERT: H 100 ASP cc_start: 0.8256 (t0) cc_final: 0.8030 (t0) REVERT: I 36 TYR cc_start: 0.7937 (m-80) cc_final: 0.7720 (m-10) REVERT: I 42 GLN cc_start: 0.7483 (mm-40) cc_final: 0.6861 (mp10) REVERT: D 368 ASP cc_start: 0.7198 (m-30) cc_final: 0.6942 (m-30) REVERT: E 633 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8604 (mtmm) REVERT: G 12 LYS cc_start: 0.8220 (mmmm) cc_final: 0.7879 (mmmt) REVERT: G 101 LYS cc_start: 0.8824 (tptt) cc_final: 0.8454 (tptp) REVERT: O 36 TYR cc_start: 0.6993 (m-80) cc_final: 0.6451 (m-80) REVERT: O 37 GLN cc_start: 0.5081 (OUTLIER) cc_final: 0.4566 (tm-30) REVERT: O 95 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7984 (mmm-85) REVERT: K 629 MET cc_start: 0.7749 (mtm) cc_final: 0.6420 (mtp) REVERT: J 100 MET cc_start: 0.8782 (mtp) cc_final: 0.8404 (mtm) REVERT: J 280 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.6688 (t0) REVERT: J 333 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8473 (tt) REVERT: J 434 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7786 (ttt) REVERT: J 435 TYR cc_start: 0.8085 (m-80) cc_final: 0.7797 (m-10) REVERT: J 475 MET cc_start: 0.7928 (mmt) cc_final: 0.7477 (mmt) REVERT: J 486 TYR cc_start: 0.8861 (m-80) cc_final: 0.8403 (m-10) REVERT: M 24 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7979 (pt) REVERT: M 85 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7408 (tm-30) REVERT: M 89 GLN cc_start: 0.8423 (mp10) cc_final: 0.8102 (mp10) REVERT: F 73 ASN cc_start: 0.8005 (t0) cc_final: 0.7788 (t0) outliers start: 51 outliers final: 26 residues processed: 335 average time/residue: 0.1443 time to fit residues: 75.7088 Evaluate side-chains 289 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 53 PHE Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 82 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 119 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 185 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 175 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN B 575 GLN A 114 GLN H 39 GLN I 90 GLN I 93 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.099259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079229 restraints weight = 64606.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082096 restraints weight = 32592.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083907 restraints weight = 21957.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085052 restraints weight = 17224.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.085760 restraints weight = 14742.310| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22421 Z= 0.150 Angle : 0.702 13.180 30645 Z= 0.343 Chirality : 0.047 0.480 3770 Planarity : 0.004 0.046 3672 Dihedral : 8.316 75.750 5381 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.65 % Allowed : 11.00 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.20 (0.16), residues: 2511 helix: 1.83 (0.25), residues: 454 sheet: 0.37 (0.19), residues: 736 loop : -0.59 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.023 0.002 TYR L 91 PHE 0.031 0.002 PHE H 29 TRP 0.066 0.002 TRP J 96 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00335 (22260) covalent geometry : angle 0.65779 (30201) SS BOND : bond 0.00261 ( 39) SS BOND : angle 1.14559 ( 78) hydrogen bonds : bond 0.04179 ( 836) hydrogen bonds : angle 5.57300 ( 2253) link_ALPHA1-2 : bond 0.00138 ( 5) link_ALPHA1-2 : angle 1.70174 ( 15) link_ALPHA1-3 : bond 0.01229 ( 6) link_ALPHA1-3 : angle 1.33253 ( 18) link_ALPHA1-6 : bond 0.00842 ( 4) link_ALPHA1-6 : angle 1.82666 ( 12) link_BETA1-4 : bond 0.00565 ( 50) link_BETA1-4 : angle 1.91583 ( 150) link_NAG-ASN : bond 0.00380 ( 57) link_NAG-ASN : angle 2.73747 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 282 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLU cc_start: 0.8430 (tp30) cc_final: 0.8203 (tp30) REVERT: L 70 GLU cc_start: 0.8111 (mp0) cc_final: 0.7826 (mp0) REVERT: B 647 GLU cc_start: 0.7963 (tt0) cc_final: 0.7604 (tt0) REVERT: A 107 ASP cc_start: 0.8580 (t0) cc_final: 0.8370 (t0) REVERT: A 368 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6845 (t0) REVERT: A 400 ARG cc_start: 0.6342 (ttt180) cc_final: 0.6033 (ttt90) REVERT: A 426 MET cc_start: 0.8799 (mtp) cc_final: 0.8587 (mtm) REVERT: A 475 MET cc_start: 0.8113 (mmp) cc_final: 0.7392 (mmt) REVERT: A 479 TRP cc_start: 0.7939 (m-10) cc_final: 0.7571 (m-90) REVERT: H 13 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8168 (tppt) REVERT: H 100 LEU cc_start: 0.8398 (mp) cc_final: 0.8190 (mp) REVERT: I 42 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6972 (mp10) REVERT: I 90 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: D 80 ASN cc_start: 0.8582 (t0) cc_final: 0.8370 (t0) REVERT: E 633 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8693 (mtmm) REVERT: G 101 LYS cc_start: 0.8776 (tptt) cc_final: 0.8394 (tptp) REVERT: O 36 TYR cc_start: 0.6989 (m-80) cc_final: 0.6648 (m-80) REVERT: O 37 GLN cc_start: 0.5201 (OUTLIER) cc_final: 0.4696 (tm-30) REVERT: K 633 LYS cc_start: 0.8949 (tppt) cc_final: 0.8565 (mppt) REVERT: J 280 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.6759 (t0) REVERT: J 333 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (tt) REVERT: J 475 MET cc_start: 0.7988 (mmt) cc_final: 0.7499 (mmt) REVERT: J 486 TYR cc_start: 0.8918 (m-80) cc_final: 0.8468 (m-10) REVERT: M 24 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8111 (pt) REVERT: M 66 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8551 (t0) REVERT: M 85 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7429 (tm-30) REVERT: F 73 ASN cc_start: 0.7967 (t0) cc_final: 0.7755 (t0) REVERT: F 87 GLU cc_start: 0.7063 (mp0) cc_final: 0.6785 (mp0) outliers start: 59 outliers final: 34 residues processed: 317 average time/residue: 0.1464 time to fit residues: 72.7971 Evaluate side-chains 294 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 61 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain K residue 661 LEU Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 162 optimal weight: 0.0970 chunk 88 optimal weight: 10.0000 chunk 238 optimal weight: 0.0170 chunk 232 optimal weight: 30.0000 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.099553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.079541 restraints weight = 64577.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082400 restraints weight = 32718.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084228 restraints weight = 22061.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085376 restraints weight = 17312.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086030 restraints weight = 14814.685| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22421 Z= 0.128 Angle : 0.673 20.445 30645 Z= 0.326 Chirality : 0.047 0.664 3770 Planarity : 0.004 0.053 3672 Dihedral : 7.693 74.142 5381 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.20 % Allowed : 12.16 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.17 (0.17), residues: 2511 helix: 1.93 (0.25), residues: 457 sheet: 0.31 (0.19), residues: 745 loop : -0.64 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 95B TYR 0.030 0.002 TYR H 90 PHE 0.030 0.002 PHE H 29 TRP 0.034 0.001 TRP J 45 HIS 0.005 0.001 HIS N 62 Details of bonding type rmsd covalent geometry : bond 0.00284 (22260) covalent geometry : angle 0.62186 (30201) SS BOND : bond 0.00444 ( 39) SS BOND : angle 1.05390 ( 78) hydrogen bonds : bond 0.03926 ( 836) hydrogen bonds : angle 5.42618 ( 2253) link_ALPHA1-2 : bond 0.00149 ( 5) link_ALPHA1-2 : angle 1.69015 ( 15) link_ALPHA1-3 : bond 0.01178 ( 6) link_ALPHA1-3 : angle 1.24169 ( 18) link_ALPHA1-6 : bond 0.00872 ( 4) link_ALPHA1-6 : angle 1.81579 ( 12) link_BETA1-4 : bond 0.00552 ( 50) link_BETA1-4 : angle 1.69644 ( 150) link_NAG-ASN : bond 0.00414 ( 57) link_NAG-ASN : angle 3.03876 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 70 GLU cc_start: 0.8145 (mp0) cc_final: 0.7856 (mp0) REVERT: B 647 GLU cc_start: 0.7947 (tt0) cc_final: 0.7570 (tt0) REVERT: A 107 ASP cc_start: 0.8536 (t0) cc_final: 0.8318 (t0) REVERT: A 368 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6889 (t0) REVERT: A 475 MET cc_start: 0.8057 (mmp) cc_final: 0.7649 (mmp) REVERT: A 479 TRP cc_start: 0.7867 (m-10) cc_final: 0.7501 (m-90) REVERT: H 13 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8234 (tppt) REVERT: H 39 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: I 42 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7236 (mp10) REVERT: D 80 ASN cc_start: 0.8557 (t0) cc_final: 0.8346 (t0) REVERT: E 633 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8680 (mtmm) REVERT: E 655 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (tppp) REVERT: G 12 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7490 (mttm) REVERT: G 101 LYS cc_start: 0.8774 (tptt) cc_final: 0.8428 (tptp) REVERT: O 36 TYR cc_start: 0.6892 (m-80) cc_final: 0.6586 (m-80) REVERT: O 37 GLN cc_start: 0.5057 (OUTLIER) cc_final: 0.4661 (tm-30) REVERT: J 280 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.6786 (t0) REVERT: J 333 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8434 (tt) REVERT: J 475 MET cc_start: 0.7979 (mmt) cc_final: 0.7508 (mmt) REVERT: M 10 ASP cc_start: 0.7996 (t0) cc_final: 0.7771 (t0) REVERT: M 24 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8132 (pt) REVERT: M 66 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8564 (t0) REVERT: M 89 GLN cc_start: 0.8369 (mp10) cc_final: 0.8128 (mp10) REVERT: N 2 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7845 (t) REVERT: F 73 ASN cc_start: 0.8004 (t0) cc_final: 0.7787 (t0) REVERT: F 87 GLU cc_start: 0.7325 (mp0) cc_final: 0.6956 (mp0) outliers start: 49 outliers final: 28 residues processed: 307 average time/residue: 0.1401 time to fit residues: 68.1841 Evaluate side-chains 291 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 61 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN H 39 GLN I 93 ASN D 105 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 GLN J 66 HIS ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS J 462 GLN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.090409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.071519 restraints weight = 64006.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073979 restraints weight = 34348.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075555 restraints weight = 23853.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076523 restraints weight = 19073.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077141 restraints weight = 16591.244| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 22421 Z= 0.377 Angle : 0.892 16.565 30645 Z= 0.438 Chirality : 0.053 0.736 3770 Planarity : 0.006 0.056 3672 Dihedral : 8.135 68.131 5381 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 3.14 % Allowed : 12.21 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.35 (0.16), residues: 2511 helix: 1.48 (0.24), residues: 448 sheet: -0.06 (0.18), residues: 790 loop : -0.94 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 480 TYR 0.039 0.003 TYR H 90 PHE 0.041 0.003 PHE D 376 TRP 0.044 0.003 TRP J 45 HIS 0.011 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00874 (22260) covalent geometry : angle 0.84533 (30201) SS BOND : bond 0.00516 ( 39) SS BOND : angle 1.54987 ( 78) hydrogen bonds : bond 0.05273 ( 836) hydrogen bonds : angle 5.83366 ( 2253) link_ALPHA1-2 : bond 0.00647 ( 5) link_ALPHA1-2 : angle 2.03669 ( 15) link_ALPHA1-3 : bond 0.01141 ( 6) link_ALPHA1-3 : angle 2.18319 ( 18) link_ALPHA1-6 : bond 0.00758 ( 4) link_ALPHA1-6 : angle 2.03897 ( 12) link_BETA1-4 : bond 0.00530 ( 50) link_BETA1-4 : angle 1.92681 ( 150) link_NAG-ASN : bond 0.00745 ( 57) link_NAG-ASN : angle 3.31283 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 GLU cc_start: 0.8685 (tp30) cc_final: 0.8475 (tp30) REVERT: L 70 GLU cc_start: 0.8284 (mp0) cc_final: 0.7967 (mp0) REVERT: A 368 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7049 (t70) REVERT: H 100 ASP cc_start: 0.8380 (t0) cc_final: 0.7961 (t0) REVERT: I 39 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6276 (mtmm) REVERT: I 42 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7254 (mp10) REVERT: D 80 ASN cc_start: 0.8681 (t0) cc_final: 0.8477 (t0) REVERT: E 633 LYS cc_start: 0.9094 (mtmm) cc_final: 0.8719 (mtmm) REVERT: E 655 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8814 (tppp) REVERT: G 12 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8107 (mtpp) REVERT: G 100 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (t80) REVERT: O 36 TYR cc_start: 0.6932 (m-80) cc_final: 0.6392 (m-80) REVERT: O 37 GLN cc_start: 0.5286 (OUTLIER) cc_final: 0.4881 (tm-30) REVERT: O 70 GLU cc_start: 0.7963 (pp20) cc_final: 0.7605 (pp20) REVERT: K 633 LYS cc_start: 0.9066 (tppt) cc_final: 0.8705 (mppt) REVERT: K 659 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7981 (tm-30) REVERT: J 280 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.6673 (t0) REVERT: J 333 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8383 (tt) REVERT: J 486 TYR cc_start: 0.8991 (m-10) cc_final: 0.8669 (m-10) REVERT: M 24 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8507 (pt) REVERT: M 66 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8473 (t0) REVERT: M 85 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7262 (tm-30) REVERT: F 73 ASN cc_start: 0.8249 (t0) cc_final: 0.7882 (t0) REVERT: F 74 LEU cc_start: 0.8837 (tp) cc_final: 0.8558 (tp) REVERT: F 87 GLU cc_start: 0.7341 (mp0) cc_final: 0.7028 (mp0) outliers start: 70 outliers final: 43 residues processed: 300 average time/residue: 0.1498 time to fit residues: 70.2907 Evaluate side-chains 289 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain K residue 535 MET Chi-restraints excluded: chain K residue 566 LEU Chi-restraints excluded: chain K residue 629 MET Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain J residue 491 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 176 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.096534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.076460 restraints weight = 65042.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.079179 restraints weight = 33376.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080909 restraints weight = 22726.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082008 restraints weight = 17963.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.082705 restraints weight = 15484.335| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22421 Z= 0.136 Angle : 0.684 13.752 30645 Z= 0.336 Chirality : 0.046 0.444 3770 Planarity : 0.004 0.044 3672 Dihedral : 7.531 64.914 5381 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 2.24 % Allowed : 13.15 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.16 (0.17), residues: 2511 helix: 1.88 (0.25), residues: 456 sheet: 0.05 (0.19), residues: 779 loop : -0.94 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 95B TYR 0.029 0.002 TYR O 96 PHE 0.025 0.002 PHE H 29 TRP 0.032 0.002 TRP J 45 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00304 (22260) covalent geometry : angle 0.64627 (30201) SS BOND : bond 0.00248 ( 39) SS BOND : angle 0.92960 ( 78) hydrogen bonds : bond 0.04084 ( 836) hydrogen bonds : angle 5.47931 ( 2253) link_ALPHA1-2 : bond 0.00242 ( 5) link_ALPHA1-2 : angle 1.82121 ( 15) link_ALPHA1-3 : bond 0.01149 ( 6) link_ALPHA1-3 : angle 1.36305 ( 18) link_ALPHA1-6 : bond 0.00984 ( 4) link_ALPHA1-6 : angle 1.86720 ( 12) link_BETA1-4 : bond 0.00510 ( 50) link_BETA1-4 : angle 1.57767 ( 150) link_NAG-ASN : bond 0.00363 ( 57) link_NAG-ASN : angle 2.60392 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5115 (mtmm) REVERT: L 70 GLU cc_start: 0.8172 (mp0) cc_final: 0.7910 (mp0) REVERT: B 629 MET cc_start: 0.7786 (mtp) cc_final: 0.6694 (mtt) REVERT: B 647 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 368 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6990 (t70) REVERT: A 479 TRP cc_start: 0.7902 (m-10) cc_final: 0.7502 (m-90) REVERT: H 13 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8230 (tppt) REVERT: H 38 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7890 (ttp80) REVERT: H 100 ASP cc_start: 0.8172 (t0) cc_final: 0.7873 (t0) REVERT: H 100 LEU cc_start: 0.8250 (mp) cc_final: 0.7950 (mp) REVERT: I 42 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7339 (mp10) REVERT: D 80 ASN cc_start: 0.8528 (t0) cc_final: 0.8312 (t0) REVERT: E 633 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8634 (mtmm) REVERT: E 655 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8667 (tppp) REVERT: G 12 LYS cc_start: 0.8268 (mmmm) cc_final: 0.8004 (mtpp) REVERT: O 36 TYR cc_start: 0.6731 (m-80) cc_final: 0.6342 (m-80) REVERT: O 37 GLN cc_start: 0.5278 (OUTLIER) cc_final: 0.4890 (tm-30) REVERT: K 633 LYS cc_start: 0.8948 (tppt) cc_final: 0.8499 (mppt) REVERT: K 645 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9037 (mm) REVERT: K 659 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7914 (tm-30) REVERT: J 280 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.6813 (t0) REVERT: J 333 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8402 (tt) REVERT: J 475 MET cc_start: 0.8075 (mmt) cc_final: 0.7799 (mmt) REVERT: J 486 TYR cc_start: 0.8912 (m-10) cc_final: 0.8696 (m-10) REVERT: M 24 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8403 (pt) REVERT: M 66 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8438 (t0) REVERT: M 89 GLN cc_start: 0.8456 (mp10) cc_final: 0.8180 (mp10) REVERT: F 73 ASN cc_start: 0.8082 (t0) cc_final: 0.7781 (t0) REVERT: F 74 LEU cc_start: 0.8792 (tp) cc_final: 0.8417 (tp) REVERT: F 87 GLU cc_start: 0.7365 (mp0) cc_final: 0.7050 (mp0) outliers start: 50 outliers final: 33 residues processed: 304 average time/residue: 0.1514 time to fit residues: 71.6085 Evaluate side-chains 284 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 166 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 75 optimal weight: 0.0170 chunk 193 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068832 restraints weight = 62353.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070862 restraints weight = 37207.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.072186 restraints weight = 27162.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073050 restraints weight = 22224.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073542 restraints weight = 19514.762| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22421 Z= 0.176 Angle : 0.702 13.017 30645 Z= 0.347 Chirality : 0.046 0.396 3770 Planarity : 0.004 0.050 3672 Dihedral : 7.326 60.534 5381 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.51 % Allowed : 13.38 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.19 (0.17), residues: 2511 helix: 1.88 (0.25), residues: 450 sheet: 0.09 (0.19), residues: 772 loop : -0.99 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.026 0.002 TYR O 96 PHE 0.026 0.002 PHE H 29 TRP 0.054 0.002 TRP A 45 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00408 (22260) covalent geometry : angle 0.66593 (30201) SS BOND : bond 0.00287 ( 39) SS BOND : angle 1.37920 ( 78) hydrogen bonds : bond 0.04054 ( 836) hydrogen bonds : angle 5.41085 ( 2253) link_ALPHA1-2 : bond 0.00262 ( 5) link_ALPHA1-2 : angle 1.89532 ( 15) link_ALPHA1-3 : bond 0.01049 ( 6) link_ALPHA1-3 : angle 1.48997 ( 18) link_ALPHA1-6 : bond 0.00909 ( 4) link_ALPHA1-6 : angle 1.82865 ( 12) link_BETA1-4 : bond 0.00506 ( 50) link_BETA1-4 : angle 1.58084 ( 150) link_NAG-ASN : bond 0.00379 ( 57) link_NAG-ASN : angle 2.48912 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5164 (mtmm) REVERT: L 49 TYR cc_start: 0.6123 (t80) cc_final: 0.5893 (t80) REVERT: L 70 GLU cc_start: 0.8107 (mp0) cc_final: 0.7690 (mp0) REVERT: B 519 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 368 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7041 (t70) REVERT: A 479 TRP cc_start: 0.7910 (m-10) cc_final: 0.7531 (m-90) REVERT: H 100 ASP cc_start: 0.8074 (t0) cc_final: 0.7612 (t0) REVERT: H 100 LEU cc_start: 0.8320 (mp) cc_final: 0.8002 (mp) REVERT: E 633 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8580 (mtmm) REVERT: G 17 SER cc_start: 0.8696 (p) cc_final: 0.8333 (m) REVERT: O 36 TYR cc_start: 0.6814 (m-80) cc_final: 0.6505 (m-80) REVERT: O 37 GLN cc_start: 0.5778 (OUTLIER) cc_final: 0.5342 (tm-30) REVERT: J 280 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.6814 (t0) REVERT: J 333 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8453 (tt) REVERT: J 434 MET cc_start: 0.8268 (tmm) cc_final: 0.7852 (tmm) REVERT: J 475 MET cc_start: 0.8087 (mmt) cc_final: 0.7781 (mmt) REVERT: J 486 TYR cc_start: 0.8893 (m-10) cc_final: 0.8618 (m-10) REVERT: M 24 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8355 (pt) REVERT: M 66 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8299 (t0) REVERT: F 73 ASN cc_start: 0.7921 (t0) cc_final: 0.7670 (t0) REVERT: F 74 LEU cc_start: 0.8628 (tp) cc_final: 0.8352 (tp) REVERT: F 87 GLU cc_start: 0.7300 (mp0) cc_final: 0.6994 (mp0) outliers start: 56 outliers final: 41 residues processed: 281 average time/residue: 0.1463 time to fit residues: 64.8902 Evaluate side-chains 286 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 98 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 43 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 219 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069644 restraints weight = 62686.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072286 restraints weight = 37496.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072897 restraints weight = 25739.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073188 restraints weight = 22788.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073356 restraints weight = 21260.067| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22421 Z= 0.154 Angle : 0.692 14.459 30645 Z= 0.341 Chirality : 0.047 0.701 3770 Planarity : 0.004 0.046 3672 Dihedral : 7.139 59.840 5381 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.29 % Allowed : 13.60 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.16 (0.17), residues: 2511 helix: 1.98 (0.25), residues: 457 sheet: 0.09 (0.19), residues: 735 loop : -0.98 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.026 0.002 TYR O 96 PHE 0.026 0.002 PHE H 29 TRP 0.051 0.002 TRP A 45 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00355 (22260) covalent geometry : angle 0.65225 (30201) SS BOND : bond 0.00275 ( 39) SS BOND : angle 1.23918 ( 78) hydrogen bonds : bond 0.03887 ( 836) hydrogen bonds : angle 5.33895 ( 2253) link_ALPHA1-2 : bond 0.00231 ( 5) link_ALPHA1-2 : angle 1.82905 ( 15) link_ALPHA1-3 : bond 0.01036 ( 6) link_ALPHA1-3 : angle 1.38492 ( 18) link_ALPHA1-6 : bond 0.00922 ( 4) link_ALPHA1-6 : angle 1.65549 ( 12) link_BETA1-4 : bond 0.00501 ( 50) link_BETA1-4 : angle 1.52214 ( 150) link_NAG-ASN : bond 0.00374 ( 57) link_NAG-ASN : angle 2.67424 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5196 (mtmm) REVERT: L 70 GLU cc_start: 0.7940 (mp0) cc_final: 0.7594 (mp0) REVERT: B 519 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 629 MET cc_start: 0.8084 (mmm) cc_final: 0.7287 (mtt) REVERT: A 368 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7032 (t70) REVERT: A 479 TRP cc_start: 0.7830 (m-10) cc_final: 0.7474 (m-90) REVERT: H 55 ASP cc_start: 0.7696 (t0) cc_final: 0.7360 (m-30) REVERT: H 100 LEU cc_start: 0.8292 (mp) cc_final: 0.7985 (mp) REVERT: E 633 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8566 (mtmm) REVERT: G 83 ARG cc_start: 0.7352 (mtp-110) cc_final: 0.7133 (mtm110) REVERT: O 36 TYR cc_start: 0.6767 (m-80) cc_final: 0.6488 (m-80) REVERT: O 37 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5510 (tm-30) REVERT: J 280 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.6873 (t0) REVERT: J 333 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8437 (tt) REVERT: J 434 MET cc_start: 0.8252 (tmm) cc_final: 0.7791 (tmm) REVERT: J 475 MET cc_start: 0.8065 (mmt) cc_final: 0.7753 (mmt) REVERT: J 486 TYR cc_start: 0.8887 (m-10) cc_final: 0.8553 (m-10) REVERT: M 24 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8401 (pt) REVERT: M 66 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8298 (t0) REVERT: F 74 LEU cc_start: 0.8655 (tp) cc_final: 0.8401 (tp) REVERT: F 87 GLU cc_start: 0.7436 (mp0) cc_final: 0.7092 (mp0) outliers start: 51 outliers final: 35 residues processed: 278 average time/residue: 0.1542 time to fit residues: 67.1385 Evaluate side-chains 278 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068510 restraints weight = 62450.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070515 restraints weight = 37481.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071831 restraints weight = 27337.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.072685 restraints weight = 22447.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073254 restraints weight = 19734.225| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22421 Z= 0.189 Angle : 0.713 13.280 30645 Z= 0.353 Chirality : 0.047 0.519 3770 Planarity : 0.004 0.048 3672 Dihedral : 7.059 59.834 5381 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.97 % Allowed : 14.41 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.17), residues: 2511 helix: 1.96 (0.25), residues: 451 sheet: 0.12 (0.19), residues: 721 loop : -1.03 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.023 0.002 TYR O 96 PHE 0.025 0.002 PHE H 29 TRP 0.048 0.002 TRP A 45 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00437 (22260) covalent geometry : angle 0.67669 (30201) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.28265 ( 78) hydrogen bonds : bond 0.04012 ( 836) hydrogen bonds : angle 5.33203 ( 2253) link_ALPHA1-2 : bond 0.00266 ( 5) link_ALPHA1-2 : angle 1.87082 ( 15) link_ALPHA1-3 : bond 0.00954 ( 6) link_ALPHA1-3 : angle 1.47609 ( 18) link_ALPHA1-6 : bond 0.00907 ( 4) link_ALPHA1-6 : angle 1.62629 ( 12) link_BETA1-4 : bond 0.00486 ( 50) link_BETA1-4 : angle 1.54231 ( 150) link_NAG-ASN : bond 0.00390 ( 57) link_NAG-ASN : angle 2.58828 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 39 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5152 (mtmm) REVERT: L 49 TYR cc_start: 0.6124 (t80) cc_final: 0.5879 (t80) REVERT: L 70 GLU cc_start: 0.7885 (mp0) cc_final: 0.7625 (mp0) REVERT: B 519 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 629 MET cc_start: 0.8027 (mmm) cc_final: 0.7440 (mtt) REVERT: A 368 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7069 (t70) REVERT: A 479 TRP cc_start: 0.7882 (m-10) cc_final: 0.7484 (m-90) REVERT: H 38 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7776 (ttp80) REVERT: H 55 ASP cc_start: 0.7752 (t0) cc_final: 0.7456 (m-30) REVERT: H 100 ASP cc_start: 0.8080 (t0) cc_final: 0.7805 (t0) REVERT: G 79 TYR cc_start: 0.8745 (m-80) cc_final: 0.8510 (m-10) REVERT: O 36 TYR cc_start: 0.6842 (m-80) cc_final: 0.6481 (m-80) REVERT: O 37 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5451 (tm-30) REVERT: J 280 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.6932 (t0) REVERT: J 333 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (tt) REVERT: J 434 MET cc_start: 0.8206 (tmm) cc_final: 0.7810 (tmm) REVERT: J 475 MET cc_start: 0.8113 (mmt) cc_final: 0.7796 (mmt) REVERT: J 486 TYR cc_start: 0.8921 (m-10) cc_final: 0.8639 (m-10) REVERT: M 10 ASP cc_start: 0.8156 (t0) cc_final: 0.7813 (p0) REVERT: M 24 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8407 (pt) REVERT: M 66 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8247 (t0) REVERT: F 74 LEU cc_start: 0.8578 (tp) cc_final: 0.8353 (tp) REVERT: F 87 GLU cc_start: 0.7504 (mp0) cc_final: 0.7168 (mp0) outliers start: 44 outliers final: 34 residues processed: 262 average time/residue: 0.1419 time to fit residues: 58.7941 Evaluate side-chains 269 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain K residue 645 LEU Chi-restraints excluded: chain J residue 45 TRP Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 333 ILE Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain F residue 16 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 87 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 230 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069807 restraints weight = 62231.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071837 restraints weight = 37085.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073182 restraints weight = 26962.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074058 restraints weight = 21998.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074614 restraints weight = 19278.729| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22421 Z= 0.142 Angle : 0.685 12.367 30645 Z= 0.339 Chirality : 0.046 0.491 3770 Planarity : 0.004 0.046 3672 Dihedral : 6.840 59.499 5381 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.24 % Allowed : 14.68 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.11 (0.17), residues: 2511 helix: 2.19 (0.25), residues: 448 sheet: 0.14 (0.19), residues: 731 loop : -1.01 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 95B TYR 0.024 0.002 TYR N 90 PHE 0.025 0.001 PHE H 29 TRP 0.045 0.002 TRP A 45 HIS 0.005 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00326 (22260) covalent geometry : angle 0.65208 (30201) SS BOND : bond 0.00251 ( 39) SS BOND : angle 1.08825 ( 78) hydrogen bonds : bond 0.03706 ( 836) hydrogen bonds : angle 5.21776 ( 2253) link_ALPHA1-2 : bond 0.00247 ( 5) link_ALPHA1-2 : angle 1.86030 ( 15) link_ALPHA1-3 : bond 0.00987 ( 6) link_ALPHA1-3 : angle 1.33282 ( 18) link_ALPHA1-6 : bond 0.00935 ( 4) link_ALPHA1-6 : angle 1.50967 ( 12) link_BETA1-4 : bond 0.00499 ( 50) link_BETA1-4 : angle 1.46035 ( 150) link_NAG-ASN : bond 0.00328 ( 57) link_NAG-ASN : angle 2.43765 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.46 seconds wall clock time: 60 minutes 50.27 seconds (3650.27 seconds total)