Starting phenix.real_space_refine on Thu Feb 5 21:55:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rso_24676/02_2026/7rso_24676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rso_24676/02_2026/7rso_24676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rso_24676/02_2026/7rso_24676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rso_24676/02_2026/7rso_24676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rso_24676/02_2026/7rso_24676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rso_24676/02_2026/7rso_24676.map" } resolution = 4.1 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= 0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12888 2.51 5 N 3348 2.21 5 O 4212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3453 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.77, per 1000 atoms: 0.23 Number of scatterers: 20568 At special positions: 0 Unit cell: (146.72, 150.65, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4212 8.00 N 3348 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.06 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.06 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 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 F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN b 4 " - " MAN b 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA Q 3 " - " MAN Q 5 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 5 " " BMA n 3 " - " MAN n 6 " " BMA o 3 " - " MAN o 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " 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 k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " 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 197 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 230 " " NAG A 604 " - " ASN A 325 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 405 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 188 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 462 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 230 " " NAG C 604 " - " ASN C 325 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 405 " " NAG C 609 " - " ASN C 289 " " NAG C 610 " - " ASN C 188 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 462 " " NAG D 601 " - " ASN D 197 " " NAG D 602 " - " ASN D 88 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 325 " " NAG D 605 " - " ASN D 355 " " NAG D 606 " - " ASN D 392 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 405 " " NAG D 609 " - " ASN D 289 " " NAG D 610 " - " ASN D 188 " " NAG D 611 " - " ASN D 160 " " NAG D 612 " - " ASN D 462 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 625 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 339 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 295 " " NAG W 1 " - " ASN A 413 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN C 339 " " NAG f 1 " - " ASN C 386 " " NAG g 1 " - " ASN C 130 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 413 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN D 156 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 241 " " NAG n 1 " - " ASN D 262 " " NAG o 1 " - " ASN D 276 " " NAG p 1 " - " ASN D 448 " " NAG q 1 " - " ASN D 339 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 130 " " NAG t 1 " - " ASN D 295 " " NAG u 1 " - " ASN D 413 " " NAG v 1 " - " ASN D 332 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 864.7 milliseconds 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 23.3% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.787A pdb=" N GLN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.658A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.342A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.659A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.052A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 3.937A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.343A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.788A pdb=" N GLN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.521A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 99 through 100C Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'I' and resid 25 through 30 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 100C Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.209A pdb=" N ASN A 67 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS A 296 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.210A pdb=" N ASN C 67 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'C' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC7, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS C 296 " --> pdb=" O GLN C 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.399A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.209A pdb=" N ASN D 67 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 120 through 121 removed outlier: 6.261A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'D' and resid 154 through 162 Processing sheet with id=AE1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.481A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.808A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N VAL D 292 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N CYS D 296 " --> pdb=" O GLN D 442 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLN D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE D 468 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.565A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.638A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.740A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.632A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.564A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.986A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 1926 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: 3.22 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 6118 1.35 - 1.50: 7224 1.50 - 1.66: 7475 1.66 - 1.81: 108 1.81 - 1.97: 54 Bond restraints: 20979 Sorted by residual: bond pdb=" CB TYR G 100E" pdb=" CG TYR G 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.56e+01 bond pdb=" CB TYR I 100E" pdb=" CG TYR I 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.55e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.54e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 20974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 28391 7.28 - 14.56: 61 14.56 - 21.85: 0 21.85 - 29.13: 0 29.13 - 36.41: 6 Bond angle restraints: 28458 Sorted by residual: angle pdb=" C2 NAG C 609 " pdb=" N2 NAG C 609 " pdb=" C7 NAG C 609 " ideal model delta sigma weight residual 124.56 160.97 -36.41 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG D 609 " pdb=" N2 NAG D 609 " pdb=" C7 NAG D 609 " ideal model delta sigma weight residual 124.56 160.96 -36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG v 2 " pdb=" N2 NAG v 2 " pdb=" C7 NAG v 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C2 NAG j 2 " pdb=" N2 NAG j 2 " pdb=" C7 NAG j 2 " ideal model delta sigma weight residual 124.56 160.37 -35.81 3.00e+00 1.11e-01 1.42e+02 ... (remaining 28453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 13737 21.14 - 42.27: 360 42.27 - 63.40: 114 63.40 - 84.54: 90 84.54 - 105.67: 60 Dihedral angle restraints: 14361 sinusoidal: 7605 harmonic: 6756 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 74 " pdb=" CB CYS D 74 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 14358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2096 0.100 - 0.200: 813 0.200 - 0.300: 358 0.300 - 0.399: 195 0.399 - 0.499: 120 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.13e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.12e+02 ... (remaining 3579 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG p 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG R 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.211 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.163 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG d 1 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.211 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7714 2.91 - 3.40: 18478 3.40 - 3.90: 34610 3.90 - 4.40: 39772 4.40 - 4.90: 61451 Nonbonded interactions: 162025 Sorted by model distance: nonbonded pdb=" OD1 ASP C 113 " pdb=" NZ LYS C 432 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 432 " model vdw 2.407 3.120 nonbonded pdb=" OD1 ASP D 113 " pdb=" NZ LYS D 432 " model vdw 2.407 3.120 nonbonded pdb=" OE2 GLU A 290 " pdb=" NZ LYS A 337 " model vdw 2.429 3.120 nonbonded pdb=" OE2 GLU C 290 " pdb=" NZ LYS C 337 " model vdw 2.429 3.120 ... (remaining 162020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'W' selection = chain 'a' selection = chain 'i' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'c' selection = chain 'o' } 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: 0.010 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.220 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.024 0.164 21156 Z= 1.228 Angle : 1.900 36.410 28956 Z= 1.152 Chirality : 0.161 0.499 3582 Planarity : 0.009 0.133 3417 Dihedral : 14.246 105.674 9906 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.15 % Allowed : 0.87 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.79 (0.16), residues: 2307 helix: 0.03 (0.22), residues: 444 sheet: 0.89 (0.18), residues: 738 loop : 0.67 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.047 0.009 TYR I 100E PHE 0.036 0.005 PHE G 76 TRP 0.050 0.010 TRP K 35 HIS 0.008 0.003 HIS G 35A Details of bonding type rmsd covalent geometry : bond 0.02293 (20979) covalent geometry : angle 1.85268 (28458) SS BOND : bond 0.01027 ( 33) SS BOND : angle 3.35506 ( 66) hydrogen bonds : bond 0.18357 ( 735) hydrogen bonds : angle 7.38723 ( 1926) link_ALPHA1-2 : bond 0.07707 ( 3) link_ALPHA1-2 : angle 4.30365 ( 9) link_ALPHA1-3 : bond 0.08550 ( 6) link_ALPHA1-3 : angle 4.75559 ( 18) link_ALPHA1-6 : bond 0.05886 ( 6) link_ALPHA1-6 : angle 3.23750 ( 18) link_BETA1-4 : bond 0.07711 ( 48) link_BETA1-4 : angle 5.05283 ( 144) link_NAG-ASN : bond 0.08409 ( 81) link_NAG-ASN : angle 2.63756 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 899 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7636 (ptm) cc_final: 0.7141 (ptm) REVERT: A 98 ASN cc_start: 0.8542 (t0) cc_final: 0.7524 (m-40) REVERT: A 100 MET cc_start: 0.7323 (mtp) cc_final: 0.6822 (ttm) REVERT: A 110 SER cc_start: 0.9470 (m) cc_final: 0.9136 (t) REVERT: A 129 LEU cc_start: 0.9263 (mt) cc_final: 0.8768 (mp) REVERT: A 131 CYS cc_start: 0.5903 (p) cc_final: 0.5649 (p) REVERT: A 338 TRP cc_start: 0.9110 (t-100) cc_final: 0.8732 (t-100) REVERT: A 377 ASN cc_start: 0.8320 (t0) cc_final: 0.8068 (t0) REVERT: B 584 GLU cc_start: 0.8891 (tt0) cc_final: 0.8666 (tt0) REVERT: B 601 LYS cc_start: 0.8816 (mttt) cc_final: 0.8610 (mtmm) REVERT: B 634 GLU cc_start: 0.8132 (tt0) cc_final: 0.7622 (tp30) REVERT: H 9 SER cc_start: 0.8153 (m) cc_final: 0.7824 (p) REVERT: H 33 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7345 (mp0) REVERT: H 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.7908 (tt0) REVERT: H 100 TRP cc_start: 0.8294 (m-10) cc_final: 0.7922 (m-10) REVERT: H 108 LEU cc_start: 0.9201 (tp) cc_final: 0.8995 (tp) REVERT: L 78 MET cc_start: 0.8379 (mmm) cc_final: 0.8116 (mmm) REVERT: L 96 GLU cc_start: 0.8311 (pt0) cc_final: 0.7609 (pt0) REVERT: C 95 MET cc_start: 0.8138 (ptm) cc_final: 0.7348 (ptm) REVERT: C 98 ASN cc_start: 0.8340 (t0) cc_final: 0.7289 (m110) REVERT: C 100 MET cc_start: 0.7952 (mtp) cc_final: 0.7316 (ttm) REVERT: C 110 SER cc_start: 0.9462 (m) cc_final: 0.9186 (t) REVERT: C 297 THR cc_start: 0.9273 (m) cc_final: 0.9017 (p) REVERT: C 377 ASN cc_start: 0.8348 (t0) cc_final: 0.8067 (t0) REVERT: C 427 TRP cc_start: 0.8415 (m-90) cc_final: 0.8078 (m-90) REVERT: C 474 ASP cc_start: 0.7449 (t0) cc_final: 0.7199 (t0) REVERT: E 540 GLN cc_start: 0.8320 (mm110) cc_final: 0.7839 (mm-40) REVERT: E 590 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9043 (tp40) REVERT: E 592 LEU cc_start: 0.9399 (tp) cc_final: 0.9146 (mt) REVERT: E 593 LEU cc_start: 0.8957 (mt) cc_final: 0.8709 (mm) REVERT: E 601 LYS cc_start: 0.8919 (mttt) cc_final: 0.8628 (mtmm) REVERT: E 616 ASN cc_start: 0.8100 (p0) cc_final: 0.7812 (p0) REVERT: E 634 GLU cc_start: 0.7871 (tt0) cc_final: 0.7505 (tp30) REVERT: E 639 THR cc_start: 0.8550 (m) cc_final: 0.8265 (p) REVERT: D 95 MET cc_start: 0.7950 (ptm) cc_final: 0.7670 (ptm) REVERT: D 98 ASN cc_start: 0.8295 (t0) cc_final: 0.7316 (m110) REVERT: D 104 MET cc_start: 0.8444 (ttm) cc_final: 0.7832 (tpp) REVERT: D 110 SER cc_start: 0.9344 (m) cc_final: 0.9019 (t) REVERT: D 165 VAL cc_start: 0.7750 (t) cc_final: 0.7513 (t) REVERT: D 217 TYR cc_start: 0.8133 (m-80) cc_final: 0.7189 (m-80) REVERT: D 352 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8413 (mm-40) REVERT: D 371 ILE cc_start: 0.8501 (mm) cc_final: 0.8201 (mm) REVERT: D 377 ASN cc_start: 0.8574 (t0) cc_final: 0.8155 (t0) REVERT: F 540 GLN cc_start: 0.8257 (mm110) cc_final: 0.7681 (mm-40) REVERT: F 601 LYS cc_start: 0.8918 (mttt) cc_final: 0.8499 (mttm) REVERT: F 634 GLU cc_start: 0.8339 (tt0) cc_final: 0.7926 (tp30) REVERT: G 36 TRP cc_start: 0.9295 (m100) cc_final: 0.8609 (m100) REVERT: G 89 THR cc_start: 0.9350 (m) cc_final: 0.8932 (p) REVERT: G 99 THR cc_start: 0.6348 (p) cc_final: 0.6077 (p) REVERT: G 100 GLN cc_start: 0.8285 (tt0) cc_final: 0.7561 (tt0) REVERT: J 33 MET cc_start: 0.8009 (ttm) cc_final: 0.7446 (mpp) REVERT: I 33 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7311 (mp0) REVERT: I 57 ASN cc_start: 0.9065 (t0) cc_final: 0.8804 (t0) REVERT: I 89 THR cc_start: 0.9405 (m) cc_final: 0.8984 (p) REVERT: I 100 GLN cc_start: 0.8392 (tt0) cc_final: 0.8114 (tt0) REVERT: K 96 GLU cc_start: 0.8508 (pt0) cc_final: 0.8290 (pt0) outliers start: 3 outliers final: 0 residues processed: 902 average time/residue: 0.1694 time to fit residues: 224.0655 Evaluate side-chains 455 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN H 57 ASN L 32 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN E 575 GLN E 653 GLN D 99 ASN D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 32 HIS J 42 GLN I 39 GLN I 95 GLN K 6 GLN K 32 HIS K 42 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102293 restraints weight = 42726.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105652 restraints weight = 27711.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107906 restraints weight = 21037.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109403 restraints weight = 17598.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110425 restraints weight = 15647.915| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21156 Z= 0.196 Angle : 0.894 22.095 28956 Z= 0.426 Chirality : 0.057 0.842 3582 Planarity : 0.006 0.059 3417 Dihedral : 11.621 80.724 5478 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.19 % Allowed : 3.00 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.67 (0.17), residues: 2307 helix: 1.10 (0.23), residues: 432 sheet: 0.54 (0.18), residues: 777 loop : 0.25 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 31 TYR 0.034 0.002 TYR E 643 PHE 0.034 0.002 PHE I 58 TRP 0.019 0.002 TRP C 112 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00413 (20979) covalent geometry : angle 0.78725 (28458) SS BOND : bond 0.00348 ( 33) SS BOND : angle 1.04873 ( 66) hydrogen bonds : bond 0.05769 ( 735) hydrogen bonds : angle 6.22939 ( 1926) link_ALPHA1-2 : bond 0.01499 ( 3) link_ALPHA1-2 : angle 2.13667 ( 9) link_ALPHA1-3 : bond 0.01946 ( 6) link_ALPHA1-3 : angle 1.60116 ( 18) link_ALPHA1-6 : bond 0.00980 ( 6) link_ALPHA1-6 : angle 1.56844 ( 18) link_BETA1-4 : bond 0.01179 ( 48) link_BETA1-4 : angle 3.06374 ( 144) link_NAG-ASN : bond 0.00907 ( 81) link_NAG-ASN : angle 4.02614 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 632 time to evaluate : 0.760 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: A 78 ASP cc_start: 0.8218 (m-30) cc_final: 0.7466 (p0) REVERT: A 104 MET cc_start: 0.8457 (tpp) cc_final: 0.6961 (tpp) REVERT: A 217 TYR cc_start: 0.7576 (m-80) cc_final: 0.6647 (m-80) REVERT: A 302 ASN cc_start: 0.8437 (m110) cc_final: 0.8134 (m-40) REVERT: A 333 ILE cc_start: 0.9233 (mt) cc_final: 0.8923 (tp) REVERT: A 414 ILE cc_start: 0.8808 (mt) cc_final: 0.8572 (mt) REVERT: B 634 GLU cc_start: 0.8315 (tt0) cc_final: 0.7941 (tp30) REVERT: B 644 ASN cc_start: 0.8030 (m110) cc_final: 0.7775 (m-40) REVERT: B 653 GLN cc_start: 0.8922 (tm130) cc_final: 0.8169 (tm-30) REVERT: H 33 GLU cc_start: 0.7705 (mm-30) cc_final: 0.6549 (mp0) REVERT: H 39 GLN cc_start: 0.8828 (tp40) cc_final: 0.8622 (tp40) REVERT: H 89 THR cc_start: 0.9113 (m) cc_final: 0.8738 (p) REVERT: H 100 TRP cc_start: 0.8032 (m-10) cc_final: 0.7817 (m-10) REVERT: H 108 LEU cc_start: 0.9276 (tp) cc_final: 0.9042 (tp) REVERT: L 5 THR cc_start: 0.7879 (m) cc_final: 0.7146 (p) REVERT: L 17 GLU cc_start: 0.7894 (pt0) cc_final: 0.7529 (pm20) REVERT: L 96 GLU cc_start: 0.8220 (pt0) cc_final: 0.7487 (pt0) REVERT: C 95 MET cc_start: 0.8060 (ptm) cc_final: 0.7839 (ptm) REVERT: C 217 TYR cc_start: 0.7834 (m-10) cc_final: 0.7597 (m-10) REVERT: C 430 VAL cc_start: 0.8895 (t) cc_final: 0.8630 (m) REVERT: E 539 VAL cc_start: 0.9212 (t) cc_final: 0.8905 (p) REVERT: E 540 GLN cc_start: 0.8471 (mm110) cc_final: 0.7627 (mm-40) REVERT: E 601 LYS cc_start: 0.8703 (mttt) cc_final: 0.8253 (mtmm) REVERT: E 616 ASN cc_start: 0.7957 (p0) cc_final: 0.7545 (p0) REVERT: E 634 GLU cc_start: 0.8316 (tt0) cc_final: 0.7813 (tp30) REVERT: E 639 THR cc_start: 0.8929 (m) cc_final: 0.8203 (p) REVERT: E 653 GLN cc_start: 0.8466 (tm130) cc_final: 0.8136 (tm-30) REVERT: D 69 TRP cc_start: 0.6181 (p-90) cc_final: 0.5327 (p-90) REVERT: D 78 ASP cc_start: 0.8335 (m-30) cc_final: 0.7386 (p0) REVERT: D 111 LEU cc_start: 0.8873 (tp) cc_final: 0.8360 (tp) REVERT: D 180 ASP cc_start: 0.8559 (m-30) cc_final: 0.8298 (m-30) REVERT: D 217 TYR cc_start: 0.7866 (m-80) cc_final: 0.7044 (m-80) REVERT: D 373 MET cc_start: 0.8401 (mtm) cc_final: 0.8187 (mtm) REVERT: D 430 VAL cc_start: 0.8946 (t) cc_final: 0.8740 (m) REVERT: F 540 GLN cc_start: 0.8415 (mm110) cc_final: 0.7551 (mm-40) REVERT: F 584 GLU cc_start: 0.8653 (tt0) cc_final: 0.8410 (tt0) REVERT: F 601 LYS cc_start: 0.8670 (mttt) cc_final: 0.8174 (mttm) REVERT: F 634 GLU cc_start: 0.8533 (tt0) cc_final: 0.8192 (tp30) REVERT: F 644 ASN cc_start: 0.8297 (m110) cc_final: 0.7725 (m110) REVERT: G 26 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7541 (tm-30) REVERT: G 33 GLU cc_start: 0.8348 (mm-30) cc_final: 0.6417 (mp0) REVERT: G 36 TRP cc_start: 0.9131 (m100) cc_final: 0.8313 (m100) REVERT: G 39 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8189 (tm-30) REVERT: G 45 LEU cc_start: 0.7755 (mp) cc_final: 0.7508 (mp) REVERT: G 50 TRP cc_start: 0.9115 (p-90) cc_final: 0.8459 (p-90) REVERT: G 86 ASP cc_start: 0.8113 (m-30) cc_final: 0.7585 (t0) REVERT: G 89 THR cc_start: 0.9116 (m) cc_final: 0.8675 (p) REVERT: G 99 THR cc_start: 0.6008 (p) cc_final: 0.5749 (p) REVERT: G 108 LEU cc_start: 0.9288 (tp) cc_final: 0.8943 (tp) REVERT: J 33 MET cc_start: 0.8014 (ttm) cc_final: 0.7773 (mtt) REVERT: J 37 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7962 (pp30) REVERT: J 81 GLU cc_start: 0.8903 (tt0) cc_final: 0.8607 (tm-30) REVERT: J 96 GLU cc_start: 0.8453 (pt0) cc_final: 0.7817 (pt0) REVERT: I 33 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7035 (mp0) REVERT: I 50 TRP cc_start: 0.9189 (p-90) cc_final: 0.8751 (p-90) REVERT: I 89 THR cc_start: 0.9208 (m) cc_final: 0.8748 (p) REVERT: I 99 THR cc_start: 0.6204 (p) cc_final: 0.5330 (t) REVERT: I 100 GLN cc_start: 0.8041 (tt0) cc_final: 0.7366 (tt0) REVERT: I 108 LEU cc_start: 0.9298 (tp) cc_final: 0.8974 (tp) REVERT: K 5 THR cc_start: 0.7477 (m) cc_final: 0.6777 (p) REVERT: K 81 GLU cc_start: 0.8818 (tt0) cc_final: 0.8488 (tm-30) REVERT: K 82 ASP cc_start: 0.8392 (m-30) cc_final: 0.8124 (m-30) REVERT: K 96 GLU cc_start: 0.8500 (pt0) cc_final: 0.8232 (pt0) outliers start: 4 outliers final: 3 residues processed: 635 average time/residue: 0.1355 time to fit residues: 133.9582 Evaluate side-chains 468 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 465 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 46 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 70 GLN C 374 HIS E 575 GLN D 374 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 70 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.127401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099503 restraints weight = 43451.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102878 restraints weight = 27122.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105159 restraints weight = 20138.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106676 restraints weight = 16627.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107580 restraints weight = 14637.081| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21156 Z= 0.174 Angle : 0.777 17.915 28956 Z= 0.376 Chirality : 0.053 0.672 3582 Planarity : 0.005 0.055 3417 Dihedral : 9.990 73.931 5478 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.24 % Allowed : 2.81 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.52 (0.17), residues: 2307 helix: 0.91 (0.24), residues: 432 sheet: 0.70 (0.18), residues: 762 loop : -0.03 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 103 TYR 0.036 0.002 TYR E 643 PHE 0.026 0.002 PHE A 233 TRP 0.019 0.002 TRP I 36 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00375 (20979) covalent geometry : angle 0.69422 (28458) SS BOND : bond 0.00428 ( 33) SS BOND : angle 1.13815 ( 66) hydrogen bonds : bond 0.05149 ( 735) hydrogen bonds : angle 5.85890 ( 1926) link_ALPHA1-2 : bond 0.01040 ( 3) link_ALPHA1-2 : angle 2.45212 ( 9) link_ALPHA1-3 : bond 0.01437 ( 6) link_ALPHA1-3 : angle 1.15937 ( 18) link_ALPHA1-6 : bond 0.01005 ( 6) link_ALPHA1-6 : angle 1.70141 ( 18) link_BETA1-4 : bond 0.00878 ( 48) link_BETA1-4 : angle 2.51450 ( 144) link_NAG-ASN : bond 0.00654 ( 81) link_NAG-ASN : angle 3.29748 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 573 time to evaluate : 0.808 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: A 69 TRP cc_start: 0.6573 (p-90) cc_final: 0.6080 (p-90) REVERT: A 78 ASP cc_start: 0.8180 (m-30) cc_final: 0.7468 (p0) REVERT: A 292 VAL cc_start: 0.8556 (t) cc_final: 0.8040 (t) REVERT: A 333 ILE cc_start: 0.9233 (mt) cc_final: 0.8872 (tp) REVERT: A 414 ILE cc_start: 0.8768 (mt) cc_final: 0.8387 (mp) REVERT: B 584 GLU cc_start: 0.8755 (tt0) cc_final: 0.8427 (tt0) REVERT: B 634 GLU cc_start: 0.8730 (tt0) cc_final: 0.8479 (tt0) REVERT: B 644 ASN cc_start: 0.8138 (m110) cc_final: 0.7842 (m-40) REVERT: H 33 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6811 (mp0) REVERT: H 50 TRP cc_start: 0.9185 (p-90) cc_final: 0.8447 (p-90) REVERT: H 100 GLN cc_start: 0.7537 (tt0) cc_final: 0.7252 (tm-30) REVERT: H 100 TRP cc_start: 0.8341 (m-10) cc_final: 0.7698 (m-10) REVERT: L 3 VAL cc_start: 0.8880 (t) cc_final: 0.8538 (t) REVERT: L 27 SER cc_start: 0.7334 (t) cc_final: 0.7058 (t) REVERT: L 30 TYR cc_start: 0.6951 (m-80) cc_final: 0.6374 (m-10) REVERT: L 37 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7969 (pp30) REVERT: L 42 GLN cc_start: 0.8445 (tp40) cc_final: 0.8183 (tp-100) REVERT: L 78 MET cc_start: 0.8125 (tpp) cc_final: 0.7718 (tpp) REVERT: L 96 GLU cc_start: 0.8274 (pt0) cc_final: 0.7951 (pt0) REVERT: C 95 MET cc_start: 0.8009 (ptm) cc_final: 0.7767 (ptm) REVERT: C 217 TYR cc_start: 0.8026 (m-10) cc_final: 0.7602 (m-10) REVERT: C 426 LEU cc_start: 0.8546 (mt) cc_final: 0.8328 (mt) REVERT: C 430 VAL cc_start: 0.8635 (t) cc_final: 0.8377 (m) REVERT: E 530 MET cc_start: 0.8883 (mmm) cc_final: 0.8522 (tpt) REVERT: E 539 VAL cc_start: 0.9281 (t) cc_final: 0.9072 (t) REVERT: E 540 GLN cc_start: 0.8528 (mm110) cc_final: 0.7651 (mm-40) REVERT: E 601 LYS cc_start: 0.8637 (mttt) cc_final: 0.8173 (mtmm) REVERT: E 616 ASN cc_start: 0.8005 (p0) cc_final: 0.7630 (p0) REVERT: E 634 GLU cc_start: 0.8416 (tt0) cc_final: 0.7965 (tp30) REVERT: E 638 TYR cc_start: 0.7182 (m-80) cc_final: 0.6920 (m-80) REVERT: E 639 THR cc_start: 0.8989 (m) cc_final: 0.8275 (p) REVERT: E 643 TYR cc_start: 0.9011 (m-80) cc_final: 0.8777 (m-80) REVERT: D 53 PHE cc_start: 0.8361 (p90) cc_final: 0.7978 (p90) REVERT: D 69 TRP cc_start: 0.6297 (p-90) cc_final: 0.5160 (p-90) REVERT: D 111 LEU cc_start: 0.8919 (tp) cc_final: 0.8449 (tp) REVERT: D 180 ASP cc_start: 0.8487 (m-30) cc_final: 0.8277 (m-30) REVERT: D 217 TYR cc_start: 0.8062 (m-80) cc_final: 0.7482 (m-80) REVERT: D 373 MET cc_start: 0.8451 (mtm) cc_final: 0.8228 (mtm) REVERT: D 434 MET cc_start: 0.7934 (ttp) cc_final: 0.7700 (ttp) REVERT: F 530 MET cc_start: 0.8758 (mmm) cc_final: 0.8472 (tpp) REVERT: F 540 GLN cc_start: 0.8498 (mm110) cc_final: 0.7440 (mm-40) REVERT: F 617 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8444 (ttmt) REVERT: F 621 ASN cc_start: 0.8627 (t0) cc_final: 0.7976 (t0) REVERT: F 634 GLU cc_start: 0.8553 (tt0) cc_final: 0.7981 (tp30) REVERT: F 643 TYR cc_start: 0.8791 (m-80) cc_final: 0.8513 (m-80) REVERT: G 26 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7752 (tm-30) REVERT: G 36 TRP cc_start: 0.9115 (m100) cc_final: 0.8179 (m100) REVERT: G 39 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8128 (tm-30) REVERT: G 45 LEU cc_start: 0.7773 (mp) cc_final: 0.7491 (mp) REVERT: G 50 TRP cc_start: 0.9147 (p-90) cc_final: 0.8502 (p-90) REVERT: G 86 ASP cc_start: 0.8297 (m-30) cc_final: 0.7967 (t0) REVERT: G 89 THR cc_start: 0.9183 (m) cc_final: 0.8648 (p) REVERT: G 96 LYS cc_start: 0.7097 (pttp) cc_final: 0.6415 (pttp) REVERT: G 99 THR cc_start: 0.5906 (p) cc_final: 0.5019 (p) REVERT: G 101 ASP cc_start: 0.7774 (t70) cc_final: 0.7396 (t70) REVERT: G 108 LEU cc_start: 0.9193 (tp) cc_final: 0.8923 (tp) REVERT: J 3 VAL cc_start: 0.8798 (t) cc_final: 0.8413 (t) REVERT: J 42 GLN cc_start: 0.8346 (tp40) cc_final: 0.8120 (tp-100) REVERT: I 46 GLU cc_start: 0.8217 (tp30) cc_final: 0.7087 (mm-30) REVERT: I 50 TRP cc_start: 0.9222 (p-90) cc_final: 0.8593 (p-90) REVERT: I 81 ASP cc_start: 0.8036 (m-30) cc_final: 0.7784 (m-30) REVERT: I 89 THR cc_start: 0.9142 (m) cc_final: 0.8712 (p) REVERT: I 99 THR cc_start: 0.6482 (p) cc_final: 0.5339 (t) REVERT: I 100 GLN cc_start: 0.7886 (tt0) cc_final: 0.7622 (tt0) REVERT: I 108 LEU cc_start: 0.9279 (tp) cc_final: 0.9076 (tp) REVERT: K 3 VAL cc_start: 0.8877 (t) cc_final: 0.8624 (t) REVERT: K 5 THR cc_start: 0.7609 (m) cc_final: 0.6845 (p) REVERT: K 17 GLU cc_start: 0.8802 (pt0) cc_final: 0.8038 (pm20) REVERT: K 37 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8039 (tm-30) REVERT: K 81 GLU cc_start: 0.8940 (tt0) cc_final: 0.8518 (tm-30) REVERT: K 82 ASP cc_start: 0.8581 (m-30) cc_final: 0.8068 (m-30) REVERT: K 103 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8160 (ttm110) outliers start: 5 outliers final: 0 residues processed: 576 average time/residue: 0.1389 time to fit residues: 123.7232 Evaluate side-chains 427 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 203 optimal weight: 0.2980 chunk 208 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 88 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 330 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN B 656 ASN L 32 HIS L 70 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 330 HIS E 653 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 330 HIS F 575 GLN J 32 HIS J 42 GLN J 70 GLN J 90 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.123864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094811 restraints weight = 44006.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098016 restraints weight = 30683.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099704 restraints weight = 22534.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100194 restraints weight = 19396.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100485 restraints weight = 18859.766| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21156 Z= 0.207 Angle : 0.762 14.840 28956 Z= 0.372 Chirality : 0.051 0.562 3582 Planarity : 0.005 0.060 3417 Dihedral : 8.761 64.921 5478 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.24 % Allowed : 1.84 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.34 (0.17), residues: 2307 helix: 0.87 (0.24), residues: 450 sheet: 0.86 (0.20), residues: 687 loop : -0.37 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 103 TYR 0.030 0.002 TYR E 643 PHE 0.023 0.002 PHE A 233 TRP 0.023 0.002 TRP F 610 HIS 0.009 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00463 (20979) covalent geometry : angle 0.70381 (28458) SS BOND : bond 0.00665 ( 33) SS BOND : angle 1.19168 ( 66) hydrogen bonds : bond 0.05068 ( 735) hydrogen bonds : angle 5.68137 ( 1926) link_ALPHA1-2 : bond 0.00846 ( 3) link_ALPHA1-2 : angle 2.28884 ( 9) link_ALPHA1-3 : bond 0.01237 ( 6) link_ALPHA1-3 : angle 1.95610 ( 18) link_ALPHA1-6 : bond 0.01158 ( 6) link_ALPHA1-6 : angle 1.83109 ( 18) link_BETA1-4 : bond 0.00732 ( 48) link_BETA1-4 : angle 2.16508 ( 144) link_NAG-ASN : bond 0.00525 ( 81) link_NAG-ASN : angle 2.69451 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 508 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6409 (p-90) cc_final: 0.5476 (p-90) REVERT: A 78 ASP cc_start: 0.8268 (m-30) cc_final: 0.7526 (p0) REVERT: A 111 LEU cc_start: 0.8926 (mt) cc_final: 0.8675 (mt) REVERT: A 333 ILE cc_start: 0.9229 (mt) cc_final: 0.8999 (tp) REVERT: A 414 ILE cc_start: 0.8655 (mt) cc_final: 0.8304 (mp) REVERT: A 466 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 584 GLU cc_start: 0.8791 (tt0) cc_final: 0.8576 (tt0) REVERT: B 631 TRP cc_start: 0.9023 (t-100) cc_final: 0.8777 (t-100) REVERT: B 634 GLU cc_start: 0.8787 (tt0) cc_final: 0.8393 (tt0) REVERT: B 647 GLU cc_start: 0.8666 (pt0) cc_final: 0.8147 (pp20) REVERT: B 653 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: H 33 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7373 (mt-10) REVERT: H 89 THR cc_start: 0.9300 (m) cc_final: 0.8880 (p) REVERT: H 100 GLN cc_start: 0.7772 (tt0) cc_final: 0.7449 (tm-30) REVERT: H 108 LEU cc_start: 0.9394 (tp) cc_final: 0.9170 (tp) REVERT: L 42 GLN cc_start: 0.8482 (tp40) cc_final: 0.8266 (tp-100) REVERT: L 47 LEU cc_start: 0.8659 (mt) cc_final: 0.8440 (mm) REVERT: L 60 ASP cc_start: 0.8587 (t0) cc_final: 0.8320 (t70) REVERT: L 86 TYR cc_start: 0.8409 (m-80) cc_final: 0.7336 (m-80) REVERT: C 348 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8032 (mmtm) REVERT: C 373 MET cc_start: 0.8744 (mtm) cc_final: 0.8506 (mtm) REVERT: C 430 VAL cc_start: 0.8745 (t) cc_final: 0.8510 (m) REVERT: E 601 LYS cc_start: 0.8704 (mttt) cc_final: 0.8229 (mtmm) REVERT: E 634 GLU cc_start: 0.8516 (tt0) cc_final: 0.8010 (tp30) REVERT: E 639 THR cc_start: 0.9120 (m) cc_final: 0.8369 (p) REVERT: E 651 ASN cc_start: 0.8261 (t0) cc_final: 0.8037 (t0) REVERT: D 53 PHE cc_start: 0.8592 (p90) cc_final: 0.8348 (p90) REVERT: D 414 ILE cc_start: 0.8799 (mt) cc_final: 0.8450 (tp) REVERT: D 466 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8105 (mm-30) REVERT: F 617 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8323 (ttmt) REVERT: F 621 ASN cc_start: 0.8575 (t0) cc_final: 0.8031 (t0) REVERT: F 634 GLU cc_start: 0.8652 (tt0) cc_final: 0.8039 (tp30) REVERT: G 26 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7596 (tm-30) REVERT: G 36 TRP cc_start: 0.9121 (m100) cc_final: 0.8165 (m100) REVERT: G 46 GLU cc_start: 0.8378 (tp30) cc_final: 0.7193 (mm-30) REVERT: G 86 ASP cc_start: 0.8400 (m-30) cc_final: 0.8107 (m-30) REVERT: G 96 LYS cc_start: 0.7186 (pttp) cc_final: 0.6981 (tptt) REVERT: G 98 TYR cc_start: 0.4355 (t80) cc_final: 0.3904 (t80) REVERT: G 108 LEU cc_start: 0.9323 (tp) cc_final: 0.9091 (tp) REVERT: J 5 THR cc_start: 0.7709 (m) cc_final: 0.6957 (p) REVERT: J 34 THR cc_start: 0.9206 (m) cc_final: 0.8635 (p) REVERT: J 42 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8202 (tp-100) REVERT: J 60 ASP cc_start: 0.7975 (t70) cc_final: 0.7070 (t70) REVERT: J 96 GLU cc_start: 0.8523 (pt0) cc_final: 0.8199 (pt0) REVERT: I 26 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7900 (tm-30) REVERT: I 39 GLN cc_start: 0.8725 (tp40) cc_final: 0.7838 (tp40) REVERT: I 89 THR cc_start: 0.9161 (m) cc_final: 0.8640 (p) REVERT: I 108 LEU cc_start: 0.9335 (tp) cc_final: 0.9069 (tp) REVERT: K 5 THR cc_start: 0.7572 (m) cc_final: 0.6893 (p) REVERT: K 37 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7286 (tm-30) REVERT: K 65 SER cc_start: 0.9122 (t) cc_final: 0.8675 (t) REVERT: K 81 GLU cc_start: 0.9219 (tt0) cc_final: 0.8748 (tm-30) REVERT: K 82 ASP cc_start: 0.8610 (m-30) cc_final: 0.7912 (m-30) REVERT: K 103 ARG cc_start: 0.8453 (ttm110) cc_final: 0.8250 (ttm110) outliers start: 5 outliers final: 0 residues processed: 511 average time/residue: 0.1246 time to fit residues: 101.1524 Evaluate side-chains 415 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 173 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN L 90 GLN C 203 GLN E 540 GLN D 203 GLN D 374 HIS F 656 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 70 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.123569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093898 restraints weight = 43581.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.097006 restraints weight = 28203.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099070 restraints weight = 21563.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100463 restraints weight = 18207.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101306 restraints weight = 16288.897| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21156 Z= 0.166 Angle : 0.695 7.727 28956 Z= 0.342 Chirality : 0.048 0.304 3582 Planarity : 0.005 0.065 3417 Dihedral : 8.059 59.479 5478 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.29 % Allowed : 1.74 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2307 helix: 1.02 (0.24), residues: 441 sheet: 0.45 (0.19), residues: 759 loop : -0.42 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 103 TYR 0.022 0.002 TYR D 384 PHE 0.027 0.002 PHE H 58 TRP 0.031 0.002 TRP I 36 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00370 (20979) covalent geometry : angle 0.65111 (28458) SS BOND : bond 0.00407 ( 33) SS BOND : angle 1.18881 ( 66) hydrogen bonds : bond 0.04700 ( 735) hydrogen bonds : angle 5.50440 ( 1926) link_ALPHA1-2 : bond 0.00827 ( 3) link_ALPHA1-2 : angle 2.33235 ( 9) link_ALPHA1-3 : bond 0.01261 ( 6) link_ALPHA1-3 : angle 2.15025 ( 18) link_ALPHA1-6 : bond 0.01141 ( 6) link_ALPHA1-6 : angle 1.85214 ( 18) link_BETA1-4 : bond 0.00623 ( 48) link_BETA1-4 : angle 1.81470 ( 144) link_NAG-ASN : bond 0.00368 ( 81) link_NAG-ASN : angle 2.19207 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 505 time to evaluate : 0.611 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: A 78 ASP cc_start: 0.8241 (m-30) cc_final: 0.7527 (p0) REVERT: A 98 ASN cc_start: 0.8234 (t0) cc_final: 0.7958 (t0) REVERT: A 211 GLU cc_start: 0.8329 (mp0) cc_final: 0.8068 (mp0) REVERT: A 414 ILE cc_start: 0.8605 (mt) cc_final: 0.8263 (mp) REVERT: A 425 ASN cc_start: 0.7910 (t0) cc_final: 0.7689 (t0) REVERT: A 466 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7840 (mm-30) REVERT: B 584 GLU cc_start: 0.8909 (tt0) cc_final: 0.8315 (tp30) REVERT: B 631 TRP cc_start: 0.8648 (t-100) cc_final: 0.8234 (t-100) REVERT: B 634 GLU cc_start: 0.8818 (tt0) cc_final: 0.8256 (tt0) REVERT: B 647 GLU cc_start: 0.8654 (pt0) cc_final: 0.8073 (pp20) REVERT: H 31 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.7091 (tpm170) REVERT: H 50 TRP cc_start: 0.9340 (p-90) cc_final: 0.8720 (p-90) REVERT: H 89 THR cc_start: 0.9241 (m) cc_final: 0.8848 (p) REVERT: H 100 GLN cc_start: 0.7682 (tt0) cc_final: 0.7301 (tm-30) REVERT: H 108 LEU cc_start: 0.9379 (tp) cc_final: 0.9151 (tp) REVERT: L 17 GLU cc_start: 0.8284 (pt0) cc_final: 0.7671 (pm20) REVERT: L 42 GLN cc_start: 0.8494 (tp40) cc_final: 0.8244 (tp-100) REVERT: L 46 LEU cc_start: 0.8420 (pt) cc_final: 0.8135 (pp) REVERT: L 60 ASP cc_start: 0.8539 (t0) cc_final: 0.8339 (t70) REVERT: C 203 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.9137 (pp30) REVERT: C 373 MET cc_start: 0.8828 (mtm) cc_final: 0.8572 (mtm) REVERT: C 430 VAL cc_start: 0.8793 (t) cc_final: 0.8561 (m) REVERT: C 474 ASP cc_start: 0.7628 (t0) cc_final: 0.7412 (t0) REVERT: E 601 LYS cc_start: 0.8733 (mttt) cc_final: 0.8276 (mtmm) REVERT: E 634 GLU cc_start: 0.8552 (tt0) cc_final: 0.8038 (tp30) REVERT: D 95 MET cc_start: 0.7888 (ptm) cc_final: 0.7328 (ppp) REVERT: D 203 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (pp30) REVERT: D 434 MET cc_start: 0.7874 (ttp) cc_final: 0.7626 (ttp) REVERT: D 466 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8057 (mm-30) REVERT: F 621 ASN cc_start: 0.8624 (t0) cc_final: 0.8015 (t0) REVERT: F 634 GLU cc_start: 0.8627 (tt0) cc_final: 0.8391 (tm-30) REVERT: G 26 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7806 (tm-30) REVERT: G 36 TRP cc_start: 0.9127 (m100) cc_final: 0.8142 (m100) REVERT: G 47 TRP cc_start: 0.8807 (t60) cc_final: 0.8283 (t60) REVERT: G 50 TRP cc_start: 0.9258 (p-90) cc_final: 0.8880 (p-90) REVERT: G 72 ASP cc_start: 0.8148 (t0) cc_final: 0.7665 (t0) REVERT: G 86 ASP cc_start: 0.8468 (m-30) cc_final: 0.8191 (m-30) REVERT: G 99 THR cc_start: 0.6228 (t) cc_final: 0.5394 (t) REVERT: G 108 LEU cc_start: 0.9269 (tp) cc_final: 0.9056 (tp) REVERT: J 5 THR cc_start: 0.7868 (m) cc_final: 0.7315 (p) REVERT: J 34 THR cc_start: 0.9294 (m) cc_final: 0.8956 (p) REVERT: J 60 ASP cc_start: 0.8098 (t70) cc_final: 0.7800 (t70) REVERT: J 96 GLU cc_start: 0.8607 (pt0) cc_final: 0.7529 (pt0) REVERT: I 26 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7933 (tm-30) REVERT: I 99 THR cc_start: 0.6493 (t) cc_final: 0.5961 (t) REVERT: I 108 LEU cc_start: 0.9347 (tp) cc_final: 0.9110 (tp) REVERT: K 5 THR cc_start: 0.7581 (m) cc_final: 0.6885 (p) REVERT: K 17 GLU cc_start: 0.8333 (pt0) cc_final: 0.7259 (pm20) REVERT: K 42 GLN cc_start: 0.8724 (tp-100) cc_final: 0.8517 (tp-100) REVERT: K 81 GLU cc_start: 0.9273 (tt0) cc_final: 0.8923 (tm-30) REVERT: K 82 ASP cc_start: 0.8688 (m-30) cc_final: 0.8222 (t0) REVERT: K 103 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8233 (ttm110) outliers start: 6 outliers final: 1 residues processed: 509 average time/residue: 0.1241 time to fit residues: 101.0559 Evaluate side-chains 407 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 404 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 104 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 178 optimal weight: 0.0670 chunk 210 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 154 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 543 GLN B 653 GLN L 70 GLN E 653 GLN E 658 GLN D 374 HIS F 575 GLN F 650 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 70 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096747 restraints weight = 43329.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100082 restraints weight = 27426.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102274 restraints weight = 20646.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103710 restraints weight = 17293.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104561 restraints weight = 15411.192| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21156 Z= 0.128 Angle : 0.643 7.573 28956 Z= 0.321 Chirality : 0.047 0.282 3582 Planarity : 0.005 0.064 3417 Dihedral : 7.488 55.030 5478 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.15 % Allowed : 1.70 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.15 (0.17), residues: 2307 helix: 1.29 (0.25), residues: 420 sheet: 0.32 (0.19), residues: 780 loop : -0.45 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 103 TYR 0.011 0.001 TYR K 86 PHE 0.022 0.002 PHE A 233 TRP 0.033 0.002 TRP I 36 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00278 (20979) covalent geometry : angle 0.60580 (28458) SS BOND : bond 0.00491 ( 33) SS BOND : angle 1.11321 ( 66) hydrogen bonds : bond 0.04195 ( 735) hydrogen bonds : angle 5.44017 ( 1926) link_ALPHA1-2 : bond 0.00883 ( 3) link_ALPHA1-2 : angle 2.39123 ( 9) link_ALPHA1-3 : bond 0.01278 ( 6) link_ALPHA1-3 : angle 1.61255 ( 18) link_ALPHA1-6 : bond 0.01031 ( 6) link_ALPHA1-6 : angle 1.89365 ( 18) link_BETA1-4 : bond 0.00558 ( 48) link_BETA1-4 : angle 1.65816 ( 144) link_NAG-ASN : bond 0.00370 ( 81) link_NAG-ASN : angle 1.91398 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 510 time to evaluate : 0.517 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: A 78 ASP cc_start: 0.8207 (m-30) cc_final: 0.7562 (p0) REVERT: A 203 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 211 GLU cc_start: 0.8314 (mp0) cc_final: 0.8081 (mp0) REVERT: A 425 ASN cc_start: 0.7709 (t0) cc_final: 0.7468 (t0) REVERT: A 466 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 584 GLU cc_start: 0.8865 (tt0) cc_final: 0.8263 (tp30) REVERT: B 621 ASN cc_start: 0.8421 (p0) cc_final: 0.8026 (t0) REVERT: B 631 TRP cc_start: 0.8721 (t-100) cc_final: 0.8450 (t-100) REVERT: B 634 GLU cc_start: 0.8782 (tt0) cc_final: 0.8259 (tt0) REVERT: B 647 GLU cc_start: 0.8615 (pt0) cc_final: 0.8068 (pp20) REVERT: B 653 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: H 31 ARG cc_start: 0.8439 (ptp-110) cc_final: 0.7093 (tpm170) REVERT: H 32 THR cc_start: 0.8517 (p) cc_final: 0.8301 (p) REVERT: H 50 TRP cc_start: 0.9199 (p-90) cc_final: 0.8600 (p-90) REVERT: H 89 THR cc_start: 0.9195 (m) cc_final: 0.8784 (p) REVERT: H 100 GLN cc_start: 0.7951 (tt0) cc_final: 0.7090 (tm-30) REVERT: H 108 LEU cc_start: 0.9352 (tp) cc_final: 0.9133 (tp) REVERT: L 42 GLN cc_start: 0.8378 (tp40) cc_final: 0.8137 (tp-100) REVERT: L 46 LEU cc_start: 0.8243 (pt) cc_final: 0.7967 (pp) REVERT: L 60 ASP cc_start: 0.8351 (t0) cc_final: 0.8149 (t70) REVERT: L 66 GLN cc_start: 0.8090 (pt0) cc_final: 0.7889 (pt0) REVERT: L 105 GLU cc_start: 0.7413 (tp30) cc_final: 0.7198 (tp30) REVERT: C 203 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8786 (tm-30) REVERT: C 242 VAL cc_start: 0.9162 (m) cc_final: 0.8942 (p) REVERT: C 373 MET cc_start: 0.8800 (mtm) cc_final: 0.8595 (mtm) REVERT: C 430 VAL cc_start: 0.8774 (t) cc_final: 0.8546 (m) REVERT: E 584 GLU cc_start: 0.8900 (tt0) cc_final: 0.8440 (tp30) REVERT: E 601 LYS cc_start: 0.8707 (mttt) cc_final: 0.8260 (mtmm) REVERT: E 634 GLU cc_start: 0.8678 (tt0) cc_final: 0.8271 (tp30) REVERT: E 648 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7744 (tm-30) REVERT: D 53 PHE cc_start: 0.8348 (p90) cc_final: 0.7930 (p90) REVERT: D 69 TRP cc_start: 0.5633 (p-90) cc_final: 0.4986 (p-90) REVERT: D 203 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8510 (tm-30) REVERT: D 395 TRP cc_start: 0.7126 (m100) cc_final: 0.6921 (m100) REVERT: D 434 MET cc_start: 0.7934 (ttp) cc_final: 0.7599 (ttp) REVERT: D 466 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8052 (mm-30) REVERT: F 614 TRP cc_start: 0.8347 (m-10) cc_final: 0.7909 (m-10) REVERT: F 634 GLU cc_start: 0.8625 (tt0) cc_final: 0.8423 (tm-30) REVERT: G 36 TRP cc_start: 0.9132 (m100) cc_final: 0.8101 (m100) REVERT: G 47 TRP cc_start: 0.8832 (t60) cc_final: 0.8265 (t60) REVERT: G 50 TRP cc_start: 0.9164 (p-90) cc_final: 0.8775 (p-90) REVERT: G 86 ASP cc_start: 0.8440 (m-30) cc_final: 0.8132 (m-30) REVERT: G 98 TYR cc_start: 0.4586 (t80) cc_final: 0.4198 (t80) REVERT: G 108 LEU cc_start: 0.9241 (tp) cc_final: 0.8982 (tp) REVERT: J 34 THR cc_start: 0.8975 (m) cc_final: 0.8555 (p) REVERT: J 60 ASP cc_start: 0.8100 (t70) cc_final: 0.7869 (t70) REVERT: J 96 GLU cc_start: 0.8579 (pt0) cc_final: 0.7491 (pt0) REVERT: I 50 TRP cc_start: 0.9162 (p-90) cc_final: 0.8477 (p-90) REVERT: I 89 THR cc_start: 0.9019 (m) cc_final: 0.8617 (p) REVERT: I 101 ASP cc_start: 0.7882 (t0) cc_final: 0.7448 (t0) REVERT: I 108 LEU cc_start: 0.9344 (tp) cc_final: 0.9067 (tp) REVERT: K 5 THR cc_start: 0.7607 (m) cc_final: 0.6932 (p) REVERT: K 65 SER cc_start: 0.9106 (t) cc_final: 0.8683 (t) REVERT: K 82 ASP cc_start: 0.8720 (m-30) cc_final: 0.8260 (t0) REVERT: K 96 GLU cc_start: 0.8441 (pt0) cc_final: 0.8083 (pt0) outliers start: 3 outliers final: 0 residues processed: 511 average time/residue: 0.1319 time to fit residues: 106.4651 Evaluate side-chains 403 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 9.9990 chunk 112 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 0.0980 chunk 206 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 193 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN D 374 HIS F 650 GLN F 652 GLN G 100BGLN J 32 HIS J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.125687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097596 restraints weight = 43703.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100782 restraints weight = 27756.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102890 restraints weight = 20870.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104279 restraints weight = 17445.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105207 restraints weight = 15514.536| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21156 Z= 0.134 Angle : 0.672 9.951 28956 Z= 0.330 Chirality : 0.047 0.290 3582 Planarity : 0.004 0.062 3417 Dihedral : 7.210 59.976 5478 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 0.10 % Allowed : 1.02 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.09 (0.17), residues: 2307 helix: 1.30 (0.25), residues: 420 sheet: 0.33 (0.19), residues: 777 loop : -0.57 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 103 TYR 0.018 0.001 TYR I 100E PHE 0.024 0.002 PHE H 58 TRP 0.035 0.001 TRP I 36 HIS 0.004 0.001 HIS H 35A Details of bonding type rmsd covalent geometry : bond 0.00293 (20979) covalent geometry : angle 0.62824 (28458) SS BOND : bond 0.00521 ( 33) SS BOND : angle 1.43094 ( 66) hydrogen bonds : bond 0.04158 ( 735) hydrogen bonds : angle 5.26790 ( 1926) link_ALPHA1-2 : bond 0.00849 ( 3) link_ALPHA1-2 : angle 2.33576 ( 9) link_ALPHA1-3 : bond 0.01381 ( 6) link_ALPHA1-3 : angle 1.44418 ( 18) link_ALPHA1-6 : bond 0.00990 ( 6) link_ALPHA1-6 : angle 1.82953 ( 18) link_BETA1-4 : bond 0.00593 ( 48) link_BETA1-4 : angle 1.71808 ( 144) link_NAG-ASN : bond 0.00396 ( 81) link_NAG-ASN : angle 2.16561 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 0.504 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: A 78 ASP cc_start: 0.8185 (m-30) cc_final: 0.7588 (p0) REVERT: A 203 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8911 (tm-30) REVERT: A 425 ASN cc_start: 0.7739 (t0) cc_final: 0.7467 (t0) REVERT: A 466 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 584 GLU cc_start: 0.8858 (tt0) cc_final: 0.8264 (tp30) REVERT: B 621 ASN cc_start: 0.8427 (p0) cc_final: 0.8159 (t0) REVERT: B 634 GLU cc_start: 0.8848 (tt0) cc_final: 0.8378 (tt0) REVERT: B 647 GLU cc_start: 0.8682 (pt0) cc_final: 0.8130 (pp20) REVERT: H 31 ARG cc_start: 0.8446 (ptp-110) cc_final: 0.7063 (tpm170) REVERT: H 50 TRP cc_start: 0.9289 (p-90) cc_final: 0.8516 (p-90) REVERT: H 89 THR cc_start: 0.9162 (m) cc_final: 0.8736 (p) REVERT: H 108 LEU cc_start: 0.9360 (tp) cc_final: 0.9138 (tp) REVERT: L 5 THR cc_start: 0.8162 (m) cc_final: 0.7614 (p) REVERT: L 22 SER cc_start: 0.8947 (m) cc_final: 0.8662 (m) REVERT: L 42 GLN cc_start: 0.8293 (tp40) cc_final: 0.8064 (tp-100) REVERT: L 46 LEU cc_start: 0.8169 (pt) cc_final: 0.7912 (pp) REVERT: L 60 ASP cc_start: 0.8449 (t0) cc_final: 0.8231 (t70) REVERT: L 66 GLN cc_start: 0.8267 (pt0) cc_final: 0.7966 (pt0) REVERT: L 70 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7307 (pp30) REVERT: L 75 ILE cc_start: 0.7754 (tp) cc_final: 0.7494 (tp) REVERT: C 104 MET cc_start: 0.8756 (tpp) cc_final: 0.8541 (tpp) REVERT: C 203 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8768 (tm-30) REVERT: C 242 VAL cc_start: 0.9208 (m) cc_final: 0.8978 (p) REVERT: C 373 MET cc_start: 0.8780 (mtm) cc_final: 0.8564 (mtm) REVERT: C 430 VAL cc_start: 0.8763 (t) cc_final: 0.8535 (m) REVERT: E 584 GLU cc_start: 0.8720 (tt0) cc_final: 0.8470 (tp30) REVERT: E 601 LYS cc_start: 0.8727 (mttt) cc_final: 0.8264 (mtmm) REVERT: E 634 GLU cc_start: 0.8663 (tt0) cc_final: 0.8213 (tp30) REVERT: E 648 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 53 PHE cc_start: 0.8329 (p90) cc_final: 0.7954 (p90) REVERT: D 69 TRP cc_start: 0.5573 (p-90) cc_final: 0.4908 (p-90) REVERT: D 203 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8492 (tm-30) REVERT: D 434 MET cc_start: 0.7956 (ttp) cc_final: 0.7618 (ttp) REVERT: D 466 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7996 (mm-30) REVERT: F 614 TRP cc_start: 0.8301 (m-10) cc_final: 0.7869 (m-10) REVERT: F 634 GLU cc_start: 0.8656 (tt0) cc_final: 0.8423 (tm-30) REVERT: F 643 TYR cc_start: 0.8960 (m-80) cc_final: 0.8477 (m-80) REVERT: G 36 TRP cc_start: 0.9101 (m100) cc_final: 0.8267 (m100) REVERT: G 47 TRP cc_start: 0.8915 (t60) cc_final: 0.8324 (t60) REVERT: G 50 TRP cc_start: 0.9209 (p-90) cc_final: 0.8611 (p-90) REVERT: G 72 ASP cc_start: 0.8172 (t0) cc_final: 0.7767 (t0) REVERT: G 86 ASP cc_start: 0.8408 (m-30) cc_final: 0.8177 (m-30) REVERT: G 108 LEU cc_start: 0.9238 (tp) cc_final: 0.8985 (tp) REVERT: J 5 THR cc_start: 0.7840 (m) cc_final: 0.7261 (p) REVERT: J 34 THR cc_start: 0.9059 (m) cc_final: 0.8608 (p) REVERT: J 60 ASP cc_start: 0.8090 (t70) cc_final: 0.7797 (t70) REVERT: J 66 GLN cc_start: 0.8386 (pp30) cc_final: 0.6933 (tp40) REVERT: J 96 GLU cc_start: 0.8561 (pt0) cc_final: 0.7544 (pt0) REVERT: I 50 TRP cc_start: 0.9121 (p-90) cc_final: 0.8494 (p-90) REVERT: I 58 PHE cc_start: 0.8710 (m-80) cc_final: 0.8365 (m-10) REVERT: I 75 LEU cc_start: 0.7972 (mt) cc_final: 0.7545 (tp) REVERT: I 89 THR cc_start: 0.9018 (m) cc_final: 0.8582 (p) REVERT: I 99 THR cc_start: 0.6578 (t) cc_final: 0.6016 (t) REVERT: I 100 GLN cc_start: 0.7355 (tm-30) cc_final: 0.7144 (tm-30) REVERT: I 100 TYR cc_start: 0.4560 (m-80) cc_final: 0.4098 (m-80) REVERT: I 108 LEU cc_start: 0.9334 (tp) cc_final: 0.9059 (tp) REVERT: K 5 THR cc_start: 0.7593 (m) cc_final: 0.6918 (p) REVERT: K 37 GLN cc_start: 0.8109 (pp30) cc_final: 0.7773 (pp30) REVERT: K 42 GLN cc_start: 0.8526 (tp-100) cc_final: 0.8257 (tp-100) REVERT: K 82 ASP cc_start: 0.8581 (m-30) cc_final: 0.8234 (m-30) REVERT: K 96 GLU cc_start: 0.8405 (pt0) cc_final: 0.8075 (pt0) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.1185 time to fit residues: 95.6175 Evaluate side-chains 406 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 0.0020 chunk 20 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN E 651 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 650 GLN J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096978 restraints weight = 43922.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100070 restraints weight = 27757.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102173 restraints weight = 20897.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103513 restraints weight = 17475.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104389 restraints weight = 15551.558| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21156 Z= 0.136 Angle : 0.656 8.820 28956 Z= 0.327 Chirality : 0.047 0.274 3582 Planarity : 0.005 0.078 3417 Dihedral : 6.875 54.510 5478 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.10 % Allowed : 0.68 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.09 (0.17), residues: 2307 helix: 1.24 (0.25), residues: 423 sheet: 0.37 (0.19), residues: 771 loop : -0.58 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 103 TYR 0.014 0.001 TYR C 217 PHE 0.021 0.002 PHE A 233 TRP 0.031 0.001 TRP I 36 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00305 (20979) covalent geometry : angle 0.61638 (28458) SS BOND : bond 0.00350 ( 33) SS BOND : angle 1.28036 ( 66) hydrogen bonds : bond 0.04164 ( 735) hydrogen bonds : angle 5.30172 ( 1926) link_ALPHA1-2 : bond 0.00790 ( 3) link_ALPHA1-2 : angle 2.29643 ( 9) link_ALPHA1-3 : bond 0.01177 ( 6) link_ALPHA1-3 : angle 1.69529 ( 18) link_ALPHA1-6 : bond 0.00965 ( 6) link_ALPHA1-6 : angle 1.87441 ( 18) link_BETA1-4 : bond 0.00547 ( 48) link_BETA1-4 : angle 1.62333 ( 144) link_NAG-ASN : bond 0.00324 ( 81) link_NAG-ASN : angle 2.02466 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 491 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7777 (p-80) cc_final: 0.7568 (p-80) REVERT: A 78 ASP cc_start: 0.8193 (m-30) cc_final: 0.7607 (p0) REVERT: A 203 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8743 (tm-30) REVERT: A 211 GLU cc_start: 0.8421 (mp0) cc_final: 0.8188 (mp0) REVERT: A 425 ASN cc_start: 0.7787 (t0) cc_final: 0.7501 (t0) REVERT: A 466 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 584 GLU cc_start: 0.8873 (tt0) cc_final: 0.8303 (tp30) REVERT: B 634 GLU cc_start: 0.8784 (tt0) cc_final: 0.8387 (tt0) REVERT: B 647 GLU cc_start: 0.8751 (pt0) cc_final: 0.8147 (pp20) REVERT: H 47 TRP cc_start: 0.9079 (t60) cc_final: 0.8379 (t60) REVERT: H 50 TRP cc_start: 0.9326 (p-90) cc_final: 0.8588 (p-90) REVERT: H 89 THR cc_start: 0.9165 (m) cc_final: 0.8714 (p) REVERT: H 100 GLN cc_start: 0.7786 (tt0) cc_final: 0.6990 (tm-30) REVERT: H 108 LEU cc_start: 0.9342 (tp) cc_final: 0.9074 (tp) REVERT: L 5 THR cc_start: 0.8097 (m) cc_final: 0.7536 (p) REVERT: L 42 GLN cc_start: 0.8266 (tp40) cc_final: 0.8033 (tp-100) REVERT: L 46 LEU cc_start: 0.8389 (pt) cc_final: 0.8091 (pp) REVERT: L 60 ASP cc_start: 0.8397 (t0) cc_final: 0.8179 (t70) REVERT: L 66 GLN cc_start: 0.8232 (pt0) cc_final: 0.7826 (pt0) REVERT: L 96 GLU cc_start: 0.8307 (pt0) cc_final: 0.6903 (pt0) REVERT: C 180 ASP cc_start: 0.8455 (m-30) cc_final: 0.8248 (m-30) REVERT: C 203 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8721 (tm-30) REVERT: C 242 VAL cc_start: 0.9242 (m) cc_final: 0.9005 (p) REVERT: C 373 MET cc_start: 0.8823 (mtm) cc_final: 0.8622 (mtm) REVERT: C 430 VAL cc_start: 0.8786 (t) cc_final: 0.8552 (m) REVERT: E 584 GLU cc_start: 0.8697 (tt0) cc_final: 0.8491 (tp30) REVERT: E 601 LYS cc_start: 0.8720 (mttt) cc_final: 0.8244 (mtmm) REVERT: E 648 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7666 (tm-30) REVERT: E 656 ASN cc_start: 0.9313 (p0) cc_final: 0.9094 (p0) REVERT: D 53 PHE cc_start: 0.8401 (p90) cc_final: 0.8018 (p90) REVERT: D 203 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8428 (tm-30) REVERT: D 434 MET cc_start: 0.8182 (ttp) cc_final: 0.7824 (ttp) REVERT: D 466 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8078 (mm-30) REVERT: F 614 TRP cc_start: 0.8335 (m-10) cc_final: 0.7894 (m-10) REVERT: G 36 TRP cc_start: 0.9130 (m100) cc_final: 0.8198 (m100) REVERT: G 47 TRP cc_start: 0.8933 (t60) cc_final: 0.8386 (t60) REVERT: G 50 TRP cc_start: 0.9268 (p-90) cc_final: 0.8600 (p-90) REVERT: G 72 ASP cc_start: 0.8254 (t0) cc_final: 0.7851 (t0) REVERT: G 86 ASP cc_start: 0.8271 (m-30) cc_final: 0.7879 (m-30) REVERT: G 99 THR cc_start: 0.6308 (p) cc_final: 0.5691 (p) REVERT: G 108 LEU cc_start: 0.9238 (tp) cc_final: 0.8987 (tp) REVERT: J 5 THR cc_start: 0.7838 (m) cc_final: 0.7249 (p) REVERT: J 34 THR cc_start: 0.8921 (m) cc_final: 0.8679 (p) REVERT: J 60 ASP cc_start: 0.8107 (t70) cc_final: 0.7837 (t70) REVERT: J 66 GLN cc_start: 0.8423 (pp30) cc_final: 0.6594 (tp40) REVERT: J 96 GLU cc_start: 0.8568 (pt0) cc_final: 0.7584 (pt0) REVERT: I 50 TRP cc_start: 0.9083 (p-90) cc_final: 0.8419 (p-90) REVERT: I 89 THR cc_start: 0.9036 (m) cc_final: 0.8633 (p) REVERT: I 100 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6840 (tm-30) REVERT: I 108 LEU cc_start: 0.9337 (tp) cc_final: 0.9061 (tp) REVERT: K 5 THR cc_start: 0.7580 (m) cc_final: 0.6935 (p) REVERT: K 42 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8200 (tp-100) REVERT: K 96 GLU cc_start: 0.8410 (pt0) cc_final: 0.8054 (pt0) outliers start: 2 outliers final: 0 residues processed: 491 average time/residue: 0.1277 time to fit residues: 100.8261 Evaluate side-chains 400 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 153 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 70 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 650 GLN G 95 GLN J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.121209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092988 restraints weight = 43873.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096038 restraints weight = 28033.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098080 restraints weight = 21157.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099426 restraints weight = 17736.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100312 restraints weight = 15785.640| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21156 Z= 0.132 Angle : 0.644 7.379 28956 Z= 0.324 Chirality : 0.046 0.259 3582 Planarity : 0.004 0.082 3417 Dihedral : 6.612 56.546 5478 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.07 (0.17), residues: 2307 helix: 1.21 (0.25), residues: 426 sheet: 0.42 (0.18), residues: 813 loop : -0.68 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 103 TYR 0.019 0.001 TYR I 100E PHE 0.019 0.001 PHE A 233 TRP 0.037 0.002 TRP H 36 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00297 (20979) covalent geometry : angle 0.60956 (28458) SS BOND : bond 0.00311 ( 33) SS BOND : angle 1.19568 ( 66) hydrogen bonds : bond 0.04079 ( 735) hydrogen bonds : angle 5.30845 ( 1926) link_ALPHA1-2 : bond 0.00757 ( 3) link_ALPHA1-2 : angle 2.30707 ( 9) link_ALPHA1-3 : bond 0.01135 ( 6) link_ALPHA1-3 : angle 1.61838 ( 18) link_ALPHA1-6 : bond 0.00925 ( 6) link_ALPHA1-6 : angle 1.75345 ( 18) link_BETA1-4 : bond 0.00532 ( 48) link_BETA1-4 : angle 1.58067 ( 144) link_NAG-ASN : bond 0.00289 ( 81) link_NAG-ASN : angle 1.84948 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 0.787 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: A 78 ASP cc_start: 0.8217 (m-30) cc_final: 0.7601 (p0) REVERT: A 95 MET cc_start: 0.7509 (ptm) cc_final: 0.7305 (ppp) REVERT: A 100 MET cc_start: 0.7958 (mmt) cc_final: 0.7730 (mmt) REVERT: A 203 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 211 GLU cc_start: 0.8458 (mp0) cc_final: 0.8228 (mp0) REVERT: A 425 ASN cc_start: 0.7785 (t0) cc_final: 0.7447 (t0) REVERT: A 466 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 584 GLU cc_start: 0.8822 (tt0) cc_final: 0.8281 (tp30) REVERT: B 634 GLU cc_start: 0.8837 (tt0) cc_final: 0.8481 (tt0) REVERT: B 647 GLU cc_start: 0.8689 (pt0) cc_final: 0.8110 (pp20) REVERT: B 649 SER cc_start: 0.9259 (p) cc_final: 0.8585 (p) REVERT: H 47 TRP cc_start: 0.9065 (t60) cc_final: 0.8390 (t60) REVERT: H 50 TRP cc_start: 0.9179 (p-90) cc_final: 0.8432 (p-90) REVERT: H 89 THR cc_start: 0.9179 (m) cc_final: 0.8718 (p) REVERT: H 108 LEU cc_start: 0.9321 (tp) cc_final: 0.9055 (tp) REVERT: L 5 THR cc_start: 0.8053 (m) cc_final: 0.7508 (p) REVERT: L 42 GLN cc_start: 0.8222 (tp40) cc_final: 0.7976 (tp-100) REVERT: L 46 LEU cc_start: 0.8338 (pt) cc_final: 0.8086 (pp) REVERT: L 60 ASP cc_start: 0.8382 (t0) cc_final: 0.8146 (t70) REVERT: L 66 GLN cc_start: 0.8332 (pt0) cc_final: 0.6483 (tp40) REVERT: L 96 GLU cc_start: 0.8237 (pt0) cc_final: 0.6879 (pt0) REVERT: C 203 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 370 GLU cc_start: 0.7666 (mp0) cc_final: 0.7306 (pt0) REVERT: C 373 MET cc_start: 0.8869 (mtm) cc_final: 0.8652 (mtm) REVERT: C 430 VAL cc_start: 0.8910 (t) cc_final: 0.8709 (m) REVERT: E 584 GLU cc_start: 0.8699 (tt0) cc_final: 0.8480 (tp30) REVERT: E 601 LYS cc_start: 0.8735 (mttt) cc_final: 0.8230 (mtmm) REVERT: E 648 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7658 (tm-30) REVERT: D 53 PHE cc_start: 0.8396 (p90) cc_final: 0.8030 (p90) REVERT: D 95 MET cc_start: 0.7916 (ptm) cc_final: 0.6832 (ppp) REVERT: D 203 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8300 (tm-30) REVERT: D 466 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7963 (mm-30) REVERT: G 36 TRP cc_start: 0.9013 (m100) cc_final: 0.8177 (m100) REVERT: G 39 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7977 (tm-30) REVERT: G 47 TRP cc_start: 0.8917 (t60) cc_final: 0.8413 (t60) REVERT: G 72 ASP cc_start: 0.8253 (t0) cc_final: 0.7861 (t0) REVERT: G 86 ASP cc_start: 0.8305 (m-30) cc_final: 0.7869 (m-30) REVERT: G 89 THR cc_start: 0.9060 (m) cc_final: 0.8615 (p) REVERT: G 108 LEU cc_start: 0.9268 (tp) cc_final: 0.8982 (tp) REVERT: J 5 THR cc_start: 0.7684 (m) cc_final: 0.7106 (p) REVERT: J 33 MET cc_start: 0.6439 (pmm) cc_final: 0.6098 (pmm) REVERT: J 60 ASP cc_start: 0.8108 (t70) cc_final: 0.7888 (t70) REVERT: J 66 GLN cc_start: 0.8481 (pp30) cc_final: 0.6711 (tp40) REVERT: J 96 GLU cc_start: 0.8452 (pt0) cc_final: 0.7659 (pt0) REVERT: I 50 TRP cc_start: 0.9101 (p-90) cc_final: 0.8442 (p-90) REVERT: I 75 LEU cc_start: 0.7995 (mt) cc_final: 0.7551 (tp) REVERT: I 89 THR cc_start: 0.9028 (m) cc_final: 0.8685 (p) REVERT: I 99 THR cc_start: 0.6633 (t) cc_final: 0.6101 (t) REVERT: I 100 TYR cc_start: 0.4750 (m-80) cc_final: 0.4486 (m-80) REVERT: I 108 LEU cc_start: 0.9309 (tp) cc_final: 0.9041 (tp) REVERT: K 5 THR cc_start: 0.7593 (m) cc_final: 0.6917 (p) REVERT: K 65 SER cc_start: 0.9326 (t) cc_final: 0.9098 (t) REVERT: K 96 GLU cc_start: 0.8359 (pt0) cc_final: 0.8001 (pt0) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.1370 time to fit residues: 109.8106 Evaluate side-chains 408 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN L 70 GLN E 651 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN J 70 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 HIS K 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092977 restraints weight = 44052.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095744 restraints weight = 29116.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097667 restraints weight = 22512.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098938 restraints weight = 19022.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099686 restraints weight = 17036.411| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21156 Z= 0.144 Angle : 0.664 11.978 28956 Z= 0.337 Chirality : 0.046 0.255 3582 Planarity : 0.005 0.085 3417 Dihedral : 6.351 54.682 5478 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 0.15 % Favored : 99.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.14 (0.17), residues: 2307 helix: 1.24 (0.26), residues: 414 sheet: 0.59 (0.19), residues: 759 loop : -0.66 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 31 TYR 0.019 0.001 TYR C 217 PHE 0.019 0.002 PHE A 233 TRP 0.039 0.002 TRP I 36 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00323 (20979) covalent geometry : angle 0.63260 (28458) SS BOND : bond 0.00308 ( 33) SS BOND : angle 1.18646 ( 66) hydrogen bonds : bond 0.04263 ( 735) hydrogen bonds : angle 5.30756 ( 1926) link_ALPHA1-2 : bond 0.00739 ( 3) link_ALPHA1-2 : angle 2.23032 ( 9) link_ALPHA1-3 : bond 0.01100 ( 6) link_ALPHA1-3 : angle 1.56616 ( 18) link_ALPHA1-6 : bond 0.00723 ( 6) link_ALPHA1-6 : angle 1.66549 ( 18) link_BETA1-4 : bond 0.00558 ( 48) link_BETA1-4 : angle 1.61440 ( 144) link_NAG-ASN : bond 0.00298 ( 81) link_NAG-ASN : angle 1.77390 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 0.604 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: A 78 ASP cc_start: 0.8240 (m-30) cc_final: 0.7640 (p0) REVERT: A 203 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 205 CYS cc_start: 0.7673 (m) cc_final: 0.7199 (m) REVERT: A 211 GLU cc_start: 0.8613 (mp0) cc_final: 0.8392 (mp0) REVERT: A 368 ASP cc_start: 0.7594 (p0) cc_final: 0.7047 (m-30) REVERT: A 425 ASN cc_start: 0.7861 (t0) cc_final: 0.7535 (t0) REVERT: A 466 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7858 (mp0) REVERT: B 584 GLU cc_start: 0.8785 (tt0) cc_final: 0.8304 (tp30) REVERT: B 634 GLU cc_start: 0.8818 (tt0) cc_final: 0.8440 (tt0) REVERT: B 647 GLU cc_start: 0.8783 (pt0) cc_final: 0.8367 (pt0) REVERT: H 89 THR cc_start: 0.9141 (m) cc_final: 0.8688 (p) REVERT: H 95 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7598 (tm-30) REVERT: H 108 LEU cc_start: 0.9360 (tp) cc_final: 0.9087 (tp) REVERT: L 5 THR cc_start: 0.8093 (m) cc_final: 0.7600 (p) REVERT: L 33 MET cc_start: 0.5825 (pmm) cc_final: 0.5547 (pmm) REVERT: L 42 GLN cc_start: 0.8153 (tp40) cc_final: 0.7934 (tp-100) REVERT: L 46 LEU cc_start: 0.8344 (pt) cc_final: 0.8068 (pp) REVERT: L 66 GLN cc_start: 0.8362 (pt0) cc_final: 0.6513 (tp40) REVERT: L 96 GLU cc_start: 0.8250 (pt0) cc_final: 0.8006 (pt0) REVERT: C 69 TRP cc_start: 0.5803 (p-90) cc_final: 0.5545 (p-90) REVERT: C 95 MET cc_start: 0.7994 (ppp) cc_final: 0.7737 (ppp) REVERT: C 203 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8635 (tm-30) REVERT: C 370 GLU cc_start: 0.7468 (mp0) cc_final: 0.7103 (pt0) REVERT: C 373 MET cc_start: 0.8860 (mtm) cc_final: 0.8652 (mtm) REVERT: E 595 ILE cc_start: 0.9084 (tp) cc_final: 0.8786 (tt) REVERT: E 601 LYS cc_start: 0.8691 (mttt) cc_final: 0.8336 (mtmm) REVERT: E 616 ASN cc_start: 0.7761 (p0) cc_final: 0.7324 (p0) REVERT: E 648 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 53 PHE cc_start: 0.8437 (p90) cc_final: 0.8163 (p90) REVERT: D 69 TRP cc_start: 0.5719 (p-90) cc_final: 0.5430 (p-90) REVERT: D 203 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8406 (tm-30) REVERT: D 373 MET cc_start: 0.8414 (mtm) cc_final: 0.8062 (ptp) REVERT: D 466 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7971 (mm-30) REVERT: G 36 TRP cc_start: 0.9077 (m100) cc_final: 0.8076 (m100) REVERT: G 39 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8009 (tm-30) REVERT: G 47 TRP cc_start: 0.8962 (t60) cc_final: 0.8400 (t60) REVERT: G 50 TRP cc_start: 0.9217 (p-90) cc_final: 0.8848 (p-90) REVERT: G 72 ASP cc_start: 0.8361 (t0) cc_final: 0.7938 (t0) REVERT: G 86 ASP cc_start: 0.8275 (m-30) cc_final: 0.7855 (m-30) REVERT: G 89 THR cc_start: 0.9045 (m) cc_final: 0.8604 (p) REVERT: G 108 LEU cc_start: 0.9225 (tp) cc_final: 0.8987 (tp) REVERT: J 33 MET cc_start: 0.6380 (pmm) cc_final: 0.5977 (pmm) REVERT: J 60 ASP cc_start: 0.8047 (t70) cc_final: 0.7819 (t70) REVERT: J 66 GLN cc_start: 0.8536 (pp30) cc_final: 0.6579 (tp40) REVERT: J 96 GLU cc_start: 0.8473 (pt0) cc_final: 0.7856 (pt0) REVERT: I 58 PHE cc_start: 0.8601 (m-80) cc_final: 0.8304 (m-10) REVERT: I 75 LEU cc_start: 0.7965 (mt) cc_final: 0.7608 (tp) REVERT: I 89 THR cc_start: 0.8947 (m) cc_final: 0.8619 (p) REVERT: I 99 THR cc_start: 0.6797 (t) cc_final: 0.5892 (t) REVERT: I 108 LEU cc_start: 0.9371 (tp) cc_final: 0.9090 (tp) REVERT: K 5 THR cc_start: 0.7633 (m) cc_final: 0.6992 (p) REVERT: K 42 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7999 (tp-100) REVERT: K 82 ASP cc_start: 0.8814 (m-30) cc_final: 0.8262 (t0) REVERT: K 96 GLU cc_start: 0.8171 (pt0) cc_final: 0.7931 (pt0) outliers start: 2 outliers final: 0 residues processed: 480 average time/residue: 0.1213 time to fit residues: 93.5729 Evaluate side-chains 380 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 45 optimal weight: 0.0060 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 3 optimal weight: 0.0670 chunk 214 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 650 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095464 restraints weight = 43662.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098354 restraints weight = 28767.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100321 restraints weight = 22111.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101641 restraints weight = 18601.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102390 restraints weight = 16604.348| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21156 Z= 0.123 Angle : 0.637 8.643 28956 Z= 0.324 Chirality : 0.045 0.227 3582 Planarity : 0.005 0.082 3417 Dihedral : 5.939 54.250 5478 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2307 helix: 1.32 (0.26), residues: 408 sheet: 0.57 (0.19), residues: 759 loop : -0.67 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 31 TYR 0.016 0.001 TYR C 217 PHE 0.017 0.002 PHE C 233 TRP 0.054 0.002 TRP I 36 HIS 0.002 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00267 (20979) covalent geometry : angle 0.60718 (28458) SS BOND : bond 0.00309 ( 33) SS BOND : angle 1.09325 ( 66) hydrogen bonds : bond 0.03888 ( 735) hydrogen bonds : angle 5.22741 ( 1926) link_ALPHA1-2 : bond 0.00777 ( 3) link_ALPHA1-2 : angle 2.31539 ( 9) link_ALPHA1-3 : bond 0.00959 ( 6) link_ALPHA1-3 : angle 1.42596 ( 18) link_ALPHA1-6 : bond 0.00581 ( 6) link_ALPHA1-6 : angle 1.56196 ( 18) link_BETA1-4 : bond 0.00555 ( 48) link_BETA1-4 : angle 1.55204 ( 144) link_NAG-ASN : bond 0.00305 ( 81) link_NAG-ASN : angle 1.72081 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.30 seconds wall clock time: 61 minutes 8.38 seconds (3668.38 seconds total)