Starting phenix.real_space_refine on Sat Jul 4 19:51:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4g_25676/07_2026/7t4g_25676.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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 147 5.16 5 C 14367 2.51 5 N 3696 2.21 5 O 4835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23045 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "B" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "D" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3953 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "F" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1138 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 137} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1028 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 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 chiralities: 2 Chain: "Z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "f" 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 chiralities: 5 Chain: "g" 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 chiralities: 3 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 chiralities: 2 Chain: "i" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "m" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "o" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "v" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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 chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.14, per 1000 atoms: 0.18 Number of scatterers: 23045 At special positions: 0 Unit cell: (156.4, 155.25, 124.2, 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 147 16.00 O 4835 8.00 N 3696 7.00 C 14367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 211 " distance=1.78 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 168 " distance=2.02 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 255 " distance=2.06 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 459 " distance=2.04 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS H 100C" - pdb=" SG CYS H 100K" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 211 " distance=2.02 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 168 " distance=2.02 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 263 " distance=2.05 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 255 " distance=2.08 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 344 " distance=2.02 Simple disulfide: pdb=" SG CYS C 395 " - pdb=" SG CYS C 459 " distance=2.04 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS G 100C" - pdb=" SG CYS G 100K" distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 211 " distance=1.79 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 168 " distance=2.02 Simple disulfide: pdb=" SG CYS E 194 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 233 " - pdb=" SG CYS E 263 " distance=2.04 Simple disulfide: pdb=" SG CYS E 243 " - pdb=" SG CYS E 255 " distance=2.05 Simple disulfide: pdb=" SG CYS E 311 " - pdb=" SG CYS E 344 " distance=2.07 Simple disulfide: pdb=" SG CYS E 395 " - pdb=" SG CYS E 459 " distance=2.06 Simple disulfide: pdb=" SG CYS E 402 " - pdb=" SG CYS E 432 " distance=2.02 Simple disulfide: pdb=" SG CYS J 100C" - pdb=" SG CYS J 100K" 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 M 5 " - " MAN M 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN Z 5 " - " MAN Z 6 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN m 5 " - " MAN m 6 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " ALPHA1-3 " BMA M 3 " - " MAN M 8 " " MAN M 4 " - " MAN M 5 " " BMA R 3 " - " MAN R 4 " " BMA Z 3 " - " MAN Z 8 " " MAN Z 4 " - " MAN Z 5 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA m 3 " - " MAN m 8 " " MAN m 4 " - " MAN m 5 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 7 " " BMA R 3 " - " MAN R 7 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 7 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 5 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 7 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG 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 y 2 " - " BMA y 3 " BETA1-6 " NAG O 1 " - " FUC O 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG Q 1 " - " FUC Q 3 " " NAG V 1 " - " FUC V 3 " " NAG b 1 " - " FUC b 3 " " NAG c 1 " - " FUC c 3 " " NAG d 1 " - " FUC d 3 " " NAG i 1 " - " FUC i 3 " " NAG o 1 " - " FUC o 3 " " NAG p 1 " - " FUC p 3 " " NAG q 1 " - " FUC q 3 " " NAG v 1 " - " FUC v 3 " NAG-ASN " NAG A 601 " - " ASN A 70 " " NAG A 602 " - " ASN A 79 " " NAG A 603 " - " ASN A 171 " " NAG A 604 " - " ASN A 184 " " NAG A 605 " - " ASN A 198 " " NAG A 606 " - " ASN A 202 " " NAG A 607 " - " ASN A 244 " " NAG A 608 " - " ASN A 306 " " NAG A 609 " - " ASN A 476 " " NAG B 701 " - " ASN B 627 " " NAG B 702 " - " ASN B 636 " " NAG B 703 " - " ASN B 652 " " NAG C 601 " - " ASN C 70 " " NAG C 602 " - " ASN C 79 " " NAG C 603 " - " ASN C 171 " " NAG C 604 " - " ASN C 184 " " NAG C 605 " - " ASN C 198 " " NAG C 606 " - " ASN C 202 " " NAG C 607 " - " ASN C 244 " " NAG C 608 " - " ASN C 306 " " NAG C 609 " - " ASN C 476 " " NAG D 701 " - " ASN D 627 " " NAG D 702 " - " ASN D 636 " " NAG D 703 " - " ASN D 652 " " NAG E 601 " - " ASN E 70 " " NAG E 602 " - " ASN E 79 " " NAG E 603 " - " ASN E 171 " " NAG E 604 " - " ASN E 184 " " NAG E 605 " - " ASN E 198 " " NAG E 606 " - " ASN E 202 " " NAG E 607 " - " ASN E 244 " " NAG E 608 " - " ASN E 306 " " NAG E 609 " - " ASN E 476 " " NAG F 701 " - " ASN F 627 " " NAG F 702 " - " ASN F 636 " " NAG F 703 " - " ASN F 652 " " NAG M 1 " - " ASN A 37 " " NAG N 1 " - " ASN A 114 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 212 " " NAG R 1 " - " ASN A 278 " " NAG S 1 " - " ASN A 284 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 316 " " NAG V 1 " - " ASN A 371 " " NAG W 1 " - " ASN A 377 " " NAG X 1 " - " ASN A 460 " " NAG Y 1 " - " ASN A 479 " " NAG Z 1 " - " ASN C 37 " " NAG a 1 " - " ASN C 114 " " NAG b 1 " - " ASN C 146 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 212 " " NAG e 1 " - " ASN C 278 " " NAG f 1 " - " ASN C 284 " " NAG g 1 " - " ASN C 295 " " NAG h 1 " - " ASN C 316 " " NAG i 1 " - " ASN C 371 " " NAG j 1 " - " ASN C 377 " " NAG k 1 " - " ASN C 460 " " NAG l 1 " - " ASN C 479 " " NAG m 1 " - " ASN E 37 " " NAG n 1 " - " ASN E 114 " " NAG o 1 " - " ASN E 146 " " NAG p 1 " - " ASN E 156 " " NAG q 1 " - " ASN E 212 " " NAG r 1 " - " ASN E 278 " " NAG s 1 " - " ASN E 284 " " NAG t 1 " - " ASN E 295 " " NAG u 1 " - " ASN E 316 " " NAG v 1 " - " ASN E 371 " " NAG w 1 " - " ASN E 377 " " NAG x 1 " - " ASN E 460 " " NAG y 1 " - " ASN E 479 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 977.3 milliseconds 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 45 sheets defined 23.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 Processing helix chain 'A' and resid 80 through 99 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.772A pdb=" N ILE A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.564A pdb=" N PHE A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 553 through 573 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 584 through 611 removed outlier: 3.705A pdb=" N THR B 588 " --> pdb=" O THR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 646 through 674 removed outlier: 3.748A pdb=" N ASN B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.165A pdb=" N GLY L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.599A pdb=" N ILE C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 404 through 412 Processing helix chain 'C' and resid 485 through 488 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 553 through 573 Processing helix chain 'D' and resid 574 through 576 No H-bonds generated for 'chain 'D' and resid 574 through 576' Processing helix chain 'D' and resid 585 through 612 Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 646 through 674 removed outlier: 3.975A pdb=" N GLU D 651 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN D 652 " --> pdb=" O PHE D 648 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA D 655 " --> pdb=" O GLU D 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'E' and resid 51 through 57 Processing helix chain 'E' and resid 80 through 99 removed outlier: 3.663A pdb=" N ILE E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 349 through 363 Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.599A pdb=" N ILE E 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.599A pdb=" N PHE E 390 " --> pdb=" O PRO E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 485 through 488 Processing helix chain 'E' and resid 489 through 494 Processing helix chain 'F' and resid 535 through 541 removed outlier: 4.305A pdb=" N THR F 540 " --> pdb=" O PHE F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 573 Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 584 through 612 Processing helix chain 'F' and resid 638 through 644 Processing helix chain 'F' and resid 646 through 674 removed outlier: 3.942A pdb=" N GLU F 651 " --> pdb=" O ASP F 647 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN F 652 " --> pdb=" O PHE F 648 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.209A pdb=" N VAL A 258 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.668A pdb=" N CYS A 44 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.934A pdb=" N PHE A 75 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 188 Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA7, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.740A pdb=" N GLN A 217 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 277 removed outlier: 7.322A pdb=" N THR A 379 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 288 through 290 removed outlier: 5.770A pdb=" N GLY A 455 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 315 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 399 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.032A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.441A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.682A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.848A pdb=" N GLY L 13 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AB8, first strand: chain 'C' and resid 35 through 37 removed outlier: 4.099A pdb=" N VAL C 258 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AC1, first strand: chain 'C' and resid 73 through 76 removed outlier: 4.910A pdb=" N PHE C 75 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 180 through 188 Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AC4, first strand: chain 'C' and resid 217 through 218 removed outlier: 6.629A pdb=" N GLN C 217 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 275 through 277 removed outlier: 7.283A pdb=" N THR C 379 " --> pdb=" O MET C 482 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.043A pdb=" N GLY C 455 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY C 315 " --> pdb=" O GLY C 455 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 399 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 320 through 323 Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.024A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=AD2, first strand: chain 'I' and resid 4 through 7 removed outlier: 5.440A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN I 27 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N SER I 67 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N ILE I 29 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N SER I 65 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 13 removed outlier: 4.025A pdb=" N GLY I 13 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 29 through 30 Processing sheet with id=AD5, first strand: chain 'E' and resid 35 through 37 removed outlier: 4.192A pdb=" N VAL E 258 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 58 through 59 removed outlier: 6.855A pdb=" N CYS E 44 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 73 through 76 removed outlier: 4.907A pdb=" N PHE E 75 " --> pdb=" O PRO E 253 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 180 through 188 Processing sheet with id=AD9, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AE1, first strand: chain 'E' and resid 217 through 218 removed outlier: 6.644A pdb=" N GLN E 217 " --> pdb=" O TYR E 449 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 275 through 277 removed outlier: 7.387A pdb=" N THR E 379 " --> pdb=" O MET E 482 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 288 through 290 removed outlier: 5.845A pdb=" N GLY E 455 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 315 " --> pdb=" O GLY E 455 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 399 " --> pdb=" O ARG E 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 320 through 323 Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 5.992A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 removed outlier: 5.344A pdb=" N THR K 69 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLN K 27 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N SER K 67 " --> pdb=" O GLN K 27 " (cutoff:3.500A) removed outlier: 11.648A pdb=" N ILE K 29 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 11.934A pdb=" N SER K 65 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.985A pdb=" N GLY K 13 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4718 1.32 - 1.47: 8416 1.47 - 1.61: 10194 1.61 - 1.76: 37 1.76 - 1.90: 169 Bond restraints: 23534 Sorted by residual: bond pdb=" CA VAL F 573 " pdb=" CB VAL F 573 " ideal model delta sigma weight residual 1.537 1.575 -0.038 5.00e-03 4.00e+04 5.83e+01 bond pdb=" CA VAL D 573 " pdb=" CB VAL D 573 " ideal model delta sigma weight residual 1.539 1.573 -0.034 5.40e-03 3.43e+04 4.08e+01 bond pdb=" CB LEU D 674 " pdb=" CG LEU D 674 " ideal model delta sigma weight residual 1.530 1.642 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CB LEU B 674 " pdb=" CG LEU B 674 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" CB LEU F 674 " pdb=" CG LEU F 674 " ideal model delta sigma weight residual 1.530 1.637 -0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 23529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 26035 2.18 - 4.36: 4863 4.36 - 6.55: 943 6.55 - 8.73: 124 8.73 - 10.91: 30 Bond angle restraints: 31995 Sorted by residual: angle pdb=" N VAL E 32 " pdb=" CA VAL E 32 " pdb=" C VAL E 32 " ideal model delta sigma weight residual 108.63 116.68 -8.05 8.60e-01 1.35e+00 8.75e+01 angle pdb=" C VAL B 573 " pdb=" N PRO B 574 " pdb=" CA PRO B 574 " ideal model delta sigma weight residual 119.56 128.63 -9.07 1.02e+00 9.61e-01 7.91e+01 angle pdb=" C VAL D 573 " pdb=" N PRO D 574 " pdb=" CA PRO D 574 " ideal model delta sigma weight residual 119.82 127.61 -7.79 9.80e-01 1.04e+00 6.32e+01 angle pdb=" C VAL F 573 " pdb=" N PRO F 574 " pdb=" CA PRO F 574 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" N THR B 588 " pdb=" CA THR B 588 " pdb=" C THR B 588 " ideal model delta sigma weight residual 113.41 103.86 9.55 1.22e+00 6.72e-01 6.13e+01 ... (remaining 31990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 12220 18.10 - 36.19: 366 36.19 - 54.29: 109 54.29 - 72.39: 42 72.39 - 90.49: 10 Dihedral angle restraints: 12747 sinusoidal: 5124 harmonic: 7623 Sorted by residual: dihedral pdb=" CB CYS E 243 " pdb=" SG CYS E 243 " pdb=" SG CYS E 255 " pdb=" CB CYS E 255 " ideal model delta sinusoidal sigma weight residual 93.00 -176.51 -90.49 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C 243 " pdb=" SG CYS C 243 " pdb=" SG CYS C 255 " pdb=" CB CYS C 255 " ideal model delta sinusoidal sigma weight residual -86.00 -176.32 90.32 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 243 " pdb=" SG CYS A 243 " pdb=" SG CYS A 255 " pdb=" CB CYS A 255 " ideal model delta sinusoidal sigma weight residual 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+01 ... (remaining 12744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2544 0.107 - 0.214: 946 0.214 - 0.320: 361 0.320 - 0.427: 139 0.427 - 0.534: 68 Chirality restraints: 4058 Sorted by residual: chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 6.11e+02 chirality pdb=" C1 MAN R 6 " pdb=" O2 MAN R 5 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 2.02 0.38 2.00e-02 2.50e+03 3.52e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.27e+02 ... (remaining 4055 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG t 2 " 0.217 2.00e-02 2.50e+03 1.80e-01 4.07e+02 pdb=" C7 NAG t 2 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG t 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG t 2 " -0.297 2.00e-02 2.50e+03 pdb=" O7 NAG t 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.168 2.00e-02 2.50e+03 1.41e-01 2.48e+02 pdb=" C7 NAG R 1 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 371 " -0.137 2.00e-02 2.50e+03 1.36e-01 2.33e+02 pdb=" CG ASN C 371 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 371 " 0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN C 371 " 0.200 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.168 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7757 2.87 - 3.38: 20792 3.38 - 3.89: 39341 3.89 - 4.39: 45462 4.39 - 4.90: 72437 Nonbonded interactions: 185789 Sorted by model distance: nonbonded pdb=" OD1 ASP C 89 " pdb=" NZ LYS D 589 " model vdw 2.363 3.120 nonbonded pdb=" C4 BMA R 3 " pdb=" O6 BMA R 3 " model vdw 2.446 2.776 nonbonded pdb=" N THR C 246 " pdb=" N ASN C 247 " model vdw 2.447 2.560 nonbonded pdb=" N ARG B 582 " pdb=" N LEU B 583 " model vdw 2.451 2.560 nonbonded pdb=" N THR A 246 " pdb=" N ASN A 247 " model vdw 2.452 2.560 ... (remaining 185784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 2 or resid 5 through 8)) selection = (chain 'R' and (resid 1 or resid 4 through 7)) selection = (chain 'Z' and (resid 2 or resid 5 through 8)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 2 or resid 5 through 8)) selection = (chain 'r' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'u' selection = chain 'x' } ncs_group { reference = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) selection = (chain 'y' and resid 1 through 2) } ncs_group { reference = chain 'S' selection = chain 's' selection = chain 't' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.640 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.252 23742 Z= 1.194 Angle : 1.877 12.694 32586 Z= 1.175 Chirality : 0.149 0.534 4058 Planarity : 0.010 0.180 3813 Dihedral : 10.655 81.093 7740 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 1.35 % Allowed : 2.85 % Favored : 95.80 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.16), residues: 2595 helix: -0.06 (0.21), residues: 471 sheet: 0.69 (0.19), residues: 654 loop : -0.45 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 231 TYR 0.055 0.008 TYR H 91 PHE 0.039 0.007 PHE B 537 TRP 0.052 0.008 TRP F 586 HIS 0.008 0.003 HIS G 100N Details of bonding type rmsd/Z covalent geometry : bond 0.02216 / 1.16 (23534) covalent geometry : angle 1.83076 / 1.17 (31995) SS BOND : bond 0.06220 / 2.78 ( 33) SS BOND : angle 2.79276 / 1.73 ( 66) hydrogen bonds : bond 0.19221 / 12.92 ( 782) hydrogen bonds : angle 7.27097 / 5.04 ( 2049) link_ALPHA1-2 : bond 0.07063 / 4.39 ( 9) link_ALPHA1-2 : angle 4.10294 / 2.45 ( 27) link_ALPHA1-3 : bond 0.07136 / 4.49 ( 12) link_ALPHA1-3 : angle 4.09985 / 2.38 ( 36) link_ALPHA1-6 : bond 0.05372 / 3.54 ( 12) link_ALPHA1-6 : angle 3.43268 / 1.99 ( 36) link_BETA1-4 : bond 0.06553 / 4.14 ( 55) link_BETA1-4 : angle 4.23650 / 2.95 ( 165) link_BETA1-6 : bond 0.05746 / 3.70 ( 12) link_BETA1-6 : angle 3.31251 / 2.01 ( 36) link_NAG-ASN : bond 0.07541 / 4.72 ( 75) link_NAG-ASN : angle 3.14362 / 2.15 ( 225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 581 time to evaluate : 0.771 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: A 163 GLU cc_start: 0.7552 (tp30) cc_final: 0.7233 (tp30) REVERT: A 391 MET cc_start: 0.8515 (ttp) cc_final: 0.8128 (ttm) REVERT: B 545 MET cc_start: 0.7810 (mmm) cc_final: 0.7173 (tpt) REVERT: B 592 GLN cc_start: 0.6083 (tp40) cc_final: 0.5631 (tm-30) REVERT: H 55 ASP cc_start: 0.8567 (m-30) cc_final: 0.8284 (p0) REVERT: H 60 ASN cc_start: 0.8382 (t0) cc_final: 0.8155 (t0) REVERT: H 69 ILE cc_start: 0.8910 (mt) cc_final: 0.8542 (mt) REVERT: L 101 THR cc_start: 0.7782 (p) cc_final: 0.7365 (t) REVERT: C 48 ASN cc_start: 0.8024 (t0) cc_final: 0.7770 (p0) REVERT: C 265 ARG cc_start: 0.8806 (ptp90) cc_final: 0.8021 (ptp-170) REVERT: D 559 LEU cc_start: 0.8780 (tp) cc_final: 0.8425 (tt) REVERT: D 603 LYS cc_start: 0.8929 (tttm) cc_final: 0.8662 (tptt) REVERT: D 631 ILE cc_start: 0.9224 (mm) cc_final: 0.8951 (pt) REVERT: G 55 ASP cc_start: 0.8689 (m-30) cc_final: 0.8437 (m-30) REVERT: G 90 TYR cc_start: 0.7696 (m-80) cc_final: 0.7441 (m-80) REVERT: I 19 VAL cc_start: 0.6728 (t) cc_final: 0.6518 (p) REVERT: I 37 GLN cc_start: 0.8556 (tt0) cc_final: 0.8305 (tm-30) REVERT: I 74 THR cc_start: 0.7341 (m) cc_final: 0.6704 (p) REVERT: I 79 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6929 (tm-30) REVERT: I 87 TYR cc_start: 0.8943 (m-80) cc_final: 0.8621 (m-80) REVERT: E 290 TRP cc_start: 0.8699 (m100) cc_final: 0.8431 (m100) REVERT: E 391 MET cc_start: 0.8824 (ttp) cc_final: 0.8583 (ttt) REVERT: F 557 ARG cc_start: 0.7724 (ptt180) cc_final: 0.7374 (ptt90) REVERT: F 588 THR cc_start: 0.7428 (m) cc_final: 0.7157 (p) REVERT: F 633 LYS cc_start: 0.7977 (mttp) cc_final: 0.7770 (mmtt) REVERT: F 668 MET cc_start: 0.8797 (mmm) cc_final: 0.8542 (mmp) REVERT: J 54 ASN cc_start: 0.8052 (t0) cc_final: 0.7799 (p0) REVERT: J 91 TYR cc_start: 0.8017 (m-80) cc_final: 0.7673 (m-10) REVERT: J 100 TYR cc_start: 0.8719 (m-80) cc_final: 0.8466 (m-80) REVERT: K 4 LEU cc_start: 0.8586 (tp) cc_final: 0.8366 (tp) REVERT: K 19 VAL cc_start: 0.8291 (t) cc_final: 0.7992 (t) REVERT: K 24 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7542 (mtt-85) outliers start: 6 outliers final: 2 residues processed: 585 average time/residue: 0.1640 time to fit residues: 143.2130 Evaluate side-chains 289 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain E residue 476 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS A 291 HIS A 336 ASN A 394 ASN B 635 ASN B 661 GLN B 672 GLN H 56 ASN H 76 ASN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 89 GLN C 210 HIS C 270 GLN C 291 HIS C 394 ASN G 5 GLN G 76 ASN G 77 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 HIS E 433 HIS ** F 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.111629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088586 restraints weight = 51287.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088404 restraints weight = 38904.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.089317 restraints weight = 41468.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.089722 restraints weight = 31819.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090134 restraints weight = 29547.521| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23742 Z= 0.181 Angle : 0.869 13.738 32586 Z= 0.428 Chirality : 0.048 0.525 4058 Planarity : 0.005 0.063 3813 Dihedral : 5.681 35.935 2839 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.97 % Favored : 95.57 % Rotamer: Outliers : 2.25 % Allowed : 8.18 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.06 (0.16), residues: 2595 helix: 1.20 (0.24), residues: 453 sheet: 0.47 (0.20), residues: 621 loop : -0.63 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 94 TYR 0.028 0.002 TYR L 91 PHE 0.019 0.002 PHE B 537 TRP 0.019 0.002 TRP J 36 HIS 0.008 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (23534) covalent geometry : angle 0.80992 / 0.42 (31995) SS BOND : bond 0.00397 / 0.28 ( 33) SS BOND : angle 0.98053 / 0.68 ( 66) hydrogen bonds : bond 0.06716 / 4.45 ( 782) hydrogen bonds : angle 6.02476 / 4.21 ( 2049) link_ALPHA1-2 : bond 0.00439 / 0.18 ( 9) link_ALPHA1-2 : angle 2.01421 / 1.27 ( 27) link_ALPHA1-3 : bond 0.00752 / 0.46 ( 12) link_ALPHA1-3 : angle 1.72356 / 1.01 ( 36) link_ALPHA1-6 : bond 0.00563 / 0.37 ( 12) link_ALPHA1-6 : angle 1.51341 / 0.91 ( 36) link_BETA1-4 : bond 0.00808 / 0.53 ( 55) link_BETA1-4 : angle 2.32569 / 1.56 ( 165) link_BETA1-6 : bond 0.00786 / 0.49 ( 12) link_BETA1-6 : angle 1.09243 / 0.65 ( 36) link_NAG-ASN : bond 0.00671 / 0.42 ( 75) link_NAG-ASN : angle 3.23202 / 2.25 ( 225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 340 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7370 (t0) cc_final: 0.6834 (m-40) REVERT: A 391 MET cc_start: 0.8025 (ttp) cc_final: 0.7666 (ttt) REVERT: B 629 SER cc_start: 0.8166 (m) cc_final: 0.7769 (t) REVERT: H 43 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8297 (mmtm) REVERT: L 36 TYR cc_start: 0.8530 (m-80) cc_final: 0.8169 (m-80) REVERT: L 48 ILE cc_start: 0.8627 (mm) cc_final: 0.8329 (mt) REVERT: L 62 PHE cc_start: 0.8411 (m-80) cc_final: 0.8196 (m-10) REVERT: C 232 TYR cc_start: 0.8067 (m-80) cc_final: 0.7861 (m-80) REVERT: D 593 THR cc_start: 0.8789 (m) cc_final: 0.8588 (p) REVERT: D 631 ILE cc_start: 0.8942 (mm) cc_final: 0.8712 (pt) REVERT: E 391 MET cc_start: 0.8309 (ttp) cc_final: 0.8004 (ttt) REVERT: F 556 SER cc_start: 0.7230 (t) cc_final: 0.7011 (p) REVERT: F 633 LYS cc_start: 0.7564 (mttp) cc_final: 0.7345 (mmtt) REVERT: F 668 MET cc_start: 0.8651 (mmm) cc_final: 0.8423 (mmt) REVERT: J 75 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8311 (tptp) REVERT: J 89 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8918 (tt) REVERT: K 24 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7094 (mtm-85) outliers start: 52 outliers final: 25 residues processed: 374 average time/residue: 0.1420 time to fit residues: 82.9685 Evaluate side-chains 280 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 306 ASN Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain K residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 154 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN B 566 GLN B 635 ASN C 394 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100NHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084282 restraints weight = 51618.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084764 restraints weight = 41375.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085678 restraints weight = 40211.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086046 restraints weight = 31279.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086277 restraints weight = 29170.618| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23742 Z= 0.204 Angle : 0.777 10.904 32586 Z= 0.385 Chirality : 0.046 0.390 4058 Planarity : 0.004 0.044 3813 Dihedral : 5.491 36.367 2839 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.55 % Favored : 94.99 % Rotamer: Outliers : 2.42 % Allowed : 9.70 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.44 (0.16), residues: 2595 helix: 0.96 (0.23), residues: 481 sheet: 0.30 (0.18), residues: 744 loop : -1.10 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 13 TYR 0.030 0.002 TYR K 91 PHE 0.017 0.002 PHE B 537 TRP 0.018 0.002 TRP D 625 HIS 0.005 0.001 HIS J 100N Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (23534) covalent geometry : angle 0.73419 / 0.38 (31995) SS BOND : bond 0.00443 / 0.27 ( 33) SS BOND : angle 1.12529 / 0.82 ( 66) hydrogen bonds : bond 0.05521 / 3.62 ( 782) hydrogen bonds : angle 5.59148 / 3.92 ( 2049) link_ALPHA1-2 : bond 0.00423 / 0.18 ( 9) link_ALPHA1-2 : angle 1.65680 / 1.04 ( 27) link_ALPHA1-3 : bond 0.00507 / 0.32 ( 12) link_ALPHA1-3 : angle 1.63024 / 0.97 ( 36) link_ALPHA1-6 : bond 0.00550 / 0.36 ( 12) link_ALPHA1-6 : angle 1.44855 / 0.86 ( 36) link_BETA1-4 : bond 0.00512 / 0.33 ( 55) link_BETA1-4 : angle 1.70142 / 1.16 ( 165) link_BETA1-6 : bond 0.00585 / 0.38 ( 12) link_BETA1-6 : angle 1.25774 / 0.73 ( 36) link_NAG-ASN : bond 0.00425 / 0.26 ( 75) link_NAG-ASN : angle 2.64241 / 1.88 ( 225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7285 (t0) cc_final: 0.6874 (m-40) REVERT: A 391 MET cc_start: 0.8198 (ttp) cc_final: 0.7846 (ttt) REVERT: B 545 MET cc_start: 0.8407 (mmm) cc_final: 0.7735 (tpp) REVERT: B 592 GLN cc_start: 0.6421 (tm-30) cc_final: 0.6176 (tm-30) REVERT: B 668 MET cc_start: 0.8075 (mmm) cc_final: 0.7844 (tpt) REVERT: H 43 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8355 (mmtm) REVERT: L 36 TYR cc_start: 0.8616 (m-80) cc_final: 0.8348 (m-80) REVERT: L 91 TYR cc_start: 0.8314 (p90) cc_final: 0.8001 (p90) REVERT: D 556 SER cc_start: 0.8830 (m) cc_final: 0.8165 (t) REVERT: D 559 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8294 (tt) REVERT: D 603 LYS cc_start: 0.8581 (tptp) cc_final: 0.8378 (tppt) REVERT: D 631 ILE cc_start: 0.8860 (mm) cc_final: 0.8644 (pt) REVERT: G 73 MET cc_start: 0.7428 (pmm) cc_final: 0.7139 (pmm) REVERT: I 55 GLN cc_start: 0.7983 (tp40) cc_final: 0.7747 (tp-100) REVERT: E 391 MET cc_start: 0.8348 (ttp) cc_final: 0.8057 (ttt) REVERT: F 633 LYS cc_start: 0.7673 (mttp) cc_final: 0.7468 (mmtt) REVERT: F 668 MET cc_start: 0.8602 (mmm) cc_final: 0.8283 (mmt) REVERT: J 75 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8252 (tptp) REVERT: J 91 TYR cc_start: 0.7695 (m-80) cc_final: 0.7457 (m-10) REVERT: K 24 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7144 (mtm-85) outliers start: 56 outliers final: 34 residues processed: 312 average time/residue: 0.1492 time to fit residues: 73.4112 Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 181 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 394 ASN B 609 ASN B 635 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084034 restraints weight = 51471.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084270 restraints weight = 40461.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085175 restraints weight = 40716.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085491 restraints weight = 32002.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085695 restraints weight = 29838.412| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23742 Z= 0.166 Angle : 0.710 9.906 32586 Z= 0.349 Chirality : 0.043 0.344 4058 Planarity : 0.004 0.042 3813 Dihedral : 5.256 34.397 2837 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.82 % Favored : 94.72 % Rotamer: Outliers : 2.73 % Allowed : 10.39 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2595 helix: 1.18 (0.24), residues: 475 sheet: 0.18 (0.18), residues: 750 loop : -1.24 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 594 TYR 0.027 0.002 TYR K 91 PHE 0.022 0.002 PHE E 346 TRP 0.018 0.001 TRP E 345 HIS 0.004 0.001 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (23534) covalent geometry : angle 0.67251 / 0.34 (31995) SS BOND : bond 0.00364 / 0.21 ( 33) SS BOND : angle 0.81306 / 0.56 ( 66) hydrogen bonds : bond 0.04951 / 3.24 ( 782) hydrogen bonds : angle 5.34976 / 3.76 ( 2049) link_ALPHA1-2 : bond 0.00405 / 0.17 ( 9) link_ALPHA1-2 : angle 1.62235 / 1.01 ( 27) link_ALPHA1-3 : bond 0.00468 / 0.30 ( 12) link_ALPHA1-3 : angle 1.57073 / 0.94 ( 36) link_ALPHA1-6 : bond 0.00493 / 0.32 ( 12) link_ALPHA1-6 : angle 1.49483 / 0.89 ( 36) link_BETA1-4 : bond 0.00466 / 0.30 ( 55) link_BETA1-4 : angle 1.47962 / 1.01 ( 165) link_BETA1-6 : bond 0.00589 / 0.37 ( 12) link_BETA1-6 : angle 1.19357 / 0.69 ( 36) link_NAG-ASN : bond 0.00372 / 0.22 ( 75) link_NAG-ASN : angle 2.34991 / 1.68 ( 225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 267 time to evaluate : 1.039 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: A 48 ASN cc_start: 0.7361 (t0) cc_final: 0.6960 (m-40) REVERT: H 43 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8421 (mmtm) REVERT: L 36 TYR cc_start: 0.8609 (m-80) cc_final: 0.8316 (m-80) REVERT: C 497 TYR cc_start: 0.9082 (m-80) cc_final: 0.8106 (m-80) REVERT: D 556 SER cc_start: 0.8739 (m) cc_final: 0.8090 (t) REVERT: D 629 SER cc_start: 0.7944 (OUTLIER) cc_final: 0.7269 (t) REVERT: D 631 ILE cc_start: 0.8819 (mm) cc_final: 0.8607 (pt) REVERT: I 58 VAL cc_start: 0.8553 (t) cc_final: 0.8162 (p) REVERT: E 172 MET cc_start: 0.7739 (tpt) cc_final: 0.7517 (tpt) REVERT: E 391 MET cc_start: 0.8370 (ttp) cc_final: 0.8084 (ttt) REVERT: F 633 LYS cc_start: 0.7731 (mttp) cc_final: 0.7468 (mmtt) REVERT: F 668 MET cc_start: 0.8567 (mmm) cc_final: 0.8197 (mmt) REVERT: J 75 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8238 (tptp) REVERT: J 91 TYR cc_start: 0.7757 (m-80) cc_final: 0.7441 (m-10) REVERT: J 100 TYR cc_start: 0.8475 (m-80) cc_final: 0.8274 (m-80) REVERT: K 24 ARG cc_start: 0.7456 (mmm-85) cc_final: 0.7144 (mtt180) outliers start: 63 outliers final: 40 residues processed: 308 average time/residue: 0.1386 time to fit residues: 67.7603 Evaluate side-chains 274 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 231 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 199 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 394 ASN B 609 ASN B 672 GLN D 617 GLN G 77 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN J 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084676 restraints weight = 51361.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084636 restraints weight = 40231.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085558 restraints weight = 40987.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085881 restraints weight = 32365.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086110 restraints weight = 30086.237| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23742 Z= 0.129 Angle : 0.666 9.274 32586 Z= 0.326 Chirality : 0.042 0.324 4058 Planarity : 0.004 0.046 3813 Dihedral : 5.025 33.089 2837 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.89 % Favored : 94.68 % Rotamer: Outliers : 2.47 % Allowed : 11.56 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2595 helix: 1.32 (0.24), residues: 475 sheet: 0.22 (0.19), residues: 714 loop : -1.22 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 594 TYR 0.029 0.001 TYR K 91 PHE 0.020 0.001 PHE E 346 TRP 0.022 0.001 TRP E 345 HIS 0.003 0.001 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (23534) covalent geometry : angle 0.63268 / 0.32 (31995) SS BOND : bond 0.00272 / 0.15 ( 33) SS BOND : angle 0.70161 / 0.47 ( 66) hydrogen bonds : bond 0.04538 / 2.97 ( 782) hydrogen bonds : angle 5.24873 / 3.68 ( 2049) link_ALPHA1-2 : bond 0.00482 / 0.20 ( 9) link_ALPHA1-2 : angle 1.57086 / 0.97 ( 27) link_ALPHA1-3 : bond 0.00523 / 0.33 ( 12) link_ALPHA1-3 : angle 1.51521 / 0.91 ( 36) link_ALPHA1-6 : bond 0.00499 / 0.32 ( 12) link_ALPHA1-6 : angle 1.46135 / 0.87 ( 36) link_BETA1-4 : bond 0.00475 / 0.31 ( 55) link_BETA1-4 : angle 1.36569 / 0.93 ( 165) link_BETA1-6 : bond 0.00613 / 0.39 ( 12) link_BETA1-6 : angle 1.20255 / 0.69 ( 36) link_NAG-ASN : bond 0.00337 / 0.20 ( 75) link_NAG-ASN : angle 2.15107 / 1.55 ( 225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.641 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: A 48 ASN cc_start: 0.7352 (t0) cc_final: 0.6983 (m-40) REVERT: B 545 MET cc_start: 0.8464 (mmm) cc_final: 0.8216 (mmm) REVERT: B 669 TYR cc_start: 0.7687 (t80) cc_final: 0.7204 (t80) REVERT: L 18 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7262 (mmm-85) REVERT: L 91 TYR cc_start: 0.8487 (p90) cc_final: 0.7803 (p90) REVERT: C 497 TYR cc_start: 0.9025 (m-80) cc_final: 0.8064 (m-80) REVERT: D 556 SER cc_start: 0.8625 (m) cc_final: 0.7984 (t) REVERT: D 629 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7333 (t) REVERT: D 631 ILE cc_start: 0.8809 (mm) cc_final: 0.8593 (pt) REVERT: I 39 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7976 (mmmm) REVERT: I 55 GLN cc_start: 0.7798 (tp40) cc_final: 0.7551 (tp-100) REVERT: I 58 VAL cc_start: 0.8487 (t) cc_final: 0.8255 (p) REVERT: E 391 MET cc_start: 0.8364 (ttp) cc_final: 0.8032 (ttt) REVERT: F 633 LYS cc_start: 0.7635 (mttp) cc_final: 0.7396 (mmtt) REVERT: F 668 MET cc_start: 0.8511 (mmm) cc_final: 0.8164 (mmp) REVERT: J 75 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8169 (tptp) REVERT: K 24 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7153 (mtm-85) outliers start: 57 outliers final: 39 residues processed: 301 average time/residue: 0.1406 time to fit residues: 66.6049 Evaluate side-chains 268 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 210 HIS Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 553 THR Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 104 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN A 270 GLN ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN H 77 GLN L 37 GLN C 425 HIS C 433 HIS C 447 ASN D 672 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN K 6 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078044 restraints weight = 52737.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078615 restraints weight = 42769.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079379 restraints weight = 45429.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079808 restraints weight = 33105.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080129 restraints weight = 30705.963| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 23742 Z= 0.356 Angle : 0.886 8.981 32586 Z= 0.436 Chirality : 0.049 0.342 4058 Planarity : 0.006 0.068 3813 Dihedral : 5.699 35.051 2837 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.20 % Favored : 93.37 % Rotamer: Outliers : 2.94 % Allowed : 12.38 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.10 (0.16), residues: 2595 helix: 0.98 (0.24), residues: 467 sheet: -0.05 (0.19), residues: 702 loop : -1.75 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 13 TYR 0.035 0.003 TYR C 401 PHE 0.032 0.003 PHE E 346 TRP 0.026 0.002 TRP D 586 HIS 0.009 0.002 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00837 / 0.36 (23534) covalent geometry : angle 0.85325 / 0.43 (31995) SS BOND : bond 0.00733 / 0.42 ( 33) SS BOND : angle 1.37050 / 0.89 ( 66) hydrogen bonds : bond 0.05607 / 3.66 ( 782) hydrogen bonds : angle 5.54201 / 3.89 ( 2049) link_ALPHA1-2 : bond 0.00532 / 0.27 ( 9) link_ALPHA1-2 : angle 1.77924 / 1.12 ( 27) link_ALPHA1-3 : bond 0.00284 / 0.18 ( 12) link_ALPHA1-3 : angle 1.92104 / 1.15 ( 36) link_ALPHA1-6 : bond 0.00454 / 0.28 ( 12) link_ALPHA1-6 : angle 1.62810 / 0.93 ( 36) link_BETA1-4 : bond 0.00417 / 0.27 ( 55) link_BETA1-4 : angle 1.60212 / 1.12 ( 165) link_BETA1-6 : bond 0.00383 / 0.27 ( 12) link_BETA1-6 : angle 1.36291 / 0.82 ( 36) link_NAG-ASN : bond 0.00566 / 0.37 ( 75) link_NAG-ASN : angle 2.45864 / 1.72 ( 225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 225 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7430 (t0) cc_final: 0.7076 (m-40) REVERT: A 154 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: B 545 MET cc_start: 0.8660 (mmm) cc_final: 0.8097 (tpp) REVERT: H 27 ASP cc_start: 0.7748 (t0) cc_final: 0.7377 (t0) REVERT: C 404 MET cc_start: 0.7666 (mmm) cc_final: 0.7339 (mtp) REVERT: C 497 TYR cc_start: 0.9164 (m-80) cc_final: 0.8644 (m-80) REVERT: D 603 LYS cc_start: 0.8835 (tppt) cc_final: 0.8457 (tppt) REVERT: D 629 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7582 (t) REVERT: D 631 ILE cc_start: 0.8880 (mm) cc_final: 0.8672 (pt) REVERT: E 144 MET cc_start: 0.8329 (tpp) cc_final: 0.8098 (mpp) REVERT: E 391 MET cc_start: 0.8565 (ttp) cc_final: 0.8308 (ttt) REVERT: F 633 LYS cc_start: 0.7909 (mttp) cc_final: 0.7708 (mmtt) REVERT: F 668 MET cc_start: 0.8553 (mmm) cc_final: 0.8108 (mmp) REVERT: J 75 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8326 (tptp) outliers start: 68 outliers final: 45 residues processed: 266 average time/residue: 0.1398 time to fit residues: 60.0277 Evaluate side-chains 260 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 345 TRP Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 225 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN E 341 GLN ** F 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN K 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.105438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081804 restraints weight = 51734.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082931 restraints weight = 40047.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083490 restraints weight = 41398.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.083819 restraints weight = 29971.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084211 restraints weight = 27844.404| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23742 Z= 0.136 Angle : 0.709 17.050 32586 Z= 0.345 Chirality : 0.045 0.815 4058 Planarity : 0.004 0.052 3813 Dihedral : 5.270 32.906 2837 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.01 % Favored : 94.57 % Rotamer: Outliers : 1.90 % Allowed : 13.68 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.93 (0.16), residues: 2595 helix: 1.18 (0.24), residues: 468 sheet: 0.01 (0.19), residues: 687 loop : -1.60 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 594 TYR 0.037 0.002 TYR I 91 PHE 0.027 0.002 PHE F 537 TRP 0.025 0.001 TRP C 52 HIS 0.003 0.001 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (23534) covalent geometry : angle 0.66705 / 0.34 (31995) SS BOND : bond 0.00288 / 0.17 ( 33) SS BOND : angle 0.80812 / 0.53 ( 66) hydrogen bonds : bond 0.04594 / 3.02 ( 782) hydrogen bonds : angle 5.29212 / 3.71 ( 2049) link_ALPHA1-2 : bond 0.00432 / 0.20 ( 9) link_ALPHA1-2 : angle 1.58909 / 0.97 ( 27) link_ALPHA1-3 : bond 0.00532 / 0.34 ( 12) link_ALPHA1-3 : angle 1.50977 / 0.89 ( 36) link_ALPHA1-6 : bond 0.00456 / 0.28 ( 12) link_ALPHA1-6 : angle 1.49429 / 0.88 ( 36) link_BETA1-4 : bond 0.00450 / 0.30 ( 55) link_BETA1-4 : angle 1.28401 / 0.89 ( 165) link_BETA1-6 : bond 0.00626 / 0.39 ( 12) link_BETA1-6 : angle 1.20388 / 0.68 ( 36) link_NAG-ASN : bond 0.00635 / 0.27 ( 75) link_NAG-ASN : angle 2.63134 / 2.14 ( 225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7514 (t0) cc_final: 0.7152 (m-40) REVERT: A 482 MET cc_start: 0.8676 (mmt) cc_final: 0.7873 (mmm) REVERT: B 545 MET cc_start: 0.8678 (mmm) cc_final: 0.8284 (tpp) REVERT: H 27 ASP cc_start: 0.7544 (t0) cc_final: 0.7265 (t0) REVERT: H 67 ILE cc_start: 0.9027 (tt) cc_final: 0.8732 (tp) REVERT: H 89 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7957 (pp) REVERT: L 91 TYR cc_start: 0.8581 (p90) cc_final: 0.7877 (p90) REVERT: C 497 TYR cc_start: 0.9053 (m-80) cc_final: 0.8065 (m-80) REVERT: D 571 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7336 (tt) REVERT: D 603 LYS cc_start: 0.8763 (tppt) cc_final: 0.8423 (tptt) REVERT: D 629 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7524 (t) REVERT: D 631 ILE cc_start: 0.8832 (mm) cc_final: 0.8624 (pt) REVERT: D 668 MET cc_start: 0.6376 (mtt) cc_final: 0.5639 (tpt) REVERT: E 391 MET cc_start: 0.8489 (ttp) cc_final: 0.8146 (ttt) REVERT: F 620 CYS cc_start: 0.6353 (m) cc_final: 0.6136 (t) REVERT: F 633 LYS cc_start: 0.7834 (mttp) cc_final: 0.7611 (mmtp) REVERT: F 668 MET cc_start: 0.8499 (mmm) cc_final: 0.8075 (mmp) REVERT: K 3 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8205 (pp) outliers start: 44 outliers final: 29 residues processed: 265 average time/residue: 0.1388 time to fit residues: 58.9943 Evaluate side-chains 249 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 163 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN F 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.105557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082296 restraints weight = 51448.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082849 restraints weight = 40207.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083737 restraints weight = 35629.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084080 restraints weight = 29262.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084331 restraints weight = 28224.443| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23742 Z= 0.157 Angle : 0.706 16.264 32586 Z= 0.342 Chirality : 0.043 0.321 4058 Planarity : 0.004 0.052 3813 Dihedral : 5.133 32.185 2837 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.74 % Favored : 93.91 % Rotamer: Outliers : 1.90 % Allowed : 13.90 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.98 (0.16), residues: 2595 helix: 1.22 (0.24), residues: 468 sheet: -0.09 (0.19), residues: 696 loop : -1.65 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 594 TYR 0.036 0.002 TYR I 91 PHE 0.020 0.002 PHE F 537 TRP 0.024 0.001 TRP C 52 HIS 0.004 0.001 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (23534) covalent geometry : angle 0.66216 / 0.33 (31995) SS BOND : bond 0.00349 / 0.21 ( 33) SS BOND : angle 0.82083 / 0.55 ( 66) hydrogen bonds : bond 0.04495 / 2.95 ( 782) hydrogen bonds : angle 5.18970 / 3.64 ( 2049) link_ALPHA1-2 : bond 0.00372 / 0.17 ( 9) link_ALPHA1-2 : angle 1.57993 / 0.98 ( 27) link_ALPHA1-3 : bond 0.00461 / 0.30 ( 12) link_ALPHA1-3 : angle 1.55824 / 0.94 ( 36) link_ALPHA1-6 : bond 0.00429 / 0.27 ( 12) link_ALPHA1-6 : angle 1.49725 / 0.88 ( 36) link_BETA1-4 : bond 0.00426 / 0.28 ( 55) link_BETA1-4 : angle 1.26789 / 0.88 ( 165) link_BETA1-6 : bond 0.00550 / 0.35 ( 12) link_BETA1-6 : angle 1.20582 / 0.70 ( 36) link_NAG-ASN : bond 0.00487 / 0.22 ( 75) link_NAG-ASN : angle 2.69160 / 2.22 ( 225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7644 (t0) cc_final: 0.7230 (m-40) REVERT: B 545 MET cc_start: 0.8741 (mmm) cc_final: 0.8182 (tpp) REVERT: H 27 ASP cc_start: 0.7728 (t0) cc_final: 0.7485 (t0) REVERT: H 67 ILE cc_start: 0.8999 (tt) cc_final: 0.8726 (tp) REVERT: L 91 TYR cc_start: 0.8576 (p90) cc_final: 0.7909 (p90) REVERT: C 497 TYR cc_start: 0.9020 (m-80) cc_final: 0.8048 (m-80) REVERT: D 571 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7347 (tt) REVERT: D 603 LYS cc_start: 0.8789 (tppt) cc_final: 0.8415 (tppt) REVERT: D 629 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7494 (t) REVERT: D 631 ILE cc_start: 0.8801 (mm) cc_final: 0.8583 (pt) REVERT: E 202 ASN cc_start: 0.7066 (t0) cc_final: 0.6812 (p0) REVERT: E 391 MET cc_start: 0.8523 (ttp) cc_final: 0.8178 (ttt) REVERT: F 668 MET cc_start: 0.8468 (mmm) cc_final: 0.8012 (mmp) outliers start: 44 outliers final: 37 residues processed: 252 average time/residue: 0.1334 time to fit residues: 54.0974 Evaluate side-chains 251 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 394 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN K 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.104524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080869 restraints weight = 52194.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081954 restraints weight = 40926.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.082665 restraints weight = 43110.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082928 restraints weight = 30399.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083473 restraints weight = 28455.399| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23742 Z= 0.165 Angle : 0.707 13.176 32586 Z= 0.344 Chirality : 0.043 0.319 4058 Planarity : 0.004 0.050 3813 Dihedral : 5.063 32.051 2837 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.86 % Favored : 93.83 % Rotamer: Outliers : 2.03 % Allowed : 13.98 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.01 (0.16), residues: 2595 helix: 1.16 (0.24), residues: 474 sheet: -0.10 (0.19), residues: 696 loop : -1.67 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 594 TYR 0.033 0.002 TYR I 91 PHE 0.019 0.002 PHE F 537 TRP 0.025 0.001 TRP C 52 HIS 0.004 0.001 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (23534) covalent geometry : angle 0.67041 / 0.34 (31995) SS BOND : bond 0.00367 / 0.22 ( 33) SS BOND : angle 0.79920 / 0.53 ( 66) hydrogen bonds : bond 0.04401 / 2.89 ( 782) hydrogen bonds : angle 5.13753 / 3.60 ( 2049) link_ALPHA1-2 : bond 0.00363 / 0.17 ( 9) link_ALPHA1-2 : angle 1.56560 / 0.97 ( 27) link_ALPHA1-3 : bond 0.00437 / 0.29 ( 12) link_ALPHA1-3 : angle 1.58026 / 0.95 ( 36) link_ALPHA1-6 : bond 0.00409 / 0.25 ( 12) link_ALPHA1-6 : angle 1.49678 / 0.88 ( 36) link_BETA1-4 : bond 0.00400 / 0.26 ( 55) link_BETA1-4 : angle 1.25627 / 0.87 ( 165) link_BETA1-6 : bond 0.00512 / 0.33 ( 12) link_BETA1-6 : angle 1.21958 / 0.72 ( 36) link_NAG-ASN : bond 0.00511 / 0.23 ( 75) link_NAG-ASN : angle 2.40578 / 1.92 ( 225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7645 (t0) cc_final: 0.7196 (m-40) REVERT: B 545 MET cc_start: 0.8766 (mmm) cc_final: 0.8234 (tpp) REVERT: H 27 ASP cc_start: 0.7878 (t0) cc_final: 0.7574 (t0) REVERT: H 67 ILE cc_start: 0.9014 (tt) cc_final: 0.8746 (tp) REVERT: H 89 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7960 (pp) REVERT: L 91 TYR cc_start: 0.8587 (p90) cc_final: 0.7917 (p90) REVERT: C 497 TYR cc_start: 0.9015 (m-80) cc_final: 0.8028 (m-80) REVERT: D 571 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7369 (tt) REVERT: D 603 LYS cc_start: 0.8780 (tppt) cc_final: 0.8417 (tptt) REVERT: D 629 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7528 (t) REVERT: D 631 ILE cc_start: 0.8726 (mm) cc_final: 0.8511 (pt) REVERT: E 391 MET cc_start: 0.8499 (ttp) cc_final: 0.8126 (ttt) REVERT: F 668 MET cc_start: 0.8471 (mmm) cc_final: 0.7993 (mmp) outliers start: 47 outliers final: 35 residues processed: 255 average time/residue: 0.1474 time to fit residues: 59.9351 Evaluate side-chains 252 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 63 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 chunk 55 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.105795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082481 restraints weight = 51873.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082181 restraints weight = 42765.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083183 restraints weight = 42691.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083487 restraints weight = 33562.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083938 restraints weight = 31227.693| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23742 Z= 0.127 Angle : 0.688 16.525 32586 Z= 0.335 Chirality : 0.042 0.313 4058 Planarity : 0.004 0.046 3813 Dihedral : 4.944 30.771 2837 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.51 % Favored : 94.18 % Rotamer: Outliers : 1.60 % Allowed : 14.42 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.97 (0.16), residues: 2595 helix: 1.21 (0.24), residues: 474 sheet: -0.08 (0.19), residues: 705 loop : -1.65 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 594 TYR 0.026 0.001 TYR K 91 PHE 0.022 0.001 PHE E 43 TRP 0.033 0.001 TRP C 52 HIS 0.004 0.001 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (23534) covalent geometry : angle 0.65241 / 0.33 (31995) SS BOND : bond 0.00269 / 0.16 ( 33) SS BOND : angle 0.77766 / 0.50 ( 66) hydrogen bonds : bond 0.04202 / 2.76 ( 782) hydrogen bonds : angle 5.09813 / 3.58 ( 2049) link_ALPHA1-2 : bond 0.00407 / 0.19 ( 9) link_ALPHA1-2 : angle 1.53036 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00512 / 0.33 ( 12) link_ALPHA1-3 : angle 1.51204 / 0.91 ( 36) link_ALPHA1-6 : bond 0.00427 / 0.27 ( 12) link_ALPHA1-6 : angle 1.46308 / 0.87 ( 36) link_BETA1-4 : bond 0.00439 / 0.29 ( 55) link_BETA1-4 : angle 1.20589 / 0.83 ( 165) link_BETA1-6 : bond 0.00580 / 0.36 ( 12) link_BETA1-6 : angle 1.19471 / 0.70 ( 36) link_NAG-ASN : bond 0.00451 / 0.21 ( 75) link_NAG-ASN : angle 2.37338 / 1.96 ( 225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5190 Ramachandran restraints generated. 2595 Oldfield, 0 Emsley, 2595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7594 (t0) cc_final: 0.7188 (m-40) REVERT: B 545 MET cc_start: 0.8711 (mmm) cc_final: 0.8054 (tpp) REVERT: H 27 ASP cc_start: 0.7833 (t0) cc_final: 0.7517 (t0) REVERT: H 67 ILE cc_start: 0.8999 (tt) cc_final: 0.8725 (tp) REVERT: H 89 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7839 (pp) REVERT: L 18 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7597 (mmm-85) REVERT: L 91 TYR cc_start: 0.8482 (p90) cc_final: 0.7979 (p90) REVERT: C 497 TYR cc_start: 0.8928 (m-80) cc_final: 0.7941 (m-80) REVERT: D 571 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7377 (tt) REVERT: D 603 LYS cc_start: 0.8770 (tppt) cc_final: 0.8440 (tptp) REVERT: D 629 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7446 (t) REVERT: D 631 ILE cc_start: 0.8655 (mm) cc_final: 0.8446 (pt) REVERT: E 309 MET cc_start: 0.8498 (tpp) cc_final: 0.8295 (ttm) REVERT: E 391 MET cc_start: 0.8454 (ttp) cc_final: 0.8160 (ttt) REVERT: F 668 MET cc_start: 0.8361 (mmm) cc_final: 0.7982 (mmp) outliers start: 37 outliers final: 32 residues processed: 249 average time/residue: 0.1526 time to fit residues: 60.6942 Evaluate side-chains 244 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 648 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 32 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 345 TRP Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 621 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 136 optimal weight: 10.0000 chunk 225 optimal weight: 0.0040 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.105967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082716 restraints weight = 51829.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082139 restraints weight = 42507.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083152 restraints weight = 44226.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083559 restraints weight = 33953.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083971 restraints weight = 31508.220| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23742 Z= 0.128 Angle : 0.679 16.982 32586 Z= 0.331 Chirality : 0.042 0.305 4058 Planarity : 0.004 0.044 3813 Dihedral : 4.859 30.455 2837 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.90 % Favored : 93.80 % Rotamer: Outliers : 1.69 % Allowed : 14.37 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.93 (0.16), residues: 2595 helix: 1.27 (0.24), residues: 474 sheet: -0.04 (0.19), residues: 705 loop : -1.65 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 594 TYR 0.027 0.001 TYR K 91 PHE 0.026 0.001 PHE B 615 TRP 0.033 0.001 TRP C 52 HIS 0.004 0.001 HIS E 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (23534) covalent geometry : angle 0.64330 / 0.32 (31995) SS BOND : bond 0.00281 / 0.17 ( 33) SS BOND : angle 0.77202 / 0.51 ( 66) hydrogen bonds : bond 0.04113 / 2.71 ( 782) hydrogen bonds : angle 5.04122 / 3.53 ( 2049) link_ALPHA1-2 : bond 0.00378 / 0.18 ( 9) link_ALPHA1-2 : angle 1.51660 / 0.94 ( 27) link_ALPHA1-3 : bond 0.00498 / 0.33 ( 12) link_ALPHA1-3 : angle 1.51760 / 0.92 ( 36) link_ALPHA1-6 : bond 0.00415 / 0.26 ( 12) link_ALPHA1-6 : angle 1.45920 / 0.87 ( 36) link_BETA1-4 : bond 0.00433 / 0.28 ( 55) link_BETA1-4 : angle 1.19616 / 0.83 ( 165) link_BETA1-6 : bond 0.00557 / 0.35 ( 12) link_BETA1-6 : angle 1.20273 / 0.70 ( 36) link_NAG-ASN : bond 0.00419 / 0.19 ( 75) link_NAG-ASN : angle 2.32505 / 1.92 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.46 seconds wall clock time: 51 minutes 32.50 seconds (3092.50 seconds total)