Starting phenix.real_space_refine on Sun Sep 13 03:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.map" model { file = "/net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u59_20642/09_2026/6u59_20642.cif" } resolution = 3.86 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= 0.005 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12780 2.51 5 N 3342 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20439 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "B" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "F" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3562 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 24, 'TRANS': 429} Chain breaks: 3 Chain: "I" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 975 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 842 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "K" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: 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: "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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" 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: "j" 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: "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: 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: "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: 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.24, per 1000 atoms: 0.21 Number of scatterers: 20439 At special positions: 0 Unit cell: (152.95, 165.6, 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 126 16.00 O 4191 8.00 N 3342 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.13 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.13 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.13 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.05 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 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 ALPHA1-3 " BMA W 3 " - " MAN W 4 " " BMA j 3 " - " MAN j 4 " " BMA w 3 " - " MAN w 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG 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 g 1 " - " NAG g 2 " " 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 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 t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 606 " - " ASN A 197 " " NAG A 613 " - " ASN A 301 " " NAG A 614 " - " ASN A 339 " " NAG A 618 " - " ASN A 355 " " NAG A 635 " - " ASN A 396 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG B 704 " - " ASN B 611 " " NAG C 601 " - " ASN C 88 " " NAG C 606 " - " ASN C 197 " " NAG C 613 " - " ASN C 301 " " NAG C 614 " - " ASN C 339 " " NAG C 618 " - " ASN C 355 " " NAG C 635 " - " ASN C 396 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 625 " " NAG D 703 " - " ASN D 637 " " NAG D 704 " - " ASN D 611 " " NAG G 601 " - " ASN G 88 " " NAG G 606 " - " ASN G 197 " " NAG G 613 " - " ASN G 301 " " NAG G 614 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 635 " - " ASN G 396 " " NAG I 701 " - " ASN I 616 " " NAG I 702 " - " ASN I 625 " " NAG I 703 " - " ASN I 637 " " NAG I 704 " - " ASN I 611 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 362 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 241 " " NAG Y 1 " - " ASN A 413 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 295 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 362 " " NAG g 1 " - " ASN C 386 " " NAG h 1 " - " ASN C 392 " " NAG i 1 " - " ASN C 448 " " NAG j 1 " - " ASN C 262 " " NAG k 1 " - " ASN C 241 " " NAG l 1 " - " ASN C 413 " " NAG m 1 " - " ASN G 156 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN G 234 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 332 " " NAG s 1 " - " ASN G 362 " " NAG t 1 " - " ASN G 386 " " NAG u 1 " - " ASN G 392 " " NAG v 1 " - " ASN G 448 " " NAG w 1 " - " ASN G 262 " " NAG x 1 " - " ASN G 241 " " NAG y 1 " - " ASN G 413 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 790.3 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 18.9% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.587A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.790A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 530' Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 569 through 597 removed outlier: 4.037A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.587A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.791A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 530' Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 569 through 597 removed outlier: 4.037A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 651 through 662 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 116 removed outlier: 3.586A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.790A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 530 removed outlier: 4.599A pdb=" N MET I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 526 through 530' Processing helix chain 'I' and resid 538 through 543 Processing helix chain 'I' and resid 569 through 597 removed outlier: 4.036A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 648 Processing helix chain 'I' and resid 651 through 662 Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.430A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.312A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.790A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.841A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.111A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 23 removed outlier: 6.773A pdb=" N THR H 76 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.429A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.313A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.791A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 359 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 308 removed outlier: 6.842A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR E 53 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.112A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 18 through 23 removed outlier: 6.772A pdb=" N THR F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'G' and resid 75 through 76 removed outlier: 5.261A pdb=" N ILE G 215 " --> pdb=" O GLY G 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY G 250 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR G 217 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'G' and resid 169 through 176 Processing sheet with id=AD9, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.429A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 removed outlier: 10.312A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.790A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR G 357 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE G 468 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE G 359 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 301 through 308 removed outlier: 6.842A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE G 323 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY G 321 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS J 107 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 14 removed outlier: 6.650A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LYS J 107 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.112A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 23 removed outlier: 6.772A pdb=" N THR K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) 768 hydrogen bonds defined for protein. 1980 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: 4.21 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4960 1.32 - 1.46: 6549 1.46 - 1.59: 9164 1.59 - 1.73: 24 1.73 - 1.86: 156 Bond restraints: 20853 Sorted by residual: bond pdb=" CE1 HIS C 374 " pdb=" NE2 HIS C 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.84e+01 bond pdb=" CE1 HIS G 374 " pdb=" NE2 HIS G 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" CE1 HIS A 374 " pdb=" NE2 HIS A 374 " ideal model delta sigma weight residual 1.321 1.268 0.053 1.00e-02 1.00e+04 2.76e+01 bond pdb=" CB HIS G 105 " pdb=" CG HIS G 105 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" CB HIS C 105 " pdb=" CG HIS C 105 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.61e+01 ... (remaining 20848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 24014 2.39 - 4.79: 3678 4.79 - 7.18: 611 7.18 - 9.58: 38 9.58 - 11.97: 12 Bond angle restraints: 28353 Sorted by residual: angle pdb=" N GLU A 370 " pdb=" CA GLU A 370 " pdb=" C GLU A 370 " ideal model delta sigma weight residual 114.62 102.65 11.97 1.14e+00 7.69e-01 1.10e+02 angle pdb=" N GLU G 370 " pdb=" CA GLU G 370 " pdb=" C GLU G 370 " ideal model delta sigma weight residual 114.62 102.69 11.93 1.14e+00 7.69e-01 1.09e+02 angle pdb=" N GLU C 370 " pdb=" CA GLU C 370 " pdb=" C GLU C 370 " ideal model delta sigma weight residual 114.62 102.70 11.92 1.14e+00 7.69e-01 1.09e+02 angle pdb=" N ILE I 602 " pdb=" CA ILE I 602 " pdb=" C ILE I 602 " ideal model delta sigma weight residual 111.67 103.88 7.79 9.50e-01 1.11e+00 6.72e+01 angle pdb=" N ILE B 602 " pdb=" CA ILE B 602 " pdb=" C ILE B 602 " ideal model delta sigma weight residual 111.67 103.89 7.78 9.50e-01 1.11e+00 6.70e+01 ... (remaining 28348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 10934 17.64 - 35.28: 391 35.28 - 52.92: 108 52.92 - 70.56: 21 70.56 - 88.19: 15 Dihedral angle restraints: 11469 sinusoidal: 4533 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.59 32.59 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.58 32.58 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -118.56 32.56 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 11466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1736 0.065 - 0.130: 1062 0.130 - 0.195: 496 0.195 - 0.259: 181 0.259 - 0.324: 41 Chirality restraints: 3516 Sorted by residual: chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG y 2 " pdb=" O4 NAG y 1 " pdb=" C2 NAG y 2 " pdb=" O5 NAG y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.26e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 ... (remaining 3513 not shown) Planarity restraints: 3534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 107 " 0.040 2.00e-02 2.50e+03 8.11e-02 6.58e+01 pdb=" C LYS J 107 " -0.140 2.00e-02 2.50e+03 pdb=" O LYS J 107 " 0.051 2.00e-02 2.50e+03 pdb=" OXT LYS J 107 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 107 " -0.040 2.00e-02 2.50e+03 8.10e-02 6.57e+01 pdb=" C LYS E 107 " 0.140 2.00e-02 2.50e+03 pdb=" O LYS E 107 " -0.051 2.00e-02 2.50e+03 pdb=" OXT LYS E 107 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 107 " 0.040 2.00e-02 2.50e+03 8.09e-02 6.55e+01 pdb=" C LYS L 107 " -0.140 2.00e-02 2.50e+03 pdb=" O LYS L 107 " 0.051 2.00e-02 2.50e+03 pdb=" OXT LYS L 107 " 0.049 2.00e-02 2.50e+03 ... (remaining 3531 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4375 2.77 - 3.30: 18449 3.30 - 3.83: 34553 3.83 - 4.37: 40023 4.37 - 4.90: 65587 Nonbonded interactions: 162987 Sorted by model distance: nonbonded pdb=" O4 NAG k 2 " pdb=" O6 NAG k 2 " model vdw 2.234 3.040 nonbonded pdb=" O4 NAG X 2 " pdb=" O6 NAG X 2 " model vdw 2.234 3.040 nonbonded pdb=" O4 NAG x 2 " pdb=" O6 NAG x 2 " model vdw 2.234 3.040 nonbonded pdb=" O4 NAG f 2 " pdb=" O6 NAG f 2 " model vdw 2.249 3.040 nonbonded pdb=" O4 NAG S 2 " pdb=" O6 NAG S 2 " model vdw 2.249 3.040 ... (remaining 162982 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'R' selection = chain 'e' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'j' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 19.180 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.020 0.116 21003 Z= 1.051 Angle : 1.826 11.971 28770 Z= 1.158 Chirality : 0.102 0.324 3516 Planarity : 0.009 0.081 3465 Dihedral : 10.644 88.195 6918 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.34 % Rotamer: Outliers : 0.72 % Allowed : 0.58 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.59 (0.17), residues: 2364 helix: -0.50 (0.25), residues: 381 sheet: 1.10 (0.19), residues: 675 loop : 0.42 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 50 TYR 0.078 0.008 TYR L 36 PHE 0.038 0.007 PHE A 383 TRP 0.057 0.011 TRP I 610 HIS 0.019 0.003 HIS H 33 Details of bonding type rmsd/Z covalent geometry : bond 0.01915 / 1.03 (20853) covalent geometry : angle 1.80525 / 1.16 (28353) SS BOND : bond 0.03128 / 2.22 ( 33) SS BOND : angle 2.57998 / 1.87 ( 66) hydrogen bonds : bond 0.17058 / 11.36 ( 720) hydrogen bonds : angle 7.32289 / 5.05 ( 1980) link_ALPHA1-3 : bond 0.06587 / 2.93 ( 3) link_ALPHA1-3 : angle 2.80760 / 1.67 ( 9) link_BETA1-4 : bond 0.06175 / 3.85 ( 45) link_BETA1-4 : angle 3.19742 / 2.08 ( 135) link_NAG-ASN : bond 0.05096 / 3.38 ( 69) link_NAG-ASN : angle 2.83342 / 1.92 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 680 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8197 (t0) cc_final: 0.7744 (t0) REVERT: A 256 SER cc_start: 0.8648 (p) cc_final: 0.8381 (p) REVERT: A 279 ASP cc_start: 0.8479 (t0) cc_final: 0.8219 (t0) REVERT: A 317 PHE cc_start: 0.8782 (t80) cc_final: 0.8524 (t80) REVERT: A 439 ILE cc_start: 0.8866 (pt) cc_final: 0.8549 (mm) REVERT: B 542 ARG cc_start: 0.6467 (mtp180) cc_final: 0.5938 (mmt180) REVERT: B 639 THR cc_start: 0.9018 (m) cc_final: 0.8708 (p) REVERT: L 77 ASP cc_start: 0.8015 (t0) cc_final: 0.7337 (t0) REVERT: H 59 TYR cc_start: 0.7810 (m-80) cc_final: 0.7584 (m-80) REVERT: H 79 LEU cc_start: 0.8005 (tp) cc_final: 0.7205 (tp) REVERT: H 82 LEU cc_start: 0.9304 (mt) cc_final: 0.8805 (mt) REVERT: C 78 ASP cc_start: 0.8173 (t0) cc_final: 0.7777 (t0) REVERT: C 107 ASP cc_start: 0.8628 (m-30) cc_final: 0.8185 (m-30) REVERT: C 279 ASP cc_start: 0.8656 (t0) cc_final: 0.8245 (t0) REVERT: C 439 ILE cc_start: 0.9031 (pt) cc_final: 0.8738 (mm) REVERT: D 542 ARG cc_start: 0.6625 (mtp180) cc_final: 0.6072 (mmt180) REVERT: D 639 THR cc_start: 0.9000 (m) cc_final: 0.8653 (p) REVERT: E 77 ASP cc_start: 0.7885 (t0) cc_final: 0.7657 (t0) REVERT: E 95 ASP cc_start: 0.7415 (m-30) cc_final: 0.7173 (m-30) REVERT: F 39 GLN cc_start: 0.8104 (tt0) cc_final: 0.7443 (tm-30) REVERT: F 82 LEU cc_start: 0.9260 (mt) cc_final: 0.8608 (mt) REVERT: G 439 ILE cc_start: 0.8801 (pt) cc_final: 0.8498 (mm) REVERT: I 542 ARG cc_start: 0.6202 (mtp180) cc_final: 0.5839 (mmt180) REVERT: I 627 THR cc_start: 0.8920 (m) cc_final: 0.7958 (p) REVERT: I 639 THR cc_start: 0.9011 (m) cc_final: 0.8437 (p) REVERT: J 77 ASP cc_start: 0.7917 (t0) cc_final: 0.7663 (t0) REVERT: K 39 GLN cc_start: 0.8331 (tt0) cc_final: 0.7734 (tm-30) REVERT: K 82 LEU cc_start: 0.9231 (mt) cc_final: 0.8669 (mt) outliers start: 15 outliers final: 6 residues processed: 692 average time/residue: 0.1489 time to fit residues: 158.9886 Evaluate side-chains 365 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 359 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain I residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.0070 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 607 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN F 35 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072392 restraints weight = 52030.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075866 restraints weight = 25446.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078244 restraints weight = 16409.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079863 restraints weight = 12325.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080891 restraints weight = 10169.079| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21003 Z= 0.182 Angle : 0.854 9.590 28770 Z= 0.431 Chirality : 0.047 0.269 3516 Planarity : 0.005 0.045 3465 Dihedral : 5.734 38.801 2592 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.99 % Allowed : 12.14 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.26 (0.17), residues: 2364 helix: 0.56 (0.27), residues: 378 sheet: 0.58 (0.19), residues: 681 loop : -0.07 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 94 TYR 0.023 0.002 TYR K 100C PHE 0.020 0.003 PHE A 391 TRP 0.032 0.002 TRP H 36 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (20853) covalent geometry : angle 0.81618 / 0.42 (28353) SS BOND : bond 0.00204 / 0.14 ( 33) SS BOND : angle 1.16572 / 0.76 ( 66) hydrogen bonds : bond 0.05924 / 3.97 ( 720) hydrogen bonds : angle 6.03288 / 4.20 ( 1980) link_ALPHA1-3 : bond 0.00467 / 0.21 ( 3) link_ALPHA1-3 : angle 1.66927 / 0.97 ( 9) link_BETA1-4 : bond 0.00470 / 0.29 ( 45) link_BETA1-4 : angle 1.91330 / 1.23 ( 135) link_NAG-ASN : bond 0.00682 / 0.47 ( 69) link_NAG-ASN : angle 2.70097 / 1.80 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 478 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8408 (ptm) cc_final: 0.8074 (ptp) REVERT: A 116 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 117 LYS cc_start: 0.8932 (tttt) cc_final: 0.8657 (ttmm) REVERT: A 122 LEU cc_start: 0.8991 (mp) cc_final: 0.8723 (tt) REVERT: A 302 ASN cc_start: 0.7912 (t0) cc_final: 0.7701 (t0) REVERT: B 530 MET cc_start: 0.7430 (mmm) cc_final: 0.6747 (mmm) REVERT: B 566 LEU cc_start: 0.8356 (tt) cc_final: 0.8112 (tt) REVERT: B 621 GLU cc_start: 0.8311 (tt0) cc_final: 0.7986 (tt0) REVERT: B 639 THR cc_start: 0.8999 (m) cc_final: 0.8792 (p) REVERT: B 647 GLU cc_start: 0.9307 (tt0) cc_final: 0.9098 (tt0) REVERT: L 42 GLN cc_start: 0.7089 (mp10) cc_final: 0.6526 (mp10) REVERT: L 75 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.8842 (tp) REVERT: L 77 ASP cc_start: 0.7962 (t0) cc_final: 0.6854 (t0) REVERT: L 78 LEU cc_start: 0.8663 (mp) cc_final: 0.8274 (mp) REVERT: L 95 ASP cc_start: 0.7300 (m-30) cc_final: 0.6755 (m-30) REVERT: H 7 SER cc_start: 0.8474 (p) cc_final: 0.8167 (p) REVERT: H 30 SER cc_start: 0.9230 (m) cc_final: 0.8932 (m) REVERT: H 33 HIS cc_start: 0.8598 (m170) cc_final: 0.8364 (m170) REVERT: H 57 ILE cc_start: 0.9451 (pt) cc_final: 0.9126 (mp) REVERT: C 67 ASN cc_start: 0.8732 (m-40) cc_final: 0.8522 (t0) REVERT: C 370 GLU cc_start: 0.8342 (tp30) cc_final: 0.8122 (tp30) REVERT: C 424 ILE cc_start: 0.9406 (pp) cc_final: 0.9198 (pp) REVERT: D 565 MET cc_start: 0.8402 (mpp) cc_final: 0.8116 (mpp) REVERT: D 566 LEU cc_start: 0.8781 (tp) cc_final: 0.8452 (tt) REVERT: D 595 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8829 (tp) REVERT: D 603 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8404 (pt) REVERT: D 627 THR cc_start: 0.8382 (p) cc_final: 0.8171 (t) REVERT: D 630 GLN cc_start: 0.8906 (mt0) cc_final: 0.8362 (mt0) REVERT: D 647 GLU cc_start: 0.9065 (tt0) cc_final: 0.8737 (tt0) REVERT: D 653 GLN cc_start: 0.8999 (tt0) cc_final: 0.8699 (pp30) REVERT: E 42 GLN cc_start: 0.7456 (mp10) cc_final: 0.6837 (mp10) REVERT: E 77 ASP cc_start: 0.8158 (t0) cc_final: 0.7217 (t0) REVERT: E 78 LEU cc_start: 0.8757 (mp) cc_final: 0.8394 (mp) REVERT: E 95 ASP cc_start: 0.7630 (m-30) cc_final: 0.7244 (m-30) REVERT: F 7 SER cc_start: 0.8176 (p) cc_final: 0.7937 (p) REVERT: F 30 SER cc_start: 0.9238 (m) cc_final: 0.8831 (m) REVERT: F 33 HIS cc_start: 0.8495 (m170) cc_final: 0.8167 (m170) REVERT: F 57 ILE cc_start: 0.9467 (pt) cc_final: 0.9167 (mp) REVERT: F 59 TYR cc_start: 0.7763 (m-80) cc_final: 0.7289 (m-80) REVERT: F 62 TRP cc_start: 0.8655 (t-100) cc_final: 0.8150 (t-100) REVERT: G 67 ASN cc_start: 0.8603 (m-40) cc_final: 0.8211 (t0) REVERT: G 74 CYS cc_start: 0.8045 (m) cc_final: 0.7573 (m) REVERT: G 195 ASN cc_start: 0.7919 (m-40) cc_final: 0.7564 (m-40) REVERT: G 370 GLU cc_start: 0.8414 (tp30) cc_final: 0.8098 (tp30) REVERT: G 398 THR cc_start: 0.8306 (p) cc_final: 0.7766 (t) REVERT: I 530 MET cc_start: 0.7299 (mmm) cc_final: 0.6439 (mmm) REVERT: I 566 LEU cc_start: 0.8457 (tp) cc_final: 0.7991 (tt) REVERT: J 42 GLN cc_start: 0.7228 (mp10) cc_final: 0.6735 (mp10) REVERT: J 63 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8362 (mmtt) REVERT: J 77 ASP cc_start: 0.7979 (t0) cc_final: 0.7231 (t0) REVERT: J 78 LEU cc_start: 0.8466 (mp) cc_final: 0.8086 (mp) REVERT: J 95 ASP cc_start: 0.7638 (m-30) cc_final: 0.7195 (m-30) REVERT: K 7 SER cc_start: 0.8347 (p) cc_final: 0.7960 (p) REVERT: K 30 SER cc_start: 0.9281 (m) cc_final: 0.8922 (m) REVERT: K 33 HIS cc_start: 0.8597 (m170) cc_final: 0.8331 (m170) REVERT: K 36 TRP cc_start: 0.8200 (m100) cc_final: 0.7897 (m-10) REVERT: K 57 ILE cc_start: 0.9368 (pt) cc_final: 0.9063 (mp) REVERT: K 58 TYR cc_start: 0.7756 (p90) cc_final: 0.7355 (p90) REVERT: K 59 TYR cc_start: 0.7676 (m-80) cc_final: 0.7207 (m-80) REVERT: K 62 TRP cc_start: 0.8564 (t-100) cc_final: 0.8112 (t-100) outliers start: 62 outliers final: 35 residues processed: 510 average time/residue: 0.1329 time to fit residues: 108.7136 Evaluate side-chains 403 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 364 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS A 422 GLN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 330 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 203 GLN G 330 HIS ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.065957 restraints weight = 53746.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069065 restraints weight = 27342.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071214 restraints weight = 18164.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072701 restraints weight = 13962.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.073692 restraints weight = 11704.317| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 21003 Z= 0.251 Angle : 0.831 17.068 28770 Z= 0.409 Chirality : 0.049 0.250 3516 Planarity : 0.004 0.055 3465 Dihedral : 5.593 41.688 2586 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.29 % Allowed : 14.26 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2364 helix: 0.59 (0.27), residues: 363 sheet: 0.49 (0.19), residues: 666 loop : -0.60 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 28 TYR 0.029 0.002 TYR K 100C PHE 0.040 0.003 PHE L 96 TRP 0.049 0.003 TRP F 36 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (20853) covalent geometry : angle 0.79769 / 0.40 (28353) SS BOND : bond 0.00326 / 0.22 ( 33) SS BOND : angle 0.99192 / 0.63 ( 66) hydrogen bonds : bond 0.05479 / 3.70 ( 720) hydrogen bonds : angle 5.71987 / 3.98 ( 1980) link_ALPHA1-3 : bond 0.00425 / 0.19 ( 3) link_ALPHA1-3 : angle 1.28196 / 0.74 ( 9) link_BETA1-4 : bond 0.00663 / 0.43 ( 45) link_BETA1-4 : angle 1.68821 / 1.06 ( 135) link_NAG-ASN : bond 0.00583 / 0.38 ( 69) link_NAG-ASN : angle 2.58095 / 1.69 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 392 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8306 (ptm) cc_final: 0.7967 (ptp) REVERT: A 180 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8730 (t0) REVERT: A 420 ILE cc_start: 0.9260 (mp) cc_final: 0.8908 (mt) REVERT: A 468 PHE cc_start: 0.8687 (m-80) cc_final: 0.8080 (m-80) REVERT: B 530 MET cc_start: 0.7623 (mmm) cc_final: 0.7023 (mmm) REVERT: B 621 GLU cc_start: 0.8921 (tt0) cc_final: 0.8530 (tt0) REVERT: B 626 MET cc_start: 0.8229 (tpp) cc_final: 0.7599 (ttt) REVERT: L 4 MET cc_start: 0.6842 (mmm) cc_final: 0.6151 (tpp) REVERT: L 21 ILE cc_start: 0.8969 (mm) cc_final: 0.8422 (tp) REVERT: L 42 GLN cc_start: 0.6949 (mp10) cc_final: 0.6515 (mp10) REVERT: L 61 ARG cc_start: 0.8599 (ptp-170) cc_final: 0.7908 (mpp80) REVERT: L 77 ASP cc_start: 0.7735 (t0) cc_final: 0.7394 (t0) REVERT: L 82 ASP cc_start: 0.6523 (p0) cc_final: 0.6182 (p0) REVERT: L 95 ASP cc_start: 0.7418 (m-30) cc_final: 0.6857 (p0) REVERT: H 13 GLN cc_start: 0.8713 (pp30) cc_final: 0.8462 (pp30) REVERT: H 20 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8943 (mm) REVERT: H 31 ASP cc_start: 0.9005 (p0) cc_final: 0.8733 (p0) REVERT: H 33 HIS cc_start: 0.8865 (m170) cc_final: 0.8398 (m170) REVERT: H 57 ILE cc_start: 0.9582 (pt) cc_final: 0.9265 (mp) REVERT: C 67 ASN cc_start: 0.8913 (m-40) cc_final: 0.8574 (t0) REVERT: C 398 THR cc_start: 0.8360 (p) cc_final: 0.8003 (t) REVERT: C 420 ILE cc_start: 0.9217 (mp) cc_final: 0.8833 (mt) REVERT: C 424 ILE cc_start: 0.9365 (pp) cc_final: 0.9150 (pp) REVERT: D 566 LEU cc_start: 0.8930 (tp) cc_final: 0.8552 (tt) REVERT: D 595 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8845 (tp) REVERT: D 621 GLU cc_start: 0.8928 (tt0) cc_final: 0.8555 (tt0) REVERT: D 652 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8576 (mp10) REVERT: D 653 GLN cc_start: 0.9060 (tt0) cc_final: 0.8418 (tm-30) REVERT: E 24 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8377 (mm-40) REVERT: E 36 TYR cc_start: 0.7251 (m-80) cc_final: 0.6544 (m-80) REVERT: E 42 GLN cc_start: 0.7376 (mp10) cc_final: 0.6846 (mp10) REVERT: E 63 LYS cc_start: 0.8266 (mmtt) cc_final: 0.8036 (mmtt) REVERT: E 75 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8774 (tp) REVERT: E 77 ASP cc_start: 0.7868 (t0) cc_final: 0.7360 (t0) REVERT: E 82 ASP cc_start: 0.6569 (p0) cc_final: 0.6211 (p0) REVERT: E 95 ASP cc_start: 0.7816 (m-30) cc_final: 0.7305 (p0) REVERT: F 33 HIS cc_start: 0.8942 (m170) cc_final: 0.8605 (m170) REVERT: F 36 TRP cc_start: 0.8452 (m100) cc_final: 0.7961 (m-10) REVERT: F 57 ILE cc_start: 0.9583 (pt) cc_final: 0.9246 (mp) REVERT: F 59 TYR cc_start: 0.8126 (m-80) cc_final: 0.7677 (m-80) REVERT: F 62 TRP cc_start: 0.8707 (t-100) cc_final: 0.8485 (t-100) REVERT: G 67 ASN cc_start: 0.8794 (m-40) cc_final: 0.8397 (t0) REVERT: G 74 CYS cc_start: 0.8261 (m) cc_final: 0.7624 (m) REVERT: G 95 MET cc_start: 0.7601 (ptp) cc_final: 0.7210 (ptp) REVERT: G 398 THR cc_start: 0.8560 (p) cc_final: 0.8214 (t) REVERT: G 420 ILE cc_start: 0.9265 (mp) cc_final: 0.8921 (mt) REVERT: G 434 MET cc_start: 0.8562 (ttm) cc_final: 0.8190 (ttp) REVERT: I 530 MET cc_start: 0.7661 (mmm) cc_final: 0.6886 (mmm) REVERT: I 595 ILE cc_start: 0.9228 (tp) cc_final: 0.8739 (tt) REVERT: I 627 THR cc_start: 0.8714 (m) cc_final: 0.8473 (p) REVERT: I 653 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: J 42 GLN cc_start: 0.7070 (mp10) cc_final: 0.6666 (mp10) REVERT: J 63 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8381 (mmtt) REVERT: J 75 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8732 (tp) REVERT: J 77 ASP cc_start: 0.8201 (t0) cc_final: 0.7915 (t0) REVERT: J 82 ASP cc_start: 0.6533 (p0) cc_final: 0.6182 (p0) REVERT: J 95 ASP cc_start: 0.7731 (m-30) cc_final: 0.6894 (p0) REVERT: K 6 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: K 15 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8589 (tp30) REVERT: K 31 ASP cc_start: 0.9087 (p0) cc_final: 0.8851 (p0) REVERT: K 33 HIS cc_start: 0.8727 (m170) cc_final: 0.8422 (m170) REVERT: K 36 TRP cc_start: 0.8233 (m100) cc_final: 0.8007 (m-10) REVERT: K 38 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7631 (ttm170) REVERT: K 59 TYR cc_start: 0.8057 (m-80) cc_final: 0.7355 (m-80) outliers start: 89 outliers final: 45 residues processed: 449 average time/residue: 0.1362 time to fit residues: 98.1926 Evaluate side-chains 391 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain I residue 630 GLN Chi-restraints excluded: chain I residue 653 GLN Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 67 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN G 203 GLN ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068292 restraints weight = 53097.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071522 restraints weight = 27129.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073742 restraints weight = 17955.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.075240 restraints weight = 13793.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.076169 restraints weight = 11543.167| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21003 Z= 0.145 Angle : 0.732 15.158 28770 Z= 0.355 Chirality : 0.045 0.225 3516 Planarity : 0.004 0.046 3465 Dihedral : 5.304 37.577 2586 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.52 % Allowed : 14.64 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2364 helix: 0.73 (0.27), residues: 363 sheet: 0.35 (0.19), residues: 726 loop : -0.65 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 28 TYR 0.015 0.001 TYR K 58 PHE 0.021 0.002 PHE H 47 TRP 0.030 0.002 TRP H 36 HIS 0.002 0.000 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (20853) covalent geometry : angle 0.70011 / 0.35 (28353) SS BOND : bond 0.00168 / 0.12 ( 33) SS BOND : angle 0.66694 / 0.45 ( 66) hydrogen bonds : bond 0.04734 / 3.19 ( 720) hydrogen bonds : angle 5.52690 / 3.85 ( 1980) link_ALPHA1-3 : bond 0.00520 / 0.23 ( 3) link_ALPHA1-3 : angle 1.51872 / 0.83 ( 9) link_BETA1-4 : bond 0.00560 / 0.36 ( 45) link_BETA1-4 : angle 1.44408 / 0.89 ( 135) link_NAG-ASN : bond 0.00375 / 0.23 ( 69) link_NAG-ASN : angle 2.41485 / 1.54 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8342 (ptm) cc_final: 0.8001 (ptp) REVERT: A 116 LEU cc_start: 0.8653 (tt) cc_final: 0.8427 (tt) REVERT: A 180 ASP cc_start: 0.8918 (m-30) cc_final: 0.8712 (t0) REVERT: A 420 ILE cc_start: 0.9156 (mp) cc_final: 0.8811 (mt) REVERT: A 468 PHE cc_start: 0.8590 (m-80) cc_final: 0.8042 (m-10) REVERT: B 530 MET cc_start: 0.7659 (mmm) cc_final: 0.7085 (mmm) REVERT: B 586 TYR cc_start: 0.8432 (t80) cc_final: 0.8229 (t80) REVERT: B 621 GLU cc_start: 0.8966 (tt0) cc_final: 0.8603 (tt0) REVERT: B 626 MET cc_start: 0.8154 (tpp) cc_final: 0.7733 (ttt) REVERT: B 647 GLU cc_start: 0.8976 (tt0) cc_final: 0.8773 (tp30) REVERT: L 4 MET cc_start: 0.6719 (mmm) cc_final: 0.6300 (tpp) REVERT: L 21 ILE cc_start: 0.8879 (mm) cc_final: 0.8386 (tp) REVERT: L 24 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8305 (mm110) REVERT: L 42 GLN cc_start: 0.6960 (mp10) cc_final: 0.6626 (mp10) REVERT: L 61 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.7922 (mpp80) REVERT: L 75 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8718 (tp) REVERT: L 77 ASP cc_start: 0.7637 (t0) cc_final: 0.7147 (t0) REVERT: L 82 ASP cc_start: 0.6107 (p0) cc_final: 0.5501 (p0) REVERT: L 95 ASP cc_start: 0.7383 (m-30) cc_final: 0.6862 (p0) REVERT: H 5 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8010 (tm-30) REVERT: H 13 GLN cc_start: 0.8806 (pp30) cc_final: 0.8489 (pp30) REVERT: H 15 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8527 (tp30) REVERT: H 33 HIS cc_start: 0.8776 (m170) cc_final: 0.8466 (m170) REVERT: H 57 ILE cc_start: 0.9597 (pt) cc_final: 0.9311 (mp) REVERT: H 100 TYR cc_start: 0.8478 (p90) cc_final: 0.8182 (p90) REVERT: C 67 ASN cc_start: 0.8824 (m-40) cc_final: 0.8558 (t0) REVERT: C 268 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7314 (mt-10) REVERT: C 420 ILE cc_start: 0.9170 (mp) cc_final: 0.8817 (mt) REVERT: D 530 MET cc_start: 0.8196 (mmm) cc_final: 0.7179 (mmm) REVERT: D 566 LEU cc_start: 0.8893 (tp) cc_final: 0.8507 (tt) REVERT: D 595 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8781 (tp) REVERT: D 621 GLU cc_start: 0.8972 (tt0) cc_final: 0.8521 (tt0) REVERT: D 647 GLU cc_start: 0.9050 (tt0) cc_final: 0.8823 (tp30) REVERT: E 42 GLN cc_start: 0.7280 (mp10) cc_final: 0.6811 (mp10) REVERT: E 77 ASP cc_start: 0.7603 (t0) cc_final: 0.7205 (t0) REVERT: E 82 ASP cc_start: 0.6096 (p0) cc_final: 0.5789 (p0) REVERT: E 95 ASP cc_start: 0.7759 (m-30) cc_final: 0.7358 (p0) REVERT: F 5 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 28 ASP cc_start: 0.6890 (t0) cc_final: 0.6653 (t0) REVERT: F 30 SER cc_start: 0.9099 (m) cc_final: 0.8814 (m) REVERT: F 31 ASP cc_start: 0.9092 (p0) cc_final: 0.8835 (p0) REVERT: F 36 TRP cc_start: 0.8429 (m100) cc_final: 0.8073 (m-10) REVERT: F 57 ILE cc_start: 0.9570 (pt) cc_final: 0.9270 (mp) REVERT: F 59 TYR cc_start: 0.8213 (m-80) cc_final: 0.7837 (m-80) REVERT: G 67 ASN cc_start: 0.8723 (m-40) cc_final: 0.8316 (t0) REVERT: G 74 CYS cc_start: 0.8164 (m) cc_final: 0.7522 (m) REVERT: G 95 MET cc_start: 0.7495 (ptp) cc_final: 0.6968 (ptp) REVERT: G 398 THR cc_start: 0.8622 (p) cc_final: 0.8342 (t) REVERT: G 420 ILE cc_start: 0.9193 (mp) cc_final: 0.8867 (mt) REVERT: G 434 MET cc_start: 0.8484 (ttm) cc_final: 0.8068 (ttm) REVERT: I 529 THR cc_start: 0.8275 (m) cc_final: 0.8014 (m) REVERT: I 530 MET cc_start: 0.7540 (mmm) cc_final: 0.6706 (mmm) REVERT: I 595 ILE cc_start: 0.9147 (tp) cc_final: 0.8743 (tp) REVERT: I 627 THR cc_start: 0.8702 (m) cc_final: 0.8210 (p) REVERT: I 629 MET cc_start: 0.8680 (mmm) cc_final: 0.8156 (mmm) REVERT: I 647 GLU cc_start: 0.8988 (tt0) cc_final: 0.8618 (tp30) REVERT: J 42 GLN cc_start: 0.7082 (mp10) cc_final: 0.6686 (mp10) REVERT: J 75 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8692 (tp) REVERT: J 77 ASP cc_start: 0.8054 (t0) cc_final: 0.7696 (t0) REVERT: J 82 ASP cc_start: 0.5970 (p0) cc_final: 0.5490 (p0) REVERT: J 95 ASP cc_start: 0.7698 (m-30) cc_final: 0.6908 (p0) REVERT: K 5 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7874 (tm-30) REVERT: K 6 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: K 7 SER cc_start: 0.8676 (p) cc_final: 0.8471 (m) REVERT: K 15 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8613 (tp30) REVERT: K 28 ASP cc_start: 0.7210 (t0) cc_final: 0.7002 (t0) REVERT: K 30 SER cc_start: 0.9068 (m) cc_final: 0.8863 (m) REVERT: K 31 ASP cc_start: 0.9182 (p0) cc_final: 0.8976 (p0) REVERT: K 33 HIS cc_start: 0.8651 (m170) cc_final: 0.8404 (m170) REVERT: K 38 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7366 (ttm-80) REVERT: K 57 ILE cc_start: 0.9564 (pt) cc_final: 0.9184 (mp) REVERT: K 59 TYR cc_start: 0.8126 (m-80) cc_final: 0.7439 (m-80) REVERT: K 100 TYR cc_start: 0.8347 (p90) cc_final: 0.8014 (p90) outliers start: 73 outliers final: 53 residues processed: 419 average time/residue: 0.1370 time to fit residues: 92.4870 Evaluate side-chains 395 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 87 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.069354 restraints weight = 52915.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071962 restraints weight = 31318.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.073740 restraints weight = 22355.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.074959 restraints weight = 17889.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075774 restraints weight = 15371.282| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 21003 Z= 0.234 Angle : 0.765 15.583 28770 Z= 0.371 Chirality : 0.046 0.209 3516 Planarity : 0.004 0.042 3465 Dihedral : 5.146 31.326 2580 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.09 % Allowed : 15.66 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.43 (0.17), residues: 2364 helix: 0.75 (0.28), residues: 366 sheet: 0.21 (0.18), residues: 729 loop : -0.88 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 28 TYR 0.024 0.002 TYR H 90 PHE 0.025 0.003 PHE L 96 TRP 0.045 0.002 TRP H 36 HIS 0.013 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (20853) covalent geometry : angle 0.73520 / 0.37 (28353) SS BOND : bond 0.00271 / 0.18 ( 33) SS BOND : angle 0.76009 / 0.49 ( 66) hydrogen bonds : bond 0.05009 / 3.37 ( 720) hydrogen bonds : angle 5.56034 / 3.87 ( 1980) link_ALPHA1-3 : bond 0.00402 / 0.18 ( 3) link_ALPHA1-3 : angle 1.41082 / 0.81 ( 9) link_BETA1-4 : bond 0.00490 / 0.32 ( 45) link_BETA1-4 : angle 1.55409 / 0.96 ( 135) link_NAG-ASN : bond 0.00542 / 0.36 ( 69) link_NAG-ASN : angle 2.32444 / 1.49 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 351 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8615 (p) cc_final: 0.8373 (p) REVERT: A 420 ILE cc_start: 0.9191 (mp) cc_final: 0.8878 (mt) REVERT: A 468 PHE cc_start: 0.8371 (m-80) cc_final: 0.7815 (m-10) REVERT: B 530 MET cc_start: 0.7407 (mmm) cc_final: 0.7122 (mmm) REVERT: B 621 GLU cc_start: 0.8730 (tt0) cc_final: 0.8344 (tt0) REVERT: L 21 ILE cc_start: 0.8627 (mm) cc_final: 0.8347 (tp) REVERT: L 42 GLN cc_start: 0.7340 (mp10) cc_final: 0.6891 (mp10) REVERT: L 52 SER cc_start: 0.8637 (p) cc_final: 0.8421 (t) REVERT: L 75 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8542 (tp) REVERT: L 77 ASP cc_start: 0.7515 (t0) cc_final: 0.7244 (t0) REVERT: L 82 ASP cc_start: 0.6052 (p0) cc_final: 0.5653 (p0) REVERT: L 95 ASP cc_start: 0.7426 (m-30) cc_final: 0.7072 (m-30) REVERT: H 15 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8316 (tp30) REVERT: H 31 ASP cc_start: 0.8789 (p0) cc_final: 0.8535 (p0) REVERT: H 38 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8069 (ttm170) REVERT: C 67 ASN cc_start: 0.8887 (m-40) cc_final: 0.8645 (t0) REVERT: C 116 LEU cc_start: 0.8673 (tt) cc_final: 0.8438 (tt) REVERT: C 420 ILE cc_start: 0.9197 (mp) cc_final: 0.8853 (mt) REVERT: C 475 MET cc_start: 0.8433 (mmp) cc_final: 0.8119 (mmp) REVERT: C 479 TRP cc_start: 0.8358 (m-10) cc_final: 0.8128 (m-90) REVERT: D 530 MET cc_start: 0.7866 (mmm) cc_final: 0.7137 (mmm) REVERT: D 566 LEU cc_start: 0.8949 (tp) cc_final: 0.8597 (tt) REVERT: D 595 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9222 (tp) REVERT: D 602 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9054 (tp) REVERT: D 621 GLU cc_start: 0.8859 (tt0) cc_final: 0.8519 (tt0) REVERT: E 36 TYR cc_start: 0.7398 (m-80) cc_final: 0.6720 (m-80) REVERT: E 42 GLN cc_start: 0.7677 (mp10) cc_final: 0.7201 (mp10) REVERT: E 75 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8478 (tp) REVERT: E 77 ASP cc_start: 0.7681 (t0) cc_final: 0.7381 (t0) REVERT: E 82 ASP cc_start: 0.6058 (p0) cc_final: 0.5700 (p0) REVERT: E 95 ASP cc_start: 0.7841 (m-30) cc_final: 0.7548 (m-30) REVERT: F 28 ASP cc_start: 0.7003 (t0) cc_final: 0.6624 (t0) REVERT: F 30 SER cc_start: 0.9105 (m) cc_final: 0.8807 (m) REVERT: F 31 ASP cc_start: 0.8838 (p0) cc_final: 0.8541 (p0) REVERT: F 36 TRP cc_start: 0.8654 (m100) cc_final: 0.8345 (m-10) REVERT: F 46 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7634 (mp0) REVERT: F 100 TYR cc_start: 0.8582 (p90) cc_final: 0.8370 (p90) REVERT: G 67 ASN cc_start: 0.8825 (m-40) cc_final: 0.8533 (t0) REVERT: G 74 CYS cc_start: 0.7811 (m) cc_final: 0.7263 (m) REVERT: G 95 MET cc_start: 0.7491 (ptp) cc_final: 0.7206 (ptp) REVERT: G 420 ILE cc_start: 0.9312 (mp) cc_final: 0.9037 (mt) REVERT: G 434 MET cc_start: 0.8452 (ttm) cc_final: 0.8082 (ttm) REVERT: I 530 MET cc_start: 0.7164 (mmm) cc_final: 0.6614 (mmm) REVERT: I 629 MET cc_start: 0.8625 (mmm) cc_final: 0.8270 (tpp) REVERT: J 42 GLN cc_start: 0.7347 (mp10) cc_final: 0.6877 (mp10) REVERT: J 63 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8284 (mmtt) REVERT: J 75 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8511 (tp) REVERT: J 82 ASP cc_start: 0.6195 (p0) cc_final: 0.5782 (p0) REVERT: J 95 ASP cc_start: 0.7779 (m-30) cc_final: 0.7470 (m-30) REVERT: K 6 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.5639 (mp0) REVERT: K 15 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8423 (tp30) REVERT: K 28 ASP cc_start: 0.7378 (t0) cc_final: 0.7031 (t0) REVERT: K 30 SER cc_start: 0.9157 (m) cc_final: 0.8927 (m) REVERT: K 57 ILE cc_start: 0.9553 (pt) cc_final: 0.9253 (mp) REVERT: K 59 TYR cc_start: 0.7966 (m-80) cc_final: 0.7536 (m-80) outliers start: 85 outliers final: 61 residues processed: 395 average time/residue: 0.1385 time to fit residues: 87.6022 Evaluate side-chains 389 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 321 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain L residue 96 PHE Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 161 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 172 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 80 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 70 GLN F 35 GLN G 203 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 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 = 0.3447 r_free = 0.3447 target = 0.092219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071915 restraints weight = 52282.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074542 restraints weight = 30585.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076360 restraints weight = 21749.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077552 restraints weight = 17301.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078426 restraints weight = 14882.119| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21003 Z= 0.140 Angle : 0.707 15.676 28770 Z= 0.344 Chirality : 0.046 0.282 3516 Planarity : 0.004 0.040 3465 Dihedral : 4.947 28.430 2580 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.32 % Allowed : 16.96 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.39 (0.17), residues: 2364 helix: 0.67 (0.27), residues: 366 sheet: 0.30 (0.19), residues: 702 loop : -0.84 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 28 TYR 0.018 0.001 TYR K 58 PHE 0.021 0.002 PHE L 96 TRP 0.051 0.002 TRP H 36 HIS 0.018 0.001 HIS H 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (20853) covalent geometry : angle 0.68066 / 0.34 (28353) SS BOND : bond 0.00160 / 0.11 ( 33) SS BOND : angle 0.57036 / 0.38 ( 66) hydrogen bonds : bond 0.04543 / 3.05 ( 720) hydrogen bonds : angle 5.41222 / 3.77 ( 1980) link_ALPHA1-3 : bond 0.00414 / 0.19 ( 3) link_ALPHA1-3 : angle 1.47830 / 0.81 ( 9) link_BETA1-4 : bond 0.00514 / 0.33 ( 45) link_BETA1-4 : angle 1.36895 / 0.83 ( 135) link_NAG-ASN : bond 0.00382 / 0.26 ( 69) link_NAG-ASN : angle 2.14391 / 1.38 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 347 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8566 (p) cc_final: 0.8307 (p) REVERT: A 420 ILE cc_start: 0.9119 (mp) cc_final: 0.8789 (mt) REVERT: A 468 PHE cc_start: 0.8213 (m-80) cc_final: 0.7698 (m-10) REVERT: A 479 TRP cc_start: 0.8304 (m-10) cc_final: 0.7862 (m-90) REVERT: B 530 MET cc_start: 0.7170 (mmm) cc_final: 0.6933 (mmm) REVERT: B 566 LEU cc_start: 0.8827 (tt) cc_final: 0.8597 (tt) REVERT: B 595 ILE cc_start: 0.9538 (tp) cc_final: 0.9140 (tp) REVERT: B 621 GLU cc_start: 0.8600 (tt0) cc_final: 0.8283 (tt0) REVERT: L 21 ILE cc_start: 0.8653 (mm) cc_final: 0.8413 (tp) REVERT: L 42 GLN cc_start: 0.7369 (mp10) cc_final: 0.6931 (mp10) REVERT: L 52 SER cc_start: 0.8547 (p) cc_final: 0.8342 (t) REVERT: L 75 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8486 (tp) REVERT: L 82 ASP cc_start: 0.5943 (p0) cc_final: 0.5567 (p0) REVERT: L 95 ASP cc_start: 0.7456 (m-30) cc_final: 0.7220 (m-30) REVERT: H 13 GLN cc_start: 0.8492 (pp30) cc_final: 0.8288 (pp30) REVERT: H 15 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8222 (tp30) REVERT: H 38 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8073 (ttm170) REVERT: C 420 ILE cc_start: 0.9158 (mp) cc_final: 0.8836 (mt) REVERT: C 475 MET cc_start: 0.8282 (mmp) cc_final: 0.7966 (mmp) REVERT: C 479 TRP cc_start: 0.8246 (m-10) cc_final: 0.8004 (m-90) REVERT: D 530 MET cc_start: 0.7823 (mmm) cc_final: 0.7175 (mmm) REVERT: D 566 LEU cc_start: 0.8912 (tp) cc_final: 0.8586 (tt) REVERT: D 602 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9102 (tp) REVERT: D 621 GLU cc_start: 0.8841 (tt0) cc_final: 0.8505 (tt0) REVERT: E 42 GLN cc_start: 0.7684 (mp10) cc_final: 0.7279 (mp10) REVERT: E 75 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8485 (tp) REVERT: E 77 ASP cc_start: 0.7581 (t0) cc_final: 0.7363 (t0) REVERT: E 82 ASP cc_start: 0.6016 (p0) cc_final: 0.5686 (p0) REVERT: F 28 ASP cc_start: 0.6992 (t0) cc_final: 0.6603 (t0) REVERT: F 30 SER cc_start: 0.9071 (m) cc_final: 0.8762 (m) REVERT: F 31 ASP cc_start: 0.8789 (p0) cc_final: 0.8541 (p0) REVERT: G 67 ASN cc_start: 0.8712 (m-40) cc_final: 0.8442 (t0) REVERT: G 74 CYS cc_start: 0.7824 (m) cc_final: 0.7412 (m) REVERT: G 95 MET cc_start: 0.7365 (ptp) cc_final: 0.7118 (ptp) REVERT: G 420 ILE cc_start: 0.9258 (mp) cc_final: 0.8967 (mt) REVERT: G 434 MET cc_start: 0.8368 (ttm) cc_final: 0.7881 (ttm) REVERT: I 530 MET cc_start: 0.7368 (mmm) cc_final: 0.6828 (mmm) REVERT: I 595 ILE cc_start: 0.9457 (tp) cc_final: 0.9013 (tp) REVERT: I 602 ILE cc_start: 0.9514 (mm) cc_final: 0.9134 (tp) REVERT: I 629 MET cc_start: 0.8570 (mmm) cc_final: 0.7837 (mmm) REVERT: J 42 GLN cc_start: 0.7484 (mp10) cc_final: 0.7009 (mp10) REVERT: J 75 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8606 (tp) REVERT: J 82 ASP cc_start: 0.6009 (p0) cc_final: 0.5637 (p0) REVERT: J 95 PRO cc_start: 0.8806 (Cg_exo) cc_final: 0.8603 (Cg_endo) REVERT: K 5 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7110 (tm-30) REVERT: K 6 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5416 (mp0) REVERT: K 7 SER cc_start: 0.8893 (t) cc_final: 0.8626 (m) REVERT: K 15 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8449 (tp30) REVERT: K 28 ASP cc_start: 0.7461 (t0) cc_final: 0.7120 (t0) REVERT: K 30 SER cc_start: 0.9166 (m) cc_final: 0.8956 (m) REVERT: K 57 ILE cc_start: 0.9527 (pt) cc_final: 0.9287 (mp) REVERT: K 59 TYR cc_start: 0.7814 (m-80) cc_final: 0.7608 (m-80) outliers start: 69 outliers final: 43 residues processed: 385 average time/residue: 0.1382 time to fit residues: 85.0076 Evaluate side-chains 365 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 51 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 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 = 0.3435 r_free = 0.3435 target = 0.091288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.070919 restraints weight = 53439.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073527 restraints weight = 31706.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075307 restraints weight = 22693.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076525 restraints weight = 18201.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077343 restraints weight = 15654.206| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21003 Z= 0.178 Angle : 0.720 16.012 28770 Z= 0.350 Chirality : 0.046 0.256 3516 Planarity : 0.004 0.040 3465 Dihedral : 4.928 24.935 2580 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.28 % Allowed : 17.53 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.49 (0.17), residues: 2364 helix: 0.56 (0.27), residues: 366 sheet: 0.28 (0.19), residues: 702 loop : -0.92 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.023 0.001 TYR H 59 PHE 0.021 0.002 PHE H 47 TRP 0.068 0.003 TRP H 36 HIS 0.009 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (20853) covalent geometry : angle 0.69431 / 0.35 (28353) SS BOND : bond 0.00238 / 0.16 ( 33) SS BOND : angle 0.66279 / 0.44 ( 66) hydrogen bonds : bond 0.04618 / 3.11 ( 720) hydrogen bonds : angle 5.42856 / 3.77 ( 1980) link_ALPHA1-3 : bond 0.00425 / 0.19 ( 3) link_ALPHA1-3 : angle 1.40676 / 0.79 ( 9) link_BETA1-4 : bond 0.00512 / 0.33 ( 45) link_BETA1-4 : angle 1.39010 / 0.84 ( 135) link_NAG-ASN : bond 0.00399 / 0.26 ( 69) link_NAG-ASN : angle 2.12726 / 1.37 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 325 time to evaluate : 0.806 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 104 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8413 (ttm) REVERT: A 373 THR cc_start: 0.8632 (p) cc_final: 0.8359 (p) REVERT: A 420 ILE cc_start: 0.9175 (mp) cc_final: 0.8852 (mt) REVERT: A 468 PHE cc_start: 0.8222 (m-80) cc_final: 0.7744 (m-10) REVERT: B 566 LEU cc_start: 0.8836 (tt) cc_final: 0.8627 (tt) REVERT: B 621 GLU cc_start: 0.8684 (tt0) cc_final: 0.8340 (tt0) REVERT: B 647 GLU cc_start: 0.8803 (tp30) cc_final: 0.8339 (tp30) REVERT: L 21 ILE cc_start: 0.8615 (mm) cc_final: 0.8409 (tp) REVERT: L 42 GLN cc_start: 0.7316 (mp10) cc_final: 0.6835 (mp-120) REVERT: L 75 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8438 (tp) REVERT: L 82 ASP cc_start: 0.6111 (p0) cc_final: 0.5771 (p0) REVERT: H 13 GLN cc_start: 0.8518 (pp30) cc_final: 0.8151 (pp30) REVERT: H 15 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8229 (tp30) REVERT: H 38 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8040 (ttm170) REVERT: C 420 ILE cc_start: 0.9099 (mp) cc_final: 0.8783 (mt) REVERT: C 475 MET cc_start: 0.8362 (mmp) cc_final: 0.8079 (mmp) REVERT: C 479 TRP cc_start: 0.8294 (m-10) cc_final: 0.8066 (m-90) REVERT: E 4 MET cc_start: 0.7250 (mmm) cc_final: 0.6180 (tpp) REVERT: E 36 TYR cc_start: 0.7407 (m-80) cc_final: 0.6723 (m-80) REVERT: E 42 GLN cc_start: 0.7603 (mp10) cc_final: 0.7230 (mp10) REVERT: E 75 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8476 (tp) REVERT: E 82 ASP cc_start: 0.6021 (p0) cc_final: 0.5677 (p0) REVERT: F 28 ASP cc_start: 0.7115 (t0) cc_final: 0.6734 (t0) REVERT: F 30 SER cc_start: 0.9083 (m) cc_final: 0.8786 (m) REVERT: F 31 ASP cc_start: 0.8823 (p0) cc_final: 0.8543 (p0) REVERT: F 81 MET cc_start: 0.7796 (mmm) cc_final: 0.7587 (mmm) REVERT: G 74 CYS cc_start: 0.7802 (m) cc_final: 0.7411 (m) REVERT: G 420 ILE cc_start: 0.9270 (mp) cc_final: 0.8998 (mt) REVERT: G 434 MET cc_start: 0.8419 (ttm) cc_final: 0.7981 (ttm) REVERT: I 530 MET cc_start: 0.7377 (mmm) cc_final: 0.7117 (mmm) REVERT: I 602 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9169 (tp) REVERT: I 629 MET cc_start: 0.8480 (mmm) cc_final: 0.7803 (mmm) REVERT: J 19 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8101 (t) REVERT: J 42 GLN cc_start: 0.7506 (mp10) cc_final: 0.7010 (mp10) REVERT: J 63 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8187 (mmtt) REVERT: J 75 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8398 (tp) REVERT: J 82 ASP cc_start: 0.6088 (p0) cc_final: 0.5760 (p0) REVERT: K 6 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5640 (mp0) REVERT: K 15 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8509 (tp30) REVERT: K 31 ASP cc_start: 0.8633 (p0) cc_final: 0.8301 (p0) REVERT: K 81 MET cc_start: 0.8056 (mtm) cc_final: 0.7818 (mtm) outliers start: 68 outliers final: 50 residues processed: 365 average time/residue: 0.1365 time to fit residues: 79.7933 Evaluate side-chains 358 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 300 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 22 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN G 203 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 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 = 0.3461 r_free = 0.3461 target = 0.092810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.072641 restraints weight = 52757.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075343 restraints weight = 30490.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.077189 restraints weight = 21431.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078442 restraints weight = 16983.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079272 restraints weight = 14509.891| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21003 Z= 0.142 Angle : 0.708 16.326 28770 Z= 0.343 Chirality : 0.046 0.295 3516 Planarity : 0.004 0.039 3465 Dihedral : 4.789 24.012 2580 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.13 % Allowed : 17.92 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.49 (0.17), residues: 2364 helix: 0.53 (0.27), residues: 372 sheet: 0.27 (0.19), residues: 720 loop : -0.93 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 273 TYR 0.013 0.001 TYR E 49 PHE 0.020 0.002 PHE H 47 TRP 0.055 0.002 TRP F 36 HIS 0.007 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (20853) covalent geometry : angle 0.68351 / 0.34 (28353) SS BOND : bond 0.00308 / 0.23 ( 33) SS BOND : angle 0.91506 / 0.61 ( 66) hydrogen bonds : bond 0.04451 / 2.99 ( 720) hydrogen bonds : angle 5.35000 / 3.71 ( 1980) link_ALPHA1-3 : bond 0.00447 / 0.20 ( 3) link_ALPHA1-3 : angle 1.42672 / 0.79 ( 9) link_BETA1-4 : bond 0.00498 / 0.32 ( 45) link_BETA1-4 : angle 1.30807 / 0.79 ( 135) link_NAG-ASN : bond 0.00380 / 0.26 ( 69) link_NAG-ASN : angle 2.04790 / 1.33 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8625 (ttm) REVERT: A 373 THR cc_start: 0.8610 (p) cc_final: 0.8328 (p) REVERT: A 420 ILE cc_start: 0.9160 (mp) cc_final: 0.8853 (mt) REVERT: A 468 PHE cc_start: 0.8175 (m-80) cc_final: 0.7700 (m-10) REVERT: A 475 MET cc_start: 0.8096 (mmm) cc_final: 0.7806 (mmp) REVERT: A 479 TRP cc_start: 0.8386 (m-10) cc_final: 0.8061 (m-90) REVERT: B 621 GLU cc_start: 0.8653 (tt0) cc_final: 0.8312 (tt0) REVERT: B 647 GLU cc_start: 0.8744 (tp30) cc_final: 0.8334 (tp30) REVERT: L 75 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8454 (tp) REVERT: L 82 ASP cc_start: 0.6078 (p0) cc_final: 0.5758 (p0) REVERT: H 13 GLN cc_start: 0.8501 (pp30) cc_final: 0.8167 (pp30) REVERT: H 15 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8174 (tp30) REVERT: H 38 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: C 420 ILE cc_start: 0.9086 (mp) cc_final: 0.8781 (mt) REVERT: C 475 MET cc_start: 0.8277 (mmp) cc_final: 0.7943 (mmp) REVERT: C 479 TRP cc_start: 0.8223 (m-10) cc_final: 0.7932 (m-90) REVERT: D 542 ARG cc_start: 0.6888 (ttt180) cc_final: 0.5686 (mmt180) REVERT: D 595 ILE cc_start: 0.9380 (tp) cc_final: 0.9070 (tp) REVERT: D 602 ILE cc_start: 0.9477 (mm) cc_final: 0.9160 (tp) REVERT: E 4 MET cc_start: 0.7225 (mmm) cc_final: 0.6177 (tpp) REVERT: E 42 GLN cc_start: 0.7371 (mp10) cc_final: 0.7010 (mp10) REVERT: E 82 ASP cc_start: 0.5644 (p0) cc_final: 0.5331 (p0) REVERT: F 28 ASP cc_start: 0.7340 (t0) cc_final: 0.6973 (t0) REVERT: F 30 SER cc_start: 0.9138 (m) cc_final: 0.8807 (m) REVERT: F 31 ASP cc_start: 0.8853 (p0) cc_final: 0.8527 (p0) REVERT: F 35 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6721 (mt0) REVERT: G 74 CYS cc_start: 0.7755 (m) cc_final: 0.7394 (m) REVERT: G 268 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7146 (mt-10) REVERT: G 420 ILE cc_start: 0.9254 (mp) cc_final: 0.8977 (mt) REVERT: G 434 MET cc_start: 0.8381 (ttm) cc_final: 0.7840 (ttm) REVERT: I 530 MET cc_start: 0.7300 (mmm) cc_final: 0.6849 (mmm) REVERT: I 602 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9137 (tp) REVERT: I 629 MET cc_start: 0.8419 (mmm) cc_final: 0.7747 (mmm) REVERT: J 1 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.7122 (p0) REVERT: J 19 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8018 (t) REVERT: J 42 GLN cc_start: 0.7592 (mp10) cc_final: 0.7130 (mp10) REVERT: J 75 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8528 (tp) REVERT: J 82 ASP cc_start: 0.6000 (p0) cc_final: 0.5743 (p0) REVERT: K 6 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: K 15 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8465 (tp30) REVERT: K 31 ASP cc_start: 0.8730 (p0) cc_final: 0.8411 (p0) REVERT: K 81 MET cc_start: 0.7941 (mtm) cc_final: 0.7738 (mtm) outliers start: 65 outliers final: 46 residues processed: 359 average time/residue: 0.1378 time to fit residues: 79.3311 Evaluate side-chains 358 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 150 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 overall best weight: 2.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.070866 restraints weight = 53509.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073474 restraints weight = 31830.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075244 restraints weight = 22794.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076377 restraints weight = 18294.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076818 restraints weight = 15870.466| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21003 Z= 0.185 Angle : 0.734 16.286 28770 Z= 0.357 Chirality : 0.046 0.262 3516 Planarity : 0.004 0.041 3465 Dihedral : 4.797 24.046 2580 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.42 % Allowed : 18.35 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.56 (0.17), residues: 2364 helix: 0.57 (0.27), residues: 372 sheet: 0.22 (0.19), residues: 717 loop : -1.00 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 273 TYR 0.021 0.001 TYR K 58 PHE 0.024 0.002 PHE H 47 TRP 0.042 0.002 TRP K 36 HIS 0.012 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (20853) covalent geometry : angle 0.70860 / 0.35 (28353) SS BOND : bond 0.00344 / 0.24 ( 33) SS BOND : angle 1.25660 / 0.89 ( 66) hydrogen bonds : bond 0.04563 / 3.05 ( 720) hydrogen bonds : angle 5.34754 / 3.70 ( 1980) link_ALPHA1-3 : bond 0.00435 / 0.19 ( 3) link_ALPHA1-3 : angle 1.39422 / 0.79 ( 9) link_BETA1-4 : bond 0.00469 / 0.30 ( 45) link_BETA1-4 : angle 1.36578 / 0.83 ( 135) link_NAG-ASN : bond 0.00418 / 0.28 ( 69) link_NAG-ASN : angle 2.07157 / 1.34 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 318 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8693 (ttm) REVERT: A 373 THR cc_start: 0.8685 (p) cc_final: 0.8409 (p) REVERT: A 468 PHE cc_start: 0.8237 (m-80) cc_final: 0.7709 (m-10) REVERT: A 479 TRP cc_start: 0.8416 (m-10) cc_final: 0.8114 (m-90) REVERT: B 621 GLU cc_start: 0.8702 (tt0) cc_final: 0.8425 (tt0) REVERT: B 647 GLU cc_start: 0.8775 (tp30) cc_final: 0.8366 (tp30) REVERT: L 75 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8500 (tp) REVERT: L 82 ASP cc_start: 0.6122 (p0) cc_final: 0.5788 (p0) REVERT: H 13 GLN cc_start: 0.8568 (pp30) cc_final: 0.8256 (pp30) REVERT: H 15 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8236 (tp30) REVERT: C 420 ILE cc_start: 0.9119 (mp) cc_final: 0.8819 (mt) REVERT: C 475 MET cc_start: 0.8367 (mmp) cc_final: 0.8084 (mmp) REVERT: C 479 TRP cc_start: 0.8243 (m-10) cc_final: 0.8016 (m-90) REVERT: D 542 ARG cc_start: 0.6954 (ttt180) cc_final: 0.5730 (mmt180) REVERT: D 595 ILE cc_start: 0.9403 (tp) cc_final: 0.9099 (tp) REVERT: E 4 MET cc_start: 0.7164 (mmm) cc_final: 0.6216 (tpp) REVERT: E 42 GLN cc_start: 0.7460 (mp10) cc_final: 0.7097 (mp10) REVERT: E 75 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8438 (tp) REVERT: E 82 ASP cc_start: 0.5619 (p0) cc_final: 0.5281 (p0) REVERT: F 28 ASP cc_start: 0.7392 (t0) cc_final: 0.7023 (t0) REVERT: F 30 SER cc_start: 0.9085 (m) cc_final: 0.8772 (m) REVERT: F 31 ASP cc_start: 0.8821 (p0) cc_final: 0.8527 (p0) REVERT: G 74 CYS cc_start: 0.7836 (m) cc_final: 0.7420 (m) REVERT: G 420 ILE cc_start: 0.9270 (mp) cc_final: 0.8996 (mt) REVERT: G 434 MET cc_start: 0.8463 (ttm) cc_final: 0.7943 (ttm) REVERT: I 530 MET cc_start: 0.7237 (mmm) cc_final: 0.6668 (mmm) REVERT: I 602 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9215 (tp) REVERT: J 1 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7229 (p0) REVERT: J 19 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8027 (t) REVERT: J 63 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8135 (mmtt) REVERT: J 75 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8482 (tp) REVERT: J 82 ASP cc_start: 0.6132 (p0) cc_final: 0.5851 (p0) REVERT: K 6 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5495 (mp0) REVERT: K 15 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8469 (tp30) REVERT: K 31 ASP cc_start: 0.8776 (p0) cc_final: 0.8494 (p0) REVERT: K 81 MET cc_start: 0.7999 (mtm) cc_final: 0.7765 (mtm) outliers start: 71 outliers final: 54 residues processed: 358 average time/residue: 0.1386 time to fit residues: 79.6800 Evaluate side-chains 363 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 62 TRP Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 0.0370 chunk 132 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 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 = 0.3446 r_free = 0.3446 target = 0.092065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.071923 restraints weight = 52938.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074546 restraints weight = 30933.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076333 restraints weight = 21937.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077546 restraints weight = 17468.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078412 restraints weight = 14984.255| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21003 Z= 0.160 Angle : 0.742 16.451 28770 Z= 0.360 Chirality : 0.046 0.266 3516 Planarity : 0.004 0.040 3465 Dihedral : 4.764 23.436 2580 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.08 % Allowed : 18.83 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.56 (0.17), residues: 2364 helix: 0.58 (0.27), residues: 372 sheet: 0.21 (0.19), residues: 714 loop : -1.00 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 273 TYR 0.014 0.001 TYR H 59 PHE 0.028 0.002 PHE H 47 TRP 0.072 0.003 TRP K 36 HIS 0.006 0.001 HIS H 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (20853) covalent geometry : angle 0.71796 / 0.36 (28353) SS BOND : bond 0.00401 / 0.29 ( 33) SS BOND : angle 1.34763 / 0.95 ( 66) hydrogen bonds : bond 0.04482 / 2.99 ( 720) hydrogen bonds : angle 5.35254 / 3.69 ( 1980) link_ALPHA1-3 : bond 0.00446 / 0.20 ( 3) link_ALPHA1-3 : angle 1.41607 / 0.79 ( 9) link_BETA1-4 : bond 0.00496 / 0.32 ( 45) link_BETA1-4 : angle 1.31593 / 0.80 ( 135) link_NAG-ASN : bond 0.00377 / 0.25 ( 69) link_NAG-ASN : angle 2.01616 / 1.31 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 310 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8696 (ttm) REVERT: A 373 THR cc_start: 0.8662 (p) cc_final: 0.8380 (p) REVERT: A 468 PHE cc_start: 0.8189 (m-80) cc_final: 0.7712 (m-10) REVERT: A 479 TRP cc_start: 0.8390 (m-10) cc_final: 0.8130 (m-90) REVERT: B 621 GLU cc_start: 0.8646 (tt0) cc_final: 0.8348 (tt0) REVERT: B 647 GLU cc_start: 0.8706 (tp30) cc_final: 0.8323 (tp30) REVERT: L 75 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8452 (tp) REVERT: L 82 ASP cc_start: 0.6112 (p0) cc_final: 0.5742 (p0) REVERT: H 15 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8155 (tp30) REVERT: H 31 ASP cc_start: 0.8551 (p0) cc_final: 0.8238 (p0) REVERT: C 420 ILE cc_start: 0.9098 (mp) cc_final: 0.8811 (mt) REVERT: C 475 MET cc_start: 0.8286 (mmp) cc_final: 0.8004 (mmp) REVERT: C 479 TRP cc_start: 0.8185 (m-10) cc_final: 0.7927 (m-90) REVERT: D 542 ARG cc_start: 0.6881 (ttt180) cc_final: 0.5757 (mmt180) REVERT: D 595 ILE cc_start: 0.9403 (tp) cc_final: 0.9091 (tp) REVERT: D 602 ILE cc_start: 0.9503 (mm) cc_final: 0.9225 (tp) REVERT: D 629 MET cc_start: 0.8568 (mmm) cc_final: 0.7587 (mmm) REVERT: E 42 GLN cc_start: 0.7359 (mp10) cc_final: 0.7015 (mp10) REVERT: E 75 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8512 (tp) REVERT: E 82 ASP cc_start: 0.5619 (p0) cc_final: 0.5286 (p0) REVERT: F 31 ASP cc_start: 0.8831 (p0) cc_final: 0.8504 (p0) REVERT: F 68 THR cc_start: 0.8211 (m) cc_final: 0.7351 (p) REVERT: G 74 CYS cc_start: 0.7790 (m) cc_final: 0.7387 (m) REVERT: G 420 ILE cc_start: 0.9227 (mp) cc_final: 0.8970 (mt) REVERT: G 434 MET cc_start: 0.8434 (ttm) cc_final: 0.7921 (ttm) REVERT: I 530 MET cc_start: 0.7153 (mmm) cc_final: 0.6700 (mmm) REVERT: I 602 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9237 (tp) REVERT: I 629 MET cc_start: 0.8525 (mmm) cc_final: 0.7802 (mmm) REVERT: J 63 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8172 (mmtt) REVERT: J 82 ASP cc_start: 0.6136 (p0) cc_final: 0.5900 (p0) REVERT: K 6 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5222 (mp0) REVERT: K 15 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8441 (tp30) REVERT: K 31 ASP cc_start: 0.8745 (p0) cc_final: 0.8458 (p0) REVERT: K 38 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8280 (ttm-80) REVERT: K 81 MET cc_start: 0.8014 (mtm) cc_final: 0.7802 (mtm) outliers start: 64 outliers final: 53 residues processed: 348 average time/residue: 0.1430 time to fit residues: 78.4546 Evaluate side-chains 361 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 80 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain I residue 602 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 623 TRP Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 80 CYS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.069788 restraints weight = 54035.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072341 restraints weight = 32120.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074082 restraints weight = 23032.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075253 restraints weight = 18539.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075917 restraints weight = 16001.281| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21003 Z= 0.210 Angle : 0.765 16.302 28770 Z= 0.374 Chirality : 0.047 0.262 3516 Planarity : 0.004 0.041 3465 Dihedral : 4.867 24.048 2580 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.03 % Allowed : 18.88 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.66 (0.17), residues: 2364 helix: 0.59 (0.28), residues: 372 sheet: 0.16 (0.19), residues: 729 loop : -1.12 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 469 TYR 0.021 0.002 TYR E 49 PHE 0.029 0.002 PHE H 47 TRP 0.098 0.003 TRP K 36 HIS 0.005 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (20853) covalent geometry : angle 0.73998 / 0.37 (28353) SS BOND : bond 0.00366 / 0.26 ( 33) SS BOND : angle 1.37644 / 0.95 ( 66) hydrogen bonds : bond 0.04690 / 3.14 ( 720) hydrogen bonds : angle 5.45640 / 3.77 ( 1980) link_ALPHA1-3 : bond 0.00433 / 0.19 ( 3) link_ALPHA1-3 : angle 1.39419 / 0.79 ( 9) link_BETA1-4 : bond 0.00487 / 0.31 ( 45) link_BETA1-4 : angle 1.39364 / 0.85 ( 135) link_NAG-ASN : bond 0.00440 / 0.29 ( 69) link_NAG-ASN : angle 2.06781 / 1.34 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.03 seconds wall clock time: 60 minutes 23.61 seconds (3623.61 seconds total)