Starting phenix.real_space_refine on Fri Jul 3 20:23:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8d_23230/07_2026/7l8d_23230.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 99 5.16 5 C 9694 2.51 5 N 2596 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15564 Number of models: 1 Model: "" Number of chains: 49 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3408 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3422 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 4 Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3418 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 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: "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: 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: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "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: 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: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.11, per 1000 atoms: 0.20 Number of scatterers: 15564 At special positions: 0 Unit cell: (130.81, 123.6, 146.26, 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 99 16.00 O 3175 8.00 N 2596 7.00 C 9694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.11 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.15 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.02 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 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 K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA Y 3 " - " MAN Y 5 " " BMA h 3 " - " MAN h 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG 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 f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 197 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 301 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 137 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG D 604 " - " ASN D 355 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 133 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 295 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 392 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 88 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 197 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 386 " " NAG d 1 " - " ASN C 392 " " NAG e 1 " - " ASN D 133 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 197 " " NAG h 1 " - " ASN D 262 " " NAG i 1 " - " ASN D 276 " " NAG j 1 " - " ASN D 295 " " NAG k 1 " - " ASN D 301 " " NAG l 1 " - " ASN D 332 " " NAG m 1 " - " ASN D 386 " " NAG n 1 " - " ASN D 392 " " NAG o 1 " - " ASN D 448 " " NAG p 1 " - " ASN D 88 " " NAG q 1 " - " ASN D 234 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 580.7 milliseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3534 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 33 sheets defined 29.4% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.269A pdb=" N UNK H 61 " --> pdb=" O UNK H 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.706A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 483 removed outlier: 4.048A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.418A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.667A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.840A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.532A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.540A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.574A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 541 Processing helix chain 'E' and resid 542 through 544 No H-bonds generated for 'chain 'E' and resid 542 through 544' Processing helix chain 'E' and resid 571 through 595 Processing helix chain 'E' and resid 621 through 626 Processing helix chain 'E' and resid 627 through 634 Processing helix chain 'E' and resid 638 through 664 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.141A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 569 through 571 No H-bonds generated for 'chain 'F' and resid 569 through 571' Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.425A pdb=" N UNK H 18 " --> pdb=" O UNK H 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.652A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.841A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA8, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA9, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.513A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.964A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.633A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.762A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.249A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AB9, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.773A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.200A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.398A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.846A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.398A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.846A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 323 through 323A removed outlier: 3.807A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.807A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AC7, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AD1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AD2, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.703A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.633A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.633A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.443A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.633A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.443A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 315 through 323 removed outlier: 6.472A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1569 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: 2.24 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4565 1.34 - 1.49: 4901 1.49 - 1.64: 6234 1.64 - 1.79: 59 1.79 - 1.95: 73 Bond restraints: 15832 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 bond pdb=" CB THR A 37 " pdb=" OG1 THR A 37 " ideal model delta sigma weight residual 1.433 1.339 0.094 1.60e-02 3.91e+03 3.48e+01 bond pdb=" CB LEU C 34 " pdb=" CG LEU C 34 " ideal model delta sigma weight residual 1.530 1.632 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " ideal model delta sigma weight residual 1.530 1.630 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 1.502 1.389 0.113 2.30e-02 1.89e+03 2.41e+01 ... (remaining 15827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 17662 2.18 - 4.35: 3236 4.35 - 6.53: 546 6.53 - 8.71: 82 8.71 - 10.88: 9 Bond angle restraints: 21535 Sorted by residual: angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.87 128.90 -9.03 1.04e+00 9.25e-01 7.53e+01 angle pdb=" C CYS D 205 " pdb=" N PRO D 206 " pdb=" CA PRO D 206 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 angle pdb=" N PRO D 437 " pdb=" CA PRO D 437 " pdb=" C PRO D 437 " ideal model delta sigma weight residual 110.58 102.20 8.38 1.07e+00 8.73e-01 6.14e+01 angle pdb=" C GLY C 237 " pdb=" N PRO C 238 " pdb=" CA PRO C 238 " ideal model delta sigma weight residual 119.76 127.75 -7.99 1.03e+00 9.43e-01 6.02e+01 angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 120.03 127.67 -7.64 9.90e-01 1.02e+00 5.96e+01 ... (remaining 21530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8406 17.93 - 35.86: 224 35.86 - 53.80: 88 53.80 - 71.73: 17 71.73 - 89.66: 5 Dihedral angle restraints: 8740 sinusoidal: 3313 harmonic: 5427 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.34 -66.34 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CA UNK H 27 " pdb=" C UNK H 27 " pdb=" N UNK H 28 " pdb=" CA UNK H 28 " ideal model delta harmonic sigma weight residual 180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA UNK L 11 " pdb=" C UNK L 11 " pdb=" N UNK L 12 " pdb=" CA UNK L 12 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 8737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1914 0.121 - 0.242: 511 0.242 - 0.363: 228 0.363 - 0.483: 108 0.483 - 0.604: 10 Chirality restraints: 2771 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.46e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.07e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 ... (remaining 2768 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG p 1 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " -0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.346 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG K 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.156 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.343 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG A 602 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.066 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.194 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4798 2.85 - 3.36: 14729 3.36 - 3.88: 26069 3.88 - 4.39: 30348 4.39 - 4.90: 46664 Nonbonded interactions: 122608 Sorted by model distance: nonbonded pdb=" O3 NAG K 1 " pdb=" O7 NAG K 1 " model vdw 2.339 3.040 nonbonded pdb=" O PHE B 522 " pdb=" NE2 GLN B 540 " model vdw 2.366 3.120 nonbonded pdb=" OD1 ASP D 107 " pdb=" NZ LYS F 574 " model vdw 2.369 3.120 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.404 3.040 nonbonded pdb=" O3 NAG p 2 " pdb=" O7 NAG p 2 " model vdw 2.417 3.040 ... (remaining 122603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 457 or resid 463 through 604)) selection = (chain 'C' and (resid 34 through 184 or resid 189 through 397 or resid 411 throu \ gh 457 or resid 463 through 604)) selection = (chain 'D' and (resid 34 through 184 or resid 189 through 397 or resid 411 throu \ gh 604)) } ncs_group { reference = (chain 'B' and (resid 521 through 545 or resid 570 through 661 or resid 702)) selection = (chain 'E' and (resid 521 through 661 or resid 702)) selection = (chain 'F' and (resid 521 through 545 or resid 570 through 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = (chain 'H' and resid 7 through 108) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'Y' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.370 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.148 15965 Z= 1.196 Angle : 1.805 11.307 21901 Z= 1.128 Chirality : 0.151 0.604 2771 Planarity : 0.018 0.299 2623 Dihedral : 10.137 89.659 5107 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1620 helix: 0.16 (0.23), residues: 401 sheet: 0.79 (0.23), residues: 420 loop : 0.43 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 178 TYR 0.048 0.010 TYR A 384 PHE 0.032 0.006 PHE A 353 TRP 0.060 0.008 TRP A 479 HIS 0.013 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.02209 / 1.17 (15832) covalent geometry : angle 1.76196 / 1.13 (21535) SS BOND : bond 0.02568 / 1.33 ( 33) SS BOND : angle 3.09768 / 1.57 ( 66) hydrogen bonds : bond 0.16600 / 9.23 ( 565) hydrogen bonds : angle 7.77040 / 4.05 ( 1569) link_ALPHA1-3 : bond 0.07404 / 3.61 ( 3) link_ALPHA1-3 : angle 4.59908 / 2.16 ( 9) link_ALPHA1-6 : bond 0.04473 / 2.19 ( 3) link_ALPHA1-6 : angle 2.16683 / 0.97 ( 9) link_BETA1-4 : bond 0.06689 / 3.69 ( 39) link_BETA1-4 : angle 4.68418 / 2.36 ( 117) link_NAG-ASN : bond 0.07421 / 4.11 ( 55) link_NAG-ASN : angle 2.53277 / 1.28 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9102 (mt) cc_final: 0.8865 (mm) REVERT: A 164 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8255 (tt0) REVERT: A 201 ILE cc_start: 0.8934 (tp) cc_final: 0.8700 (pt) REVERT: A 261 LEU cc_start: 0.9345 (mt) cc_final: 0.9114 (mp) REVERT: A 424 ILE cc_start: 0.8930 (mm) cc_final: 0.8324 (mp) REVERT: A 434 MET cc_start: 0.9032 (tmm) cc_final: 0.8551 (tmm) REVERT: B 530 MET cc_start: 0.8868 (mtp) cc_final: 0.8368 (mtp) REVERT: B 536 THR cc_start: 0.8771 (p) cc_final: 0.8230 (t) REVERT: B 581 LEU cc_start: 0.9268 (mt) cc_final: 0.9008 (tp) REVERT: B 585 HIS cc_start: 0.9072 (m-70) cc_final: 0.8220 (m-70) REVERT: B 586 TYR cc_start: 0.9290 (t80) cc_final: 0.8481 (t80) REVERT: B 588 ARG cc_start: 0.9439 (ttp80) cc_final: 0.8954 (ttm-80) REVERT: B 610 TRP cc_start: 0.8715 (t-100) cc_final: 0.8366 (t-100) REVERT: B 625 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (t0) REVERT: B 634 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8725 (tp30) REVERT: B 635 ILE cc_start: 0.9558 (pt) cc_final: 0.8984 (pt) REVERT: B 655 LYS cc_start: 0.9523 (tptp) cc_final: 0.9300 (tptt) REVERT: C 81 PRO cc_start: 0.8318 (Cg_endo) cc_final: 0.7754 (Cg_exo) REVERT: C 104 MET cc_start: 0.8879 (mtt) cc_final: 0.8577 (mmp) REVERT: C 191 TYR cc_start: 0.8446 (m-80) cc_final: 0.7792 (m-80) REVERT: C 199 SER cc_start: 0.8869 (p) cc_final: 0.8632 (m) REVERT: C 252 LYS cc_start: 0.9324 (mttt) cc_final: 0.9094 (mttm) REVERT: C 319 TYR cc_start: 0.8905 (p90) cc_final: 0.8409 (p90) REVERT: C 342 LEU cc_start: 0.9615 (mm) cc_final: 0.9388 (tp) REVERT: E 536 THR cc_start: 0.9361 (p) cc_final: 0.9075 (t) REVERT: E 575 GLN cc_start: 0.9242 (tt0) cc_final: 0.8870 (tp40) REVERT: E 584 GLU cc_start: 0.9130 (tt0) cc_final: 0.8887 (tm-30) REVERT: E 589 ASP cc_start: 0.9351 (m-30) cc_final: 0.9118 (p0) REVERT: E 591 GLN cc_start: 0.8821 (tt0) cc_final: 0.8213 (tp40) REVERT: E 607 ASN cc_start: 0.9436 (m-40) cc_final: 0.9192 (m-40) REVERT: E 620 SER cc_start: 0.7710 (m) cc_final: 0.7467 (p) REVERT: E 630 GLN cc_start: 0.9483 (mt0) cc_final: 0.9101 (mt0) REVERT: E 634 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8646 (mt-10) REVERT: E 659 ASP cc_start: 0.9114 (m-30) cc_final: 0.8868 (t0) REVERT: D 42 VAL cc_start: 0.9609 (t) cc_final: 0.9348 (p) REVERT: D 69 TRP cc_start: 0.8255 (m-90) cc_final: 0.8001 (m-90) REVERT: D 104 MET cc_start: 0.9104 (mmm) cc_final: 0.8541 (mmp) REVERT: D 150 MET cc_start: 0.7974 (mtp) cc_final: 0.7477 (mtp) REVERT: D 199 SER cc_start: 0.8378 (p) cc_final: 0.8174 (m) REVERT: D 210 PHE cc_start: 0.8487 (m-80) cc_final: 0.8195 (m-80) REVERT: D 376 PHE cc_start: 0.8686 (p90) cc_final: 0.8214 (p90) REVERT: D 424 ILE cc_start: 0.9009 (mm) cc_final: 0.8551 (mp) REVERT: D 434 MET cc_start: 0.8914 (tmm) cc_final: 0.8200 (tmm) REVERT: F 530 MET cc_start: 0.9309 (mtp) cc_final: 0.8890 (mtp) REVERT: F 539 VAL cc_start: 0.9449 (p) cc_final: 0.9216 (t) REVERT: F 574 LYS cc_start: 0.9515 (mttt) cc_final: 0.8994 (tttm) REVERT: F 584 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8811 (tp30) REVERT: F 593 LEU cc_start: 0.9539 (mt) cc_final: 0.9293 (tp) REVERT: F 622 ILE cc_start: 0.8904 (mt) cc_final: 0.7959 (mm) REVERT: F 624 ASP cc_start: 0.8705 (m-30) cc_final: 0.8442 (t0) REVERT: F 626 MET cc_start: 0.8253 (tpp) cc_final: 0.6797 (tpp) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1210 time to fit residues: 82.2310 Evaluate side-chains 237 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 328 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 HIS E 653 GLN F 590 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.063731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053914 restraints weight = 88138.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055532 restraints weight = 50815.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056678 restraints weight = 33907.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057499 restraints weight = 24992.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058088 restraints weight = 19672.131| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15965 Z= 0.193 Angle : 0.851 13.959 21901 Z= 0.407 Chirality : 0.051 0.511 2771 Planarity : 0.005 0.047 2623 Dihedral : 5.175 22.790 1962 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.27 % Allowed : 2.30 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1620 helix: 1.07 (0.26), residues: 391 sheet: 0.60 (0.24), residues: 408 loop : -0.16 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 327 TYR 0.021 0.002 TYR D 217 PHE 0.020 0.003 PHE C 382 TRP 0.027 0.003 TRP F 610 HIS 0.006 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (15832) covalent geometry : angle 0.78909 / 0.39 (21535) SS BOND : bond 0.00266 / 0.14 ( 33) SS BOND : angle 1.05863 / 0.52 ( 66) hydrogen bonds : bond 0.05909 / 3.27 ( 565) hydrogen bonds : angle 6.18228 / 3.25 ( 1569) link_ALPHA1-3 : bond 0.01122 / 0.56 ( 3) link_ALPHA1-3 : angle 1.88553 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00795 / 0.40 ( 3) link_ALPHA1-6 : angle 1.45406 / 0.79 ( 9) link_BETA1-4 : bond 0.00509 / 0.33 ( 39) link_BETA1-4 : angle 2.50118 / 1.25 ( 117) link_NAG-ASN : bond 0.00486 / 0.26 ( 55) link_NAG-ASN : angle 3.09157 / 1.59 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 321 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8928 (t80) cc_final: 0.8589 (t80) REVERT: A 52 LEU cc_start: 0.9469 (mm) cc_final: 0.8764 (mm) REVERT: A 98 ASN cc_start: 0.9046 (t0) cc_final: 0.8778 (t0) REVERT: A 107 ASP cc_start: 0.8966 (t0) cc_final: 0.8407 (t0) REVERT: A 136 ASN cc_start: 0.8792 (m-40) cc_final: 0.8452 (p0) REVERT: A 161 MET cc_start: 0.8779 (tmm) cc_final: 0.8411 (tmm) REVERT: A 164 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7959 (tp30) REVERT: A 244 THR cc_start: 0.8989 (m) cc_final: 0.8489 (t) REVERT: A 424 ILE cc_start: 0.8660 (mm) cc_final: 0.8289 (mp) REVERT: A 427 TRP cc_start: 0.8059 (m100) cc_final: 0.7686 (m100) REVERT: B 581 LEU cc_start: 0.9280 (mt) cc_final: 0.8634 (tp) REVERT: B 584 GLU cc_start: 0.8545 (pp20) cc_final: 0.7556 (pp20) REVERT: B 585 HIS cc_start: 0.8726 (m-70) cc_final: 0.7424 (m-70) REVERT: B 586 TYR cc_start: 0.8893 (t80) cc_final: 0.8512 (t80) REVERT: B 588 ARG cc_start: 0.9390 (ttp80) cc_final: 0.8893 (ttm-80) REVERT: B 589 ASP cc_start: 0.9342 (m-30) cc_final: 0.9090 (m-30) REVERT: B 591 GLN cc_start: 0.9343 (tt0) cc_final: 0.8936 (tm-30) REVERT: B 595 ILE cc_start: 0.9514 (pt) cc_final: 0.9286 (tt) REVERT: B 610 TRP cc_start: 0.8733 (t-100) cc_final: 0.8409 (t-100) REVERT: B 622 ILE cc_start: 0.9131 (mp) cc_final: 0.8673 (mp) REVERT: B 634 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8528 (tp30) REVERT: B 635 ILE cc_start: 0.9582 (pt) cc_final: 0.9323 (pt) REVERT: B 651 ASN cc_start: 0.8774 (t0) cc_final: 0.8528 (t0) REVERT: B 654 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8591 (mt-10) REVERT: C 39 TYR cc_start: 0.7854 (m-80) cc_final: 0.7491 (m-80) REVERT: C 98 ASN cc_start: 0.8584 (t0) cc_final: 0.8223 (t0) REVERT: C 116 LEU cc_start: 0.9453 (tp) cc_final: 0.9183 (tp) REVERT: C 191 TYR cc_start: 0.8281 (m-80) cc_final: 0.7621 (m-80) REVERT: C 319 TYR cc_start: 0.9076 (p90) cc_final: 0.8301 (p90) REVERT: C 477 ASP cc_start: 0.9564 (m-30) cc_final: 0.8988 (p0) REVERT: E 536 THR cc_start: 0.9203 (p) cc_final: 0.8906 (t) REVERT: E 584 GLU cc_start: 0.9307 (tt0) cc_final: 0.8788 (tm-30) REVERT: E 589 ASP cc_start: 0.9312 (m-30) cc_final: 0.9008 (p0) REVERT: E 595 ILE cc_start: 0.9569 (tt) cc_final: 0.9315 (tp) REVERT: E 620 SER cc_start: 0.7854 (m) cc_final: 0.7591 (p) REVERT: E 645 LEU cc_start: 0.9735 (mm) cc_final: 0.9518 (mm) REVERT: E 659 ASP cc_start: 0.9151 (m-30) cc_final: 0.8888 (t0) REVERT: D 42 VAL cc_start: 0.9419 (t) cc_final: 0.8927 (p) REVERT: D 91 GLU cc_start: 0.8058 (tp30) cc_final: 0.7812 (tm-30) REVERT: D 121 LYS cc_start: 0.9157 (pptt) cc_final: 0.8818 (ptmm) REVERT: D 154 LEU cc_start: 0.9513 (mt) cc_final: 0.9023 (tt) REVERT: D 376 PHE cc_start: 0.8546 (p90) cc_final: 0.7741 (p90) REVERT: D 383 PHE cc_start: 0.9301 (m-80) cc_final: 0.8772 (m-80) REVERT: F 522 PHE cc_start: 0.8789 (t80) cc_final: 0.8460 (t80) REVERT: F 534 SER cc_start: 0.9541 (p) cc_final: 0.9316 (p) REVERT: F 574 LYS cc_start: 0.9395 (mttt) cc_final: 0.9161 (ptmm) REVERT: F 633 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8771 (mmmt) outliers start: 4 outliers final: 1 residues processed: 322 average time/residue: 0.1107 time to fit residues: 53.1120 Evaluate side-chains 232 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 chunk 127 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 302 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN E 653 GLN D 114 GLN D 425 ASN F 590 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051386 restraints weight = 92847.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052935 restraints weight = 53489.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.054054 restraints weight = 35725.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054841 restraints weight = 26176.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055406 restraints weight = 20597.097| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15965 Z= 0.225 Angle : 0.783 9.739 21901 Z= 0.383 Chirality : 0.046 0.476 2771 Planarity : 0.004 0.057 2623 Dihedral : 5.152 28.597 1962 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1620 helix: 0.88 (0.26), residues: 397 sheet: 0.48 (0.22), residues: 454 loop : -0.49 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 298 TYR 0.034 0.002 TYR A 217 PHE 0.023 0.003 PHE C 382 TRP 0.019 0.002 TRP A 427 HIS 0.008 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (15832) covalent geometry : angle 0.74286 / 0.37 (21535) SS BOND : bond 0.00556 / 0.29 ( 33) SS BOND : angle 1.22618 / 0.65 ( 66) hydrogen bonds : bond 0.05085 / 2.84 ( 565) hydrogen bonds : angle 5.92827 / 3.09 ( 1569) link_ALPHA1-3 : bond 0.00644 / 0.32 ( 3) link_ALPHA1-3 : angle 1.74014 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00579 / 0.29 ( 3) link_ALPHA1-6 : angle 1.48957 / 0.79 ( 9) link_BETA1-4 : bond 0.00493 / 0.29 ( 39) link_BETA1-4 : angle 1.97666 / 0.99 ( 117) link_NAG-ASN : bond 0.00390 / 0.21 ( 55) link_NAG-ASN : angle 2.38143 / 1.18 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9331 (mm) cc_final: 0.9104 (mm) REVERT: A 98 ASN cc_start: 0.9235 (t0) cc_final: 0.8719 (t0) REVERT: A 109 ILE cc_start: 0.9644 (mt) cc_final: 0.9369 (tp) REVERT: A 136 ASN cc_start: 0.8810 (m-40) cc_final: 0.8424 (p0) REVERT: A 244 THR cc_start: 0.8995 (m) cc_final: 0.8639 (t) REVERT: A 427 TRP cc_start: 0.8679 (m100) cc_final: 0.8377 (m100) REVERT: A 484 TYR cc_start: 0.9449 (p90) cc_final: 0.8949 (p90) REVERT: B 581 LEU cc_start: 0.9254 (mt) cc_final: 0.8775 (tp) REVERT: B 584 GLU cc_start: 0.8604 (pp20) cc_final: 0.7639 (pp20) REVERT: B 585 HIS cc_start: 0.8666 (m-70) cc_final: 0.7546 (m-70) REVERT: B 588 ARG cc_start: 0.9437 (ttp80) cc_final: 0.8902 (ttm-80) REVERT: B 589 ASP cc_start: 0.9331 (m-30) cc_final: 0.9059 (m-30) REVERT: B 591 GLN cc_start: 0.9472 (tt0) cc_final: 0.9209 (tm-30) REVERT: B 595 ILE cc_start: 0.9542 (pt) cc_final: 0.9306 (tt) REVERT: B 610 TRP cc_start: 0.8858 (t-100) cc_final: 0.8633 (t-100) REVERT: B 622 ILE cc_start: 0.9238 (mp) cc_final: 0.8934 (mp) REVERT: B 634 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8552 (tp30) REVERT: B 635 ILE cc_start: 0.9711 (pt) cc_final: 0.9487 (pt) REVERT: B 651 ASN cc_start: 0.8875 (t0) cc_final: 0.8564 (t0) REVERT: B 654 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8144 (mt-10) REVERT: C 39 TYR cc_start: 0.7997 (m-80) cc_final: 0.7518 (m-10) REVERT: C 40 TYR cc_start: 0.9228 (t80) cc_final: 0.8929 (t80) REVERT: C 116 LEU cc_start: 0.9566 (tp) cc_final: 0.9083 (tp) REVERT: C 191 TYR cc_start: 0.8449 (m-80) cc_final: 0.7811 (m-80) REVERT: C 319 TYR cc_start: 0.9199 (p90) cc_final: 0.8511 (p90) REVERT: C 434 MET cc_start: 0.8851 (tpp) cc_final: 0.8347 (tpt) REVERT: C 477 ASP cc_start: 0.9552 (m-30) cc_final: 0.9133 (p0) REVERT: E 536 THR cc_start: 0.9189 (p) cc_final: 0.8855 (t) REVERT: E 584 GLU cc_start: 0.9315 (tt0) cc_final: 0.9002 (tm-30) REVERT: E 589 ASP cc_start: 0.9385 (m-30) cc_final: 0.9026 (p0) REVERT: E 595 ILE cc_start: 0.9642 (tt) cc_final: 0.9346 (tp) REVERT: E 603 ILE cc_start: 0.9093 (mt) cc_final: 0.8799 (mt) REVERT: E 620 SER cc_start: 0.8229 (m) cc_final: 0.7885 (p) REVERT: E 654 GLU cc_start: 0.9308 (tp30) cc_final: 0.8768 (tp30) REVERT: E 655 LYS cc_start: 0.9334 (tptp) cc_final: 0.9026 (tppt) REVERT: E 659 ASP cc_start: 0.9156 (m-30) cc_final: 0.8770 (t0) REVERT: D 42 VAL cc_start: 0.9438 (t) cc_final: 0.8921 (p) REVERT: D 121 LYS cc_start: 0.9237 (pptt) cc_final: 0.8877 (ptmm) REVERT: D 154 LEU cc_start: 0.9567 (mt) cc_final: 0.9174 (tt) REVERT: D 376 PHE cc_start: 0.8692 (p90) cc_final: 0.7808 (p90) REVERT: D 383 PHE cc_start: 0.9337 (m-80) cc_final: 0.8765 (m-80) REVERT: D 424 ILE cc_start: 0.8871 (tp) cc_final: 0.8289 (tp) REVERT: F 535 MET cc_start: 0.7805 (mpp) cc_final: 0.7495 (mpp) REVERT: F 539 VAL cc_start: 0.9549 (t) cc_final: 0.9238 (p) REVERT: F 574 LYS cc_start: 0.9433 (mttt) cc_final: 0.9135 (ptmm) REVERT: F 589 ASP cc_start: 0.8986 (m-30) cc_final: 0.8784 (m-30) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.1223 time to fit residues: 50.4728 Evaluate side-chains 196 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 22 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 4 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 150 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN C 293 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN D 72 HIS D 114 GLN D 425 ASN F 590 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051367 restraints weight = 91855.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052915 restraints weight = 53135.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054011 restraints weight = 35545.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054784 restraints weight = 26211.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055361 restraints weight = 20651.131| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15965 Z= 0.172 Angle : 0.696 12.346 21901 Z= 0.337 Chirality : 0.046 0.632 2771 Planarity : 0.004 0.056 2623 Dihedral : 4.898 21.803 1962 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1620 helix: 1.22 (0.27), residues: 392 sheet: 0.35 (0.23), residues: 459 loop : -0.62 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.025 0.002 TYR A 217 PHE 0.018 0.002 PHE C 382 TRP 0.014 0.002 TRP E 628 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (15832) covalent geometry : angle 0.65358 / 0.33 (21535) SS BOND : bond 0.00302 / 0.16 ( 33) SS BOND : angle 1.13842 / 0.53 ( 66) hydrogen bonds : bond 0.04474 / 2.49 ( 565) hydrogen bonds : angle 5.59461 / 2.92 ( 1569) link_ALPHA1-3 : bond 0.00514 / 0.26 ( 3) link_ALPHA1-3 : angle 1.74363 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00520 / 0.26 ( 3) link_ALPHA1-6 : angle 1.45573 / 0.78 ( 9) link_BETA1-4 : bond 0.00367 / 0.21 ( 39) link_BETA1-4 : angle 1.73296 / 0.87 ( 117) link_NAG-ASN : bond 0.00517 / 0.28 ( 55) link_NAG-ASN : angle 2.38434 / 1.18 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.9320 (t0) cc_final: 0.8879 (t0) REVERT: A 136 ASN cc_start: 0.8900 (m-40) cc_final: 0.8491 (p0) REVERT: A 161 MET cc_start: 0.8838 (tmm) cc_final: 0.8633 (tpp) REVERT: A 217 TYR cc_start: 0.7630 (m-80) cc_final: 0.7420 (m-80) REVERT: A 244 THR cc_start: 0.8933 (m) cc_final: 0.8510 (t) REVERT: A 427 TRP cc_start: 0.8747 (m100) cc_final: 0.8494 (m100) REVERT: A 484 TYR cc_start: 0.9421 (p90) cc_final: 0.8975 (p90) REVERT: B 581 LEU cc_start: 0.9293 (mt) cc_final: 0.8693 (tp) REVERT: B 584 GLU cc_start: 0.8573 (pp20) cc_final: 0.7461 (pp20) REVERT: B 585 HIS cc_start: 0.8570 (m-70) cc_final: 0.7483 (m-70) REVERT: B 588 ARG cc_start: 0.9390 (ttp80) cc_final: 0.8793 (ttm-80) REVERT: B 591 GLN cc_start: 0.9458 (tt0) cc_final: 0.9085 (tm-30) REVERT: B 595 ILE cc_start: 0.9585 (pt) cc_final: 0.9339 (tt) REVERT: B 603 ILE cc_start: 0.8134 (pt) cc_final: 0.7376 (pt) REVERT: B 634 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8644 (tp30) REVERT: B 651 ASN cc_start: 0.8882 (t0) cc_final: 0.8539 (t0) REVERT: B 654 GLU cc_start: 0.8926 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 664 ASP cc_start: 0.7827 (t0) cc_final: 0.7131 (p0) REVERT: C 39 TYR cc_start: 0.7925 (m-80) cc_final: 0.7397 (m-10) REVERT: C 40 TYR cc_start: 0.9219 (t80) cc_final: 0.8586 (t80) REVERT: C 116 LEU cc_start: 0.9566 (tp) cc_final: 0.9007 (tp) REVERT: C 191 TYR cc_start: 0.8420 (m-80) cc_final: 0.7751 (m-80) REVERT: C 319 TYR cc_start: 0.9152 (p90) cc_final: 0.8433 (p90) REVERT: C 434 MET cc_start: 0.8605 (tpp) cc_final: 0.8306 (tpt) REVERT: C 477 ASP cc_start: 0.9532 (m-30) cc_final: 0.9127 (p0) REVERT: E 536 THR cc_start: 0.9158 (p) cc_final: 0.8838 (t) REVERT: E 537 LEU cc_start: 0.9023 (mt) cc_final: 0.8813 (mt) REVERT: E 584 GLU cc_start: 0.9295 (tt0) cc_final: 0.9010 (tm-30) REVERT: E 589 ASP cc_start: 0.9299 (m-30) cc_final: 0.8995 (p0) REVERT: E 603 ILE cc_start: 0.9096 (mt) cc_final: 0.8753 (mt) REVERT: E 620 SER cc_start: 0.8410 (m) cc_final: 0.8190 (p) REVERT: E 654 GLU cc_start: 0.9291 (tp30) cc_final: 0.8854 (tp30) REVERT: E 655 LYS cc_start: 0.9289 (tptp) cc_final: 0.9065 (tppt) REVERT: E 659 ASP cc_start: 0.9101 (m-30) cc_final: 0.8865 (t0) REVERT: D 42 VAL cc_start: 0.9480 (t) cc_final: 0.9001 (p) REVERT: D 121 LYS cc_start: 0.9271 (pptt) cc_final: 0.9037 (ptmm) REVERT: D 154 LEU cc_start: 0.9577 (mt) cc_final: 0.9169 (tt) REVERT: D 376 PHE cc_start: 0.8656 (p90) cc_final: 0.7730 (p90) REVERT: D 383 PHE cc_start: 0.9244 (m-80) cc_final: 0.8755 (m-80) REVERT: F 535 MET cc_start: 0.7922 (mpp) cc_final: 0.7523 (mpp) REVERT: F 539 VAL cc_start: 0.9444 (t) cc_final: 0.9163 (p) REVERT: F 574 LYS cc_start: 0.9362 (mttt) cc_final: 0.9083 (ptmm) REVERT: F 589 ASP cc_start: 0.8960 (m-30) cc_final: 0.8727 (m-30) REVERT: F 601 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8724 (tppt) REVERT: F 617 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8144 (mtp180) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1147 time to fit residues: 45.8058 Evaluate side-chains 197 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 607 ASN E 650 GLN D 114 GLN D 425 ASN F 590 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.051337 restraints weight = 92470.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.052852 restraints weight = 53604.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053955 restraints weight = 35971.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054735 restraints weight = 26485.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055316 restraints weight = 20858.974| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15965 Z= 0.151 Angle : 0.661 10.489 21901 Z= 0.320 Chirality : 0.045 0.547 2771 Planarity : 0.004 0.069 2623 Dihedral : 4.768 22.561 1962 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1620 helix: 1.15 (0.26), residues: 393 sheet: 0.36 (0.23), residues: 461 loop : -0.72 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 327 TYR 0.022 0.002 TYR A 217 PHE 0.016 0.002 PHE C 382 TRP 0.023 0.002 TRP A 96 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (15832) covalent geometry : angle 0.62469 / 0.31 (21535) SS BOND : bond 0.00351 / 0.18 ( 33) SS BOND : angle 0.96331 / 0.43 ( 66) hydrogen bonds : bond 0.04158 / 2.30 ( 565) hydrogen bonds : angle 5.43164 / 2.83 ( 1569) link_ALPHA1-3 : bond 0.00480 / 0.24 ( 3) link_ALPHA1-3 : angle 1.70729 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00516 / 0.26 ( 3) link_ALPHA1-6 : angle 1.44408 / 0.76 ( 9) link_BETA1-4 : bond 0.00390 / 0.23 ( 39) link_BETA1-4 : angle 1.64692 / 0.83 ( 117) link_NAG-ASN : bond 0.00354 / 0.19 ( 55) link_NAG-ASN : angle 2.13090 / 1.04 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.535 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 136 ASN cc_start: 0.8890 (m-40) cc_final: 0.8510 (p0) REVERT: A 217 TYR cc_start: 0.7532 (m-80) cc_final: 0.7234 (m-80) REVERT: A 244 THR cc_start: 0.8947 (m) cc_final: 0.8516 (t) REVERT: A 427 TRP cc_start: 0.8826 (m100) cc_final: 0.8497 (m100) REVERT: A 477 ASP cc_start: 0.9212 (m-30) cc_final: 0.8903 (m-30) REVERT: B 543 ASN cc_start: 0.9408 (m-40) cc_final: 0.8367 (t0) REVERT: B 581 LEU cc_start: 0.9321 (mt) cc_final: 0.9086 (tp) REVERT: B 584 GLU cc_start: 0.8608 (pp20) cc_final: 0.8251 (pp20) REVERT: B 585 HIS cc_start: 0.8613 (m-70) cc_final: 0.8172 (m-70) REVERT: B 586 TYR cc_start: 0.8906 (t80) cc_final: 0.8507 (t80) REVERT: B 588 ARG cc_start: 0.9374 (ttp80) cc_final: 0.8775 (ttm-80) REVERT: B 591 GLN cc_start: 0.9440 (tt0) cc_final: 0.9025 (tm-30) REVERT: B 595 ILE cc_start: 0.9594 (pt) cc_final: 0.9308 (pt) REVERT: B 603 ILE cc_start: 0.8113 (pt) cc_final: 0.7556 (pt) REVERT: B 606 THR cc_start: 0.8874 (p) cc_final: 0.8590 (t) REVERT: B 634 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8651 (tp30) REVERT: B 647 GLU cc_start: 0.8041 (pp20) cc_final: 0.7838 (pp20) REVERT: B 654 GLU cc_start: 0.8951 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 664 ASP cc_start: 0.7876 (t0) cc_final: 0.7110 (p0) REVERT: C 39 TYR cc_start: 0.7978 (m-80) cc_final: 0.7418 (m-10) REVERT: C 40 TYR cc_start: 0.9237 (t80) cc_final: 0.8574 (t80) REVERT: C 116 LEU cc_start: 0.9585 (tp) cc_final: 0.9008 (tp) REVERT: C 191 TYR cc_start: 0.8414 (m-80) cc_final: 0.7730 (m-80) REVERT: C 319 TYR cc_start: 0.9089 (p90) cc_final: 0.8348 (p90) REVERT: C 434 MET cc_start: 0.8629 (tpp) cc_final: 0.8392 (tpt) REVERT: C 477 ASP cc_start: 0.9527 (m-30) cc_final: 0.9202 (p0) REVERT: E 536 THR cc_start: 0.9169 (p) cc_final: 0.8799 (t) REVERT: E 537 LEU cc_start: 0.9021 (mt) cc_final: 0.8791 (mt) REVERT: E 571 TRP cc_start: 0.8821 (m100) cc_final: 0.8278 (m100) REVERT: E 575 GLN cc_start: 0.9441 (tt0) cc_final: 0.9127 (tm-30) REVERT: E 584 GLU cc_start: 0.9292 (tt0) cc_final: 0.8985 (tm-30) REVERT: E 589 ASP cc_start: 0.9309 (m-30) cc_final: 0.8998 (p0) REVERT: E 591 GLN cc_start: 0.9216 (pt0) cc_final: 0.8589 (pt0) REVERT: E 603 ILE cc_start: 0.9080 (mt) cc_final: 0.8734 (mt) REVERT: E 654 GLU cc_start: 0.9311 (tp30) cc_final: 0.8850 (tp30) REVERT: E 655 LYS cc_start: 0.9258 (tptp) cc_final: 0.9032 (tppt) REVERT: E 659 ASP cc_start: 0.9126 (m-30) cc_final: 0.8919 (t0) REVERT: D 42 VAL cc_start: 0.9513 (t) cc_final: 0.9021 (p) REVERT: D 121 LYS cc_start: 0.9264 (pptt) cc_final: 0.9029 (ptmm) REVERT: D 154 LEU cc_start: 0.9559 (mt) cc_final: 0.9079 (tp) REVERT: D 376 PHE cc_start: 0.8736 (p90) cc_final: 0.7901 (p90) REVERT: D 383 PHE cc_start: 0.9173 (m-80) cc_final: 0.8693 (m-80) REVERT: F 535 MET cc_start: 0.8138 (mpp) cc_final: 0.7645 (mpp) REVERT: F 539 VAL cc_start: 0.9464 (t) cc_final: 0.9245 (t) REVERT: F 574 LYS cc_start: 0.9277 (mttt) cc_final: 0.8915 (ptmm) REVERT: F 590 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: F 601 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8737 (tppt) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1194 time to fit residues: 46.0317 Evaluate side-chains 199 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 176 optimal weight: 4.9990 chunk 18 optimal weight: 50.0000 chunk 137 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050950 restraints weight = 92429.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052424 restraints weight = 53730.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.053515 restraints weight = 36382.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.054301 restraints weight = 26839.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054870 restraints weight = 21100.184| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15965 Z= 0.163 Angle : 0.675 10.638 21901 Z= 0.326 Chirality : 0.046 0.683 2771 Planarity : 0.004 0.060 2623 Dihedral : 4.726 21.080 1962 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1620 helix: 1.12 (0.27), residues: 397 sheet: 0.27 (0.23), residues: 463 loop : -0.76 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 327 TYR 0.022 0.002 TYR A 217 PHE 0.017 0.002 PHE B 522 TRP 0.015 0.002 TRP C 112 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (15832) covalent geometry : angle 0.63783 / 0.32 (21535) SS BOND : bond 0.00337 / 0.18 ( 33) SS BOND : angle 1.16944 / 0.57 ( 66) hydrogen bonds : bond 0.04039 / 2.23 ( 565) hydrogen bonds : angle 5.35037 / 2.79 ( 1569) link_ALPHA1-3 : bond 0.00443 / 0.22 ( 3) link_ALPHA1-3 : angle 1.71524 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00494 / 0.25 ( 3) link_ALPHA1-6 : angle 1.44877 / 0.77 ( 9) link_BETA1-4 : bond 0.00371 / 0.22 ( 39) link_BETA1-4 : angle 1.62130 / 0.82 ( 117) link_NAG-ASN : bond 0.00347 / 0.19 ( 55) link_NAG-ASN : angle 2.17506 / 1.09 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.647 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: A 52 LEU cc_start: 0.9483 (mm) cc_final: 0.9228 (mm) REVERT: A 82 GLN cc_start: 0.8567 (pm20) cc_final: 0.8364 (pm20) REVERT: A 136 ASN cc_start: 0.8939 (m-40) cc_final: 0.8539 (p0) REVERT: A 217 TYR cc_start: 0.7452 (m-80) cc_final: 0.7173 (m-80) REVERT: A 244 THR cc_start: 0.8974 (m) cc_final: 0.8570 (t) REVERT: A 477 ASP cc_start: 0.9194 (m-30) cc_final: 0.8900 (m-30) REVERT: B 543 ASN cc_start: 0.9452 (m-40) cc_final: 0.8465 (t0) REVERT: B 581 LEU cc_start: 0.9368 (mt) cc_final: 0.9043 (tp) REVERT: B 584 GLU cc_start: 0.8575 (pp20) cc_final: 0.8023 (pp20) REVERT: B 585 HIS cc_start: 0.8579 (m-70) cc_final: 0.8203 (m-70) REVERT: B 586 TYR cc_start: 0.8919 (t80) cc_final: 0.8523 (t80) REVERT: B 588 ARG cc_start: 0.9375 (ttp80) cc_final: 0.8769 (ttm-80) REVERT: B 591 GLN cc_start: 0.9451 (tt0) cc_final: 0.9023 (tm-30) REVERT: B 595 ILE cc_start: 0.9597 (pt) cc_final: 0.9324 (pt) REVERT: B 603 ILE cc_start: 0.8129 (pt) cc_final: 0.7575 (pt) REVERT: B 622 ILE cc_start: 0.9507 (mp) cc_final: 0.9098 (mp) REVERT: B 634 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8632 (tp30) REVERT: B 654 GLU cc_start: 0.8951 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 664 ASP cc_start: 0.8058 (t0) cc_final: 0.7257 (p0) REVERT: C 39 TYR cc_start: 0.7995 (m-80) cc_final: 0.7379 (m-10) REVERT: C 40 TYR cc_start: 0.9265 (t80) cc_final: 0.8597 (t80) REVERT: C 116 LEU cc_start: 0.9575 (tp) cc_final: 0.9088 (tp) REVERT: C 191 TYR cc_start: 0.8442 (m-80) cc_final: 0.7781 (m-80) REVERT: C 319 TYR cc_start: 0.9102 (p90) cc_final: 0.8381 (p90) REVERT: C 477 ASP cc_start: 0.9522 (m-30) cc_final: 0.9206 (p0) REVERT: E 536 THR cc_start: 0.9147 (p) cc_final: 0.8871 (t) REVERT: E 537 LEU cc_start: 0.8987 (mt) cc_final: 0.8786 (mt) REVERT: E 542 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7507 (mtm110) REVERT: E 584 GLU cc_start: 0.9294 (tt0) cc_final: 0.9004 (tm-30) REVERT: E 589 ASP cc_start: 0.9300 (m-30) cc_final: 0.9016 (p0) REVERT: E 591 GLN cc_start: 0.9200 (pt0) cc_final: 0.8573 (pt0) REVERT: E 603 ILE cc_start: 0.9100 (mt) cc_final: 0.8674 (mt) REVERT: E 654 GLU cc_start: 0.9255 (tp30) cc_final: 0.8797 (tp30) REVERT: E 655 LYS cc_start: 0.9270 (tptp) cc_final: 0.8967 (tppt) REVERT: E 658 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8742 (tm-30) REVERT: E 659 ASP cc_start: 0.8959 (m-30) cc_final: 0.8725 (t0) REVERT: D 121 LYS cc_start: 0.9228 (pptt) cc_final: 0.8936 (ptmm) REVERT: D 376 PHE cc_start: 0.8741 (p90) cc_final: 0.7909 (p90) REVERT: D 383 PHE cc_start: 0.9177 (m-80) cc_final: 0.8663 (m-80) REVERT: F 535 MET cc_start: 0.8210 (mpp) cc_final: 0.7684 (mpp) REVERT: F 589 ASP cc_start: 0.9060 (m-30) cc_final: 0.8820 (m-30) REVERT: F 601 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8778 (tppt) REVERT: F 633 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8958 (mmmt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1236 time to fit residues: 47.8267 Evaluate side-chains 201 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 12 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 77 optimal weight: 0.0570 chunk 56 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN D 328 GLN D 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047924 restraints weight = 95648.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.049345 restraints weight = 56299.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050327 restraints weight = 38209.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051081 restraints weight = 28468.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051616 restraints weight = 22564.198| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15965 Z= 0.342 Angle : 0.923 10.927 21901 Z= 0.443 Chirality : 0.051 0.680 2771 Planarity : 0.005 0.061 2623 Dihedral : 5.338 24.191 1962 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1620 helix: 0.34 (0.25), residues: 388 sheet: 0.02 (0.23), residues: 460 loop : -1.08 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 327 TYR 0.030 0.003 TYR A 217 PHE 0.036 0.003 PHE B 522 TRP 0.040 0.003 TRP C 69 HIS 0.011 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.34 (15832) covalent geometry : angle 0.88040 / 0.43 (21535) SS BOND : bond 0.00678 / 0.36 ( 33) SS BOND : angle 1.39433 / 0.69 ( 66) hydrogen bonds : bond 0.05005 / 2.79 ( 565) hydrogen bonds : angle 6.04229 / 3.13 ( 1569) link_ALPHA1-3 : bond 0.00393 / 0.21 ( 3) link_ALPHA1-3 : angle 2.10009 / 1.19 ( 9) link_ALPHA1-6 : bond 0.00403 / 0.20 ( 3) link_ALPHA1-6 : angle 1.55307 / 0.81 ( 9) link_BETA1-4 : bond 0.00531 / 0.28 ( 39) link_BETA1-4 : angle 2.04007 / 1.04 ( 117) link_NAG-ASN : bond 0.00669 / 0.36 ( 55) link_NAG-ASN : angle 2.81396 / 1.41 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.9017 (m-40) cc_final: 0.8597 (p0) REVERT: A 217 TYR cc_start: 0.7652 (m-80) cc_final: 0.7253 (m-80) REVERT: A 475 MET cc_start: 0.9220 (mmp) cc_final: 0.8959 (mmp) REVERT: A 477 ASP cc_start: 0.9189 (m-30) cc_final: 0.8855 (m-30) REVERT: B 543 ASN cc_start: 0.9502 (m-40) cc_final: 0.9029 (m-40) REVERT: B 581 LEU cc_start: 0.9475 (mt) cc_final: 0.9070 (tp) REVERT: B 585 HIS cc_start: 0.8650 (m-70) cc_final: 0.7851 (m-70) REVERT: B 586 TYR cc_start: 0.9089 (t80) cc_final: 0.8660 (t80) REVERT: B 588 ARG cc_start: 0.9419 (ttp80) cc_final: 0.8807 (ttm-80) REVERT: B 591 GLN cc_start: 0.9491 (tt0) cc_final: 0.9085 (tm-30) REVERT: B 603 ILE cc_start: 0.8171 (pt) cc_final: 0.7502 (pt) REVERT: B 622 ILE cc_start: 0.9588 (mp) cc_final: 0.9271 (mp) REVERT: B 634 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8629 (tp30) REVERT: B 647 GLU cc_start: 0.8400 (pp20) cc_final: 0.8160 (pp20) REVERT: B 654 GLU cc_start: 0.8841 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 657 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8811 (tm-30) REVERT: C 39 TYR cc_start: 0.8166 (m-80) cc_final: 0.7387 (m-10) REVERT: C 40 TYR cc_start: 0.9284 (t80) cc_final: 0.8624 (t80) REVERT: C 95 MET cc_start: 0.8537 (pmm) cc_final: 0.8320 (pmm) REVERT: C 116 LEU cc_start: 0.9391 (tp) cc_final: 0.9122 (tp) REVERT: C 191 TYR cc_start: 0.8593 (m-80) cc_final: 0.8009 (m-80) REVERT: C 319 TYR cc_start: 0.9117 (p90) cc_final: 0.8444 (p90) REVERT: C 434 MET cc_start: 0.8991 (tpp) cc_final: 0.7936 (tpt) REVERT: C 477 ASP cc_start: 0.9495 (m-30) cc_final: 0.9253 (p0) REVERT: E 537 LEU cc_start: 0.9024 (mt) cc_final: 0.8786 (mt) REVERT: E 584 GLU cc_start: 0.9304 (tt0) cc_final: 0.9035 (tm-30) REVERT: E 589 ASP cc_start: 0.9392 (m-30) cc_final: 0.9097 (p0) REVERT: E 591 GLN cc_start: 0.9222 (pt0) cc_final: 0.8834 (pt0) REVERT: E 603 ILE cc_start: 0.9163 (mt) cc_final: 0.8817 (mt) REVERT: E 654 GLU cc_start: 0.9281 (tp30) cc_final: 0.8929 (tp30) REVERT: E 655 LYS cc_start: 0.9313 (tptp) cc_final: 0.9041 (tppt) REVERT: E 656 ASN cc_start: 0.9204 (m110) cc_final: 0.9001 (m-40) REVERT: E 658 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8885 (tm-30) REVERT: E 659 ASP cc_start: 0.9065 (m-30) cc_final: 0.8749 (t0) REVERT: D 121 LYS cc_start: 0.9263 (pptt) cc_final: 0.9001 (ptmm) REVERT: D 376 PHE cc_start: 0.8888 (p90) cc_final: 0.7777 (p90) REVERT: D 424 ILE cc_start: 0.8897 (tp) cc_final: 0.7735 (tp) REVERT: F 535 MET cc_start: 0.8273 (mpp) cc_final: 0.7681 (mpp) REVERT: F 539 VAL cc_start: 0.9487 (t) cc_final: 0.9154 (p) REVERT: F 589 ASP cc_start: 0.9129 (m-30) cc_final: 0.8885 (m-30) REVERT: F 601 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8723 (tppt) REVERT: F 617 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7900 (mtp85) REVERT: F 648 GLU cc_start: 0.9228 (pp20) cc_final: 0.8981 (pp20) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1254 time to fit residues: 42.6864 Evaluate side-chains 170 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS C 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 HIS ** D 195 ASN ** 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 = 0.3130 r_free = 0.3130 target = 0.058445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049169 restraints weight = 93355.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050612 restraints weight = 54620.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051681 restraints weight = 37209.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052444 restraints weight = 27490.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052970 restraints weight = 21809.292| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15965 Z= 0.196 Angle : 0.765 12.682 21901 Z= 0.364 Chirality : 0.048 0.626 2771 Planarity : 0.004 0.062 2623 Dihedral : 5.122 22.242 1962 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1620 helix: 0.53 (0.26), residues: 392 sheet: 0.01 (0.23), residues: 481 loop : -1.11 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 327 TYR 0.038 0.002 TYR D 217 PHE 0.019 0.002 PHE B 522 TRP 0.021 0.002 TRP C 112 HIS 0.004 0.001 HIS E 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (15832) covalent geometry : angle 0.71562 / 0.35 (21535) SS BOND : bond 0.00338 / 0.19 ( 33) SS BOND : angle 1.02317 / 0.48 ( 66) hydrogen bonds : bond 0.04371 / 2.42 ( 565) hydrogen bonds : angle 5.76690 / 2.99 ( 1569) link_ALPHA1-3 : bond 0.00327 / 0.17 ( 3) link_ALPHA1-3 : angle 1.91004 / 1.06 ( 9) link_ALPHA1-6 : bond 0.00423 / 0.22 ( 3) link_ALPHA1-6 : angle 1.54123 / 0.81 ( 9) link_BETA1-4 : bond 0.00373 / 0.21 ( 39) link_BETA1-4 : angle 1.73874 / 0.87 ( 117) link_NAG-ASN : bond 0.00381 / 0.20 ( 55) link_NAG-ASN : angle 2.81159 / 1.43 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9478 (mm) cc_final: 0.9272 (mm) REVERT: A 136 ASN cc_start: 0.8983 (m-40) cc_final: 0.8582 (p0) REVERT: A 161 MET cc_start: 0.8746 (tpt) cc_final: 0.8544 (tpp) REVERT: A 217 TYR cc_start: 0.7601 (m-80) cc_final: 0.7267 (m-80) REVERT: A 360 ARG cc_start: 0.7483 (mpp80) cc_final: 0.6962 (mpp80) REVERT: A 475 MET cc_start: 0.9231 (mmp) cc_final: 0.9004 (mmp) REVERT: A 477 ASP cc_start: 0.9177 (m-30) cc_final: 0.8886 (m-30) REVERT: B 543 ASN cc_start: 0.9474 (m-40) cc_final: 0.8475 (t0) REVERT: B 581 LEU cc_start: 0.9442 (mt) cc_final: 0.8706 (tp) REVERT: B 584 GLU cc_start: 0.8544 (pp20) cc_final: 0.7310 (pp20) REVERT: B 585 HIS cc_start: 0.8602 (m-70) cc_final: 0.7648 (m-70) REVERT: B 586 TYR cc_start: 0.8990 (t80) cc_final: 0.8540 (t80) REVERT: B 588 ARG cc_start: 0.9419 (ttp80) cc_final: 0.8788 (ttm-80) REVERT: B 591 GLN cc_start: 0.9475 (tt0) cc_final: 0.9026 (tm-30) REVERT: B 603 ILE cc_start: 0.8110 (pt) cc_final: 0.7560 (pt) REVERT: B 634 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8572 (tp30) REVERT: B 648 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8855 (tm-30) REVERT: B 654 GLU cc_start: 0.8918 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 657 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8871 (tm-30) REVERT: C 39 TYR cc_start: 0.8148 (m-80) cc_final: 0.7365 (m-10) REVERT: C 40 TYR cc_start: 0.9250 (t80) cc_final: 0.8546 (t80) REVERT: C 191 TYR cc_start: 0.8553 (m-80) cc_final: 0.7905 (m-80) REVERT: C 252 LYS cc_start: 0.9235 (mttt) cc_final: 0.9005 (mttt) REVERT: C 319 TYR cc_start: 0.9142 (p90) cc_final: 0.8446 (p90) REVERT: C 434 MET cc_start: 0.8905 (tpp) cc_final: 0.7720 (tpp) REVERT: C 477 ASP cc_start: 0.9478 (m-30) cc_final: 0.9236 (p0) REVERT: E 536 THR cc_start: 0.9206 (p) cc_final: 0.8886 (t) REVERT: E 537 LEU cc_start: 0.9020 (mt) cc_final: 0.8748 (mt) REVERT: E 584 GLU cc_start: 0.9269 (tt0) cc_final: 0.8969 (tm-30) REVERT: E 589 ASP cc_start: 0.9321 (m-30) cc_final: 0.9027 (p0) REVERT: E 591 GLN cc_start: 0.9206 (pt0) cc_final: 0.8552 (pt0) REVERT: E 603 ILE cc_start: 0.9135 (mt) cc_final: 0.8779 (mt) REVERT: E 632 ASP cc_start: 0.9196 (t0) cc_final: 0.8893 (p0) REVERT: E 654 GLU cc_start: 0.9243 (tp30) cc_final: 0.8985 (tp30) REVERT: E 655 LYS cc_start: 0.9294 (tptp) cc_final: 0.9029 (tppt) REVERT: E 656 ASN cc_start: 0.9073 (m110) cc_final: 0.8863 (m-40) REVERT: E 658 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8917 (tm-30) REVERT: E 659 ASP cc_start: 0.9016 (m-30) cc_final: 0.8734 (t0) REVERT: D 121 LYS cc_start: 0.9284 (pptt) cc_final: 0.9059 (ptmm) REVERT: D 376 PHE cc_start: 0.8772 (p90) cc_final: 0.7897 (p90) REVERT: D 383 PHE cc_start: 0.9086 (m-80) cc_final: 0.8585 (m-80) REVERT: D 424 ILE cc_start: 0.8918 (tp) cc_final: 0.7776 (tp) REVERT: F 535 MET cc_start: 0.8299 (mpp) cc_final: 0.7673 (mpp) REVERT: F 539 VAL cc_start: 0.9525 (t) cc_final: 0.9160 (p) REVERT: F 589 ASP cc_start: 0.9154 (m-30) cc_final: 0.8912 (m-30) REVERT: F 601 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8677 (tppt) REVERT: F 648 GLU cc_start: 0.9202 (pp20) cc_final: 0.8994 (pp20) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1131 time to fit residues: 39.8412 Evaluate side-chains 180 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 585 HIS E 625 ASN ** D 195 ASN ** 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 = 0.3139 r_free = 0.3139 target = 0.058835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.049589 restraints weight = 92958.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051011 restraints weight = 55204.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052009 restraints weight = 37731.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052805 restraints weight = 28343.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053350 restraints weight = 22352.115| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15965 Z= 0.177 Angle : 0.749 11.747 21901 Z= 0.355 Chirality : 0.047 0.597 2771 Planarity : 0.004 0.060 2623 Dihedral : 5.054 29.289 1962 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1620 helix: 0.61 (0.26), residues: 392 sheet: -0.15 (0.22), residues: 502 loop : -1.05 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 542 TYR 0.029 0.002 TYR D 217 PHE 0.016 0.002 PHE A 383 TRP 0.022 0.002 TRP C 112 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (15832) covalent geometry : angle 0.70525 / 0.35 (21535) SS BOND : bond 0.00331 / 0.18 ( 33) SS BOND : angle 1.25293 / 0.62 ( 66) hydrogen bonds : bond 0.04252 / 2.38 ( 565) hydrogen bonds : angle 5.63005 / 2.92 ( 1569) link_ALPHA1-3 : bond 0.00362 / 0.19 ( 3) link_ALPHA1-3 : angle 1.77119 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00469 / 0.24 ( 3) link_ALPHA1-6 : angle 1.49587 / 0.78 ( 9) link_BETA1-4 : bond 0.00366 / 0.21 ( 39) link_BETA1-4 : angle 1.67966 / 0.84 ( 117) link_NAG-ASN : bond 0.00430 / 0.26 ( 55) link_NAG-ASN : angle 2.59326 / 1.32 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.515 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 52 LEU cc_start: 0.9493 (mm) cc_final: 0.9291 (mm) REVERT: A 136 ASN cc_start: 0.8975 (m-40) cc_final: 0.8619 (p0) REVERT: A 161 MET cc_start: 0.8694 (tpt) cc_final: 0.8321 (tpp) REVERT: A 217 TYR cc_start: 0.7546 (m-80) cc_final: 0.7095 (m-10) REVERT: A 244 THR cc_start: 0.9051 (m) cc_final: 0.8638 (t) REVERT: A 360 ARG cc_start: 0.7465 (mpp80) cc_final: 0.6966 (mpp80) REVERT: A 477 ASP cc_start: 0.9203 (m-30) cc_final: 0.8917 (m-30) REVERT: A 484 TYR cc_start: 0.9267 (p90) cc_final: 0.9029 (p90) REVERT: B 543 ASN cc_start: 0.9478 (m-40) cc_final: 0.9252 (m110) REVERT: B 581 LEU cc_start: 0.9439 (mt) cc_final: 0.8708 (tp) REVERT: B 584 GLU cc_start: 0.8521 (pp20) cc_final: 0.7329 (pp20) REVERT: B 585 HIS cc_start: 0.8552 (m-70) cc_final: 0.7625 (m-70) REVERT: B 586 TYR cc_start: 0.8970 (t80) cc_final: 0.8505 (t80) REVERT: B 588 ARG cc_start: 0.9419 (ttp80) cc_final: 0.8746 (ttm-80) REVERT: B 591 GLN cc_start: 0.9459 (tt0) cc_final: 0.9014 (tm-30) REVERT: B 603 ILE cc_start: 0.8082 (pt) cc_final: 0.7669 (pt) REVERT: B 634 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8583 (tp30) REVERT: B 648 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 654 GLU cc_start: 0.8954 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 39 TYR cc_start: 0.8026 (m-80) cc_final: 0.7207 (m-10) REVERT: C 40 TYR cc_start: 0.9243 (t80) cc_final: 0.8887 (t80) REVERT: C 95 MET cc_start: 0.8548 (pmm) cc_final: 0.8334 (pmm) REVERT: C 191 TYR cc_start: 0.8501 (m-80) cc_final: 0.7787 (m-80) REVERT: C 252 LYS cc_start: 0.9190 (mttt) cc_final: 0.8965 (mttt) REVERT: C 319 TYR cc_start: 0.9116 (p90) cc_final: 0.8386 (p90) REVERT: C 434 MET cc_start: 0.8901 (tpp) cc_final: 0.7986 (tpp) REVERT: C 477 ASP cc_start: 0.9473 (m-30) cc_final: 0.9243 (p0) REVERT: E 536 THR cc_start: 0.9271 (p) cc_final: 0.8805 (t) REVERT: E 580 VAL cc_start: 0.9480 (m) cc_final: 0.9245 (p) REVERT: E 584 GLU cc_start: 0.9303 (tt0) cc_final: 0.9015 (tm-30) REVERT: E 589 ASP cc_start: 0.9312 (m-30) cc_final: 0.9007 (p0) REVERT: E 591 GLN cc_start: 0.9198 (pt0) cc_final: 0.8497 (pt0) REVERT: E 603 ILE cc_start: 0.9111 (mt) cc_final: 0.8726 (mt) REVERT: E 632 ASP cc_start: 0.9145 (t0) cc_final: 0.8851 (p0) REVERT: E 654 GLU cc_start: 0.9273 (tp30) cc_final: 0.8865 (tp30) REVERT: E 655 LYS cc_start: 0.9288 (tptp) cc_final: 0.9023 (tppt) REVERT: E 658 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8940 (tm-30) REVERT: E 659 ASP cc_start: 0.9031 (m-30) cc_final: 0.8822 (t0) REVERT: D 97 LYS cc_start: 0.9291 (mppt) cc_final: 0.9048 (mppt) REVERT: D 121 LYS cc_start: 0.9275 (pptt) cc_final: 0.9029 (ptmm) REVERT: D 256 SER cc_start: 0.8495 (p) cc_final: 0.7565 (t) REVERT: D 376 PHE cc_start: 0.8762 (p90) cc_final: 0.7920 (p90) REVERT: D 383 PHE cc_start: 0.9053 (m-80) cc_final: 0.8549 (m-80) REVERT: D 424 ILE cc_start: 0.8870 (tp) cc_final: 0.7787 (tp) REVERT: F 535 MET cc_start: 0.8235 (mpp) cc_final: 0.7576 (mpp) REVERT: F 539 VAL cc_start: 0.9444 (t) cc_final: 0.9112 (t) REVERT: F 589 ASP cc_start: 0.9142 (m-30) cc_final: 0.8891 (m-30) REVERT: F 601 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8714 (tppt) REVERT: F 617 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7853 (mtp85) REVERT: F 648 GLU cc_start: 0.9193 (pp20) cc_final: 0.8929 (pp20) REVERT: F 656 ASN cc_start: 0.9223 (m110) cc_final: 0.8982 (m110) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.1096 time to fit residues: 39.4245 Evaluate side-chains 183 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 167 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN E 653 GLN ** D 195 ASN ** 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 = 0.3163 r_free = 0.3163 target = 0.059882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050724 restraints weight = 93764.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052133 restraints weight = 56512.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053131 restraints weight = 38914.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053877 restraints weight = 29206.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054426 restraints weight = 23226.996| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15965 Z= 0.139 Angle : 0.698 11.723 21901 Z= 0.331 Chirality : 0.046 0.565 2771 Planarity : 0.004 0.060 2623 Dihedral : 4.823 27.168 1962 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1620 helix: 0.87 (0.27), residues: 390 sheet: -0.10 (0.23), residues: 496 loop : -0.94 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 542 TYR 0.035 0.002 TYR F 643 PHE 0.020 0.002 PHE D 233 TRP 0.025 0.002 TRP C 112 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (15832) covalent geometry : angle 0.65754 / 0.32 (21535) SS BOND : bond 0.00289 / 0.16 ( 33) SS BOND : angle 1.06724 / 0.52 ( 66) hydrogen bonds : bond 0.04035 / 2.25 ( 565) hydrogen bonds : angle 5.44136 / 2.82 ( 1569) link_ALPHA1-3 : bond 0.00397 / 0.20 ( 3) link_ALPHA1-3 : angle 1.63117 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00480 / 0.24 ( 3) link_ALPHA1-6 : angle 1.47400 / 0.78 ( 9) link_BETA1-4 : bond 0.00375 / 0.21 ( 39) link_BETA1-4 : angle 1.59692 / 0.80 ( 117) link_NAG-ASN : bond 0.00426 / 0.26 ( 55) link_NAG-ASN : angle 2.37172 / 1.19 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9510 (mm) cc_final: 0.9143 (mm) REVERT: A 136 ASN cc_start: 0.8999 (m-40) cc_final: 0.8669 (p0) REVERT: A 161 MET cc_start: 0.8742 (tpt) cc_final: 0.8404 (tpp) REVERT: A 217 TYR cc_start: 0.7499 (m-80) cc_final: 0.7073 (m-10) REVERT: A 244 THR cc_start: 0.8991 (m) cc_final: 0.8598 (t) REVERT: A 477 ASP cc_start: 0.9223 (m-30) cc_final: 0.8955 (m-30) REVERT: A 484 TYR cc_start: 0.9208 (p90) cc_final: 0.8894 (p90) REVERT: B 543 ASN cc_start: 0.9403 (m-40) cc_final: 0.8437 (t0) REVERT: B 581 LEU cc_start: 0.9388 (mt) cc_final: 0.8561 (tp) REVERT: B 584 GLU cc_start: 0.8492 (pp20) cc_final: 0.7207 (pp20) REVERT: B 585 HIS cc_start: 0.8501 (m-70) cc_final: 0.7427 (m-70) REVERT: B 586 TYR cc_start: 0.8870 (t80) cc_final: 0.8324 (t80) REVERT: B 588 ARG cc_start: 0.9394 (ttp80) cc_final: 0.8717 (ttm-80) REVERT: B 591 GLN cc_start: 0.9432 (tt0) cc_final: 0.9075 (tm-30) REVERT: B 603 ILE cc_start: 0.8043 (pt) cc_final: 0.7417 (pt) REVERT: B 634 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8584 (tp30) REVERT: B 648 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8737 (tm-30) REVERT: B 654 GLU cc_start: 0.8944 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 39 TYR cc_start: 0.7875 (m-80) cc_final: 0.7175 (m-10) REVERT: C 40 TYR cc_start: 0.9219 (t80) cc_final: 0.8868 (t80) REVERT: C 191 TYR cc_start: 0.8387 (m-80) cc_final: 0.7623 (m-80) REVERT: C 319 TYR cc_start: 0.9069 (p90) cc_final: 0.8382 (p90) REVERT: C 434 MET cc_start: 0.8878 (tpp) cc_final: 0.7831 (tpp) REVERT: C 477 ASP cc_start: 0.9449 (m-30) cc_final: 0.9223 (p0) REVERT: E 536 THR cc_start: 0.9184 (p) cc_final: 0.8740 (t) REVERT: E 538 THR cc_start: 0.8258 (p) cc_final: 0.7597 (p) REVERT: E 539 VAL cc_start: 0.8725 (t) cc_final: 0.8232 (t) REVERT: E 542 ARG cc_start: 0.8248 (ptp-110) cc_final: 0.7783 (ptm160) REVERT: E 584 GLU cc_start: 0.9241 (tt0) cc_final: 0.8976 (tm-30) REVERT: E 589 ASP cc_start: 0.9299 (m-30) cc_final: 0.9001 (p0) REVERT: E 632 ASP cc_start: 0.9004 (t0) cc_final: 0.8767 (p0) REVERT: E 655 LYS cc_start: 0.9238 (tptp) cc_final: 0.8967 (tppt) REVERT: E 658 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8933 (tm-30) REVERT: E 659 ASP cc_start: 0.9031 (m-30) cc_final: 0.8807 (t0) REVERT: D 97 LYS cc_start: 0.9111 (mppt) cc_final: 0.8903 (mppt) REVERT: D 121 LYS cc_start: 0.9278 (pptt) cc_final: 0.9016 (ptmm) REVERT: D 256 SER cc_start: 0.8330 (p) cc_final: 0.7584 (t) REVERT: D 376 PHE cc_start: 0.8716 (p90) cc_final: 0.7960 (p90) REVERT: D 383 PHE cc_start: 0.8987 (m-80) cc_final: 0.8507 (m-80) REVERT: D 424 ILE cc_start: 0.8890 (tp) cc_final: 0.7817 (tp) REVERT: F 535 MET cc_start: 0.8314 (mpp) cc_final: 0.7656 (mpp) REVERT: F 539 VAL cc_start: 0.9335 (t) cc_final: 0.9096 (t) REVERT: F 589 ASP cc_start: 0.9136 (m-30) cc_final: 0.8924 (m-30) REVERT: F 601 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8752 (tppt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1042 time to fit residues: 38.5632 Evaluate side-chains 186 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 165 optimal weight: 4.9990 chunk 28 optimal weight: 0.0010 chunk 71 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048635 restraints weight = 96211.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049967 restraints weight = 58430.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050903 restraints weight = 40444.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051513 restraints weight = 30603.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052079 restraints weight = 25209.137| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15965 Z= 0.259 Angle : 0.824 11.925 21901 Z= 0.392 Chirality : 0.049 0.607 2771 Planarity : 0.005 0.060 2623 Dihedral : 5.183 25.894 1962 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1620 helix: 0.36 (0.26), residues: 391 sheet: -0.25 (0.22), residues: 501 loop : -1.23 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 542 TYR 0.037 0.003 TYR D 217 PHE 0.031 0.003 PHE B 522 TRP 0.027 0.002 TRP F 571 HIS 0.006 0.001 HIS E 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (15832) covalent geometry : angle 0.78145 / 0.38 (21535) SS BOND : bond 0.00404 / 0.22 ( 33) SS BOND : angle 1.30497 / 0.65 ( 66) hydrogen bonds : bond 0.04495 / 2.51 ( 565) hydrogen bonds : angle 5.81480 / 3.01 ( 1569) link_ALPHA1-3 : bond 0.00322 / 0.17 ( 3) link_ALPHA1-3 : angle 1.95621 / 1.10 ( 9) link_ALPHA1-6 : bond 0.00464 / 0.24 ( 3) link_ALPHA1-6 : angle 1.50769 / 0.79 ( 9) link_BETA1-4 : bond 0.00436 / 0.24 ( 39) link_BETA1-4 : angle 1.89053 / 0.95 ( 117) link_NAG-ASN : bond 0.00494 / 0.28 ( 55) link_NAG-ASN : angle 2.60970 / 1.29 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.04 seconds wall clock time: 37 minutes 16.22 seconds (2236.22 seconds total)