Starting phenix.real_space_refine on Wed Mar 4 20:01:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8d_23230/03_2026/7l8d_23230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8d_23230/03_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_23230/03_2026/7l8d_23230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8d_23230/03_2026/7l8d_23230.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8d_23230/03_2026/7l8d_23230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8d_23230/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.23 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: 1.80 Conformation dependent library (CDL) restraints added in 588.7 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: 0.75 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: 2.93 Time building geometry restraints manager: 2.28 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 - 21.32: 10426 21.32 - 42.64: 273 42.64 - 63.96: 69 63.96 - 85.28: 34 85.28 - 106.60: 18 Dihedral angle restraints: 10820 sinusoidal: 5393 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 10817 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: 4.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 11.720 106.603 7187 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 covalent geometry : bond 0.02209 (15832) covalent geometry : angle 1.76196 (21535) SS BOND : bond 0.02568 ( 33) SS BOND : angle 3.09768 ( 66) hydrogen bonds : bond 0.16600 ( 565) hydrogen bonds : angle 7.77040 ( 1569) link_ALPHA1-3 : bond 0.07404 ( 3) link_ALPHA1-3 : angle 4.59908 ( 9) link_ALPHA1-6 : bond 0.04473 ( 3) link_ALPHA1-6 : angle 2.16683 ( 9) link_BETA1-4 : bond 0.06689 ( 39) link_BETA1-4 : angle 4.68418 ( 117) link_NAG-ASN : bond 0.07421 ( 55) link_NAG-ASN : angle 2.53277 ( 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 : 0.541 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: 0.1284 time to fit residues: 87.0167 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.063740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053922 restraints weight = 88329.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055557 restraints weight = 50995.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056707 restraints weight = 34018.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057525 restraints weight = 25015.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058125 restraints weight = 19645.955| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15965 Z= 0.200 Angle : 0.866 19.431 21901 Z= 0.413 Chirality : 0.050 0.497 2771 Planarity : 0.004 0.047 2623 Dihedral : 9.373 79.666 4042 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.27 % Allowed : 2.36 % Favored : 97.37 % 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: 1.09 (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 F 643 PHE 0.020 0.003 PHE C 382 TRP 0.027 0.002 TRP F 610 HIS 0.006 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00422 (15832) covalent geometry : angle 0.79104 (21535) SS BOND : bond 0.00260 ( 33) SS BOND : angle 1.07375 ( 66) hydrogen bonds : bond 0.05968 ( 565) hydrogen bonds : angle 6.19011 ( 1569) link_ALPHA1-3 : bond 0.01500 ( 3) link_ALPHA1-3 : angle 2.20209 ( 9) link_ALPHA1-6 : bond 0.00698 ( 3) link_ALPHA1-6 : angle 1.54233 ( 9) link_BETA1-4 : bond 0.00598 ( 39) link_BETA1-4 : angle 2.74451 ( 117) link_NAG-ASN : bond 0.00516 ( 55) link_NAG-ASN : angle 3.42465 ( 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 324 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 320 time to evaluate : 0.501 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 40 TYR cc_start: 0.8954 (t80) cc_final: 0.8580 (t80) REVERT: A 52 LEU cc_start: 0.9467 (mm) cc_final: 0.8754 (mm) REVERT: A 98 ASN cc_start: 0.9041 (t0) cc_final: 0.8775 (t0) REVERT: A 136 ASN cc_start: 0.8808 (m-40) cc_final: 0.8479 (p0) REVERT: A 161 MET cc_start: 0.8780 (tmm) cc_final: 0.8408 (tmm) REVERT: A 164 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7964 (tp30) REVERT: A 244 THR cc_start: 0.8989 (m) cc_final: 0.8495 (t) REVERT: A 424 ILE cc_start: 0.8663 (mm) cc_final: 0.8289 (mp) REVERT: A 427 TRP cc_start: 0.8060 (m100) cc_final: 0.7706 (m100) REVERT: B 581 LEU cc_start: 0.9278 (mt) cc_final: 0.8629 (tp) REVERT: B 584 GLU cc_start: 0.8550 (pp20) cc_final: 0.7561 (pp20) REVERT: B 585 HIS cc_start: 0.8727 (m-70) cc_final: 0.7427 (m-70) REVERT: B 586 TYR cc_start: 0.8900 (t80) cc_final: 0.8519 (t80) REVERT: B 588 ARG cc_start: 0.9389 (ttp80) cc_final: 0.8892 (ttm-80) REVERT: B 589 ASP cc_start: 0.9338 (m-30) cc_final: 0.9093 (m-30) REVERT: B 591 GLN cc_start: 0.9338 (tt0) cc_final: 0.8924 (tm-30) REVERT: B 595 ILE cc_start: 0.9513 (pt) cc_final: 0.9281 (tt) REVERT: B 603 ILE cc_start: 0.7806 (pt) cc_final: 0.7244 (pt) REVERT: B 610 TRP cc_start: 0.8741 (t-100) cc_final: 0.8414 (t-100) REVERT: B 622 ILE cc_start: 0.9122 (mp) cc_final: 0.8657 (mp) REVERT: B 634 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8522 (tp30) REVERT: B 635 ILE cc_start: 0.9581 (pt) cc_final: 0.9325 (pt) REVERT: B 651 ASN cc_start: 0.8776 (t0) cc_final: 0.8529 (t0) REVERT: B 654 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8588 (mt-10) REVERT: C 39 TYR cc_start: 0.7859 (m-80) cc_final: 0.7489 (m-80) REVERT: C 98 ASN cc_start: 0.8580 (t0) cc_final: 0.8219 (t0) REVERT: C 116 LEU cc_start: 0.9452 (tp) cc_final: 0.9180 (tp) REVERT: C 191 TYR cc_start: 0.8282 (m-80) cc_final: 0.7621 (m-80) REVERT: C 319 TYR cc_start: 0.9068 (p90) cc_final: 0.8298 (p90) REVERT: C 477 ASP cc_start: 0.9567 (m-30) cc_final: 0.8967 (p0) REVERT: E 536 THR cc_start: 0.9203 (p) cc_final: 0.8904 (t) REVERT: E 584 GLU cc_start: 0.9302 (tt0) cc_final: 0.8782 (tm-30) REVERT: E 589 ASP cc_start: 0.9313 (m-30) cc_final: 0.9006 (p0) REVERT: E 595 ILE cc_start: 0.9571 (tt) cc_final: 0.9308 (tp) REVERT: E 603 ILE cc_start: 0.8978 (mt) cc_final: 0.8777 (mt) REVERT: E 620 SER cc_start: 0.7832 (m) cc_final: 0.7575 (p) REVERT: E 645 LEU cc_start: 0.9735 (mm) cc_final: 0.9515 (mm) REVERT: E 654 GLU cc_start: 0.9290 (tp30) cc_final: 0.8734 (tp30) REVERT: E 659 ASP cc_start: 0.9152 (m-30) cc_final: 0.8886 (t0) REVERT: D 42 VAL cc_start: 0.9422 (t) cc_final: 0.8930 (p) REVERT: D 91 GLU cc_start: 0.8057 (tp30) cc_final: 0.7813 (tm-30) REVERT: D 121 LYS cc_start: 0.9156 (pptt) cc_final: 0.8818 (ptmm) REVERT: D 154 LEU cc_start: 0.9514 (mt) cc_final: 0.9027 (tt) REVERT: D 376 PHE cc_start: 0.8550 (p90) cc_final: 0.7749 (p90) REVERT: D 383 PHE cc_start: 0.9303 (m-80) cc_final: 0.8743 (m-80) REVERT: F 522 PHE cc_start: 0.8790 (t80) cc_final: 0.8462 (t80) REVERT: F 534 SER cc_start: 0.9537 (p) cc_final: 0.9313 (p) REVERT: F 574 LYS cc_start: 0.9396 (mttt) cc_final: 0.9158 (ptmm) REVERT: F 633 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8768 (mmmt) outliers start: 4 outliers final: 1 residues processed: 321 average time/residue: 0.1134 time to fit residues: 54.1014 Evaluate side-chains 234 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 127 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 585 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3162 r_free = 0.3162 target = 0.059537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050018 restraints weight = 94350.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051528 restraints weight = 54531.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052601 restraints weight = 36532.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053390 restraints weight = 26968.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053962 restraints weight = 21179.828| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15965 Z= 0.279 Angle : 0.883 16.781 21901 Z= 0.427 Chirality : 0.049 0.505 2771 Planarity : 0.005 0.059 2623 Dihedral : 8.851 70.268 4042 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % 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: -0.06 (0.20), residues: 1620 helix: 0.64 (0.25), residues: 397 sheet: 0.41 (0.23), residues: 455 loop : -0.61 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 298 TYR 0.031 0.003 TYR A 217 PHE 0.028 0.003 PHE B 522 TRP 0.019 0.003 TRP B 623 HIS 0.010 0.002 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00594 (15832) covalent geometry : angle 0.82883 (21535) SS BOND : bond 0.00480 ( 33) SS BOND : angle 1.38237 ( 66) hydrogen bonds : bond 0.05344 ( 565) hydrogen bonds : angle 6.11321 ( 1569) link_ALPHA1-3 : bond 0.01256 ( 3) link_ALPHA1-3 : angle 2.40393 ( 9) link_ALPHA1-6 : bond 0.00716 ( 3) link_ALPHA1-6 : angle 1.60412 ( 9) link_BETA1-4 : bond 0.00495 ( 39) link_BETA1-4 : angle 2.29513 ( 117) link_NAG-ASN : bond 0.00667 ( 55) link_NAG-ASN : angle 2.97572 ( 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 255 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9342 (mm) cc_final: 0.9130 (mm) REVERT: A 98 ASN cc_start: 0.9273 (t0) cc_final: 0.8784 (t0) REVERT: A 136 ASN cc_start: 0.8841 (m-40) cc_final: 0.8451 (p0) REVERT: A 161 MET cc_start: 0.8935 (tmm) cc_final: 0.8482 (tmm) REVERT: A 244 THR cc_start: 0.9081 (m) cc_final: 0.8656 (t) REVERT: A 345 VAL cc_start: 0.9626 (t) cc_final: 0.9248 (p) REVERT: A 427 TRP cc_start: 0.8714 (m100) cc_final: 0.8380 (m100) REVERT: A 492 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 588 ARG cc_start: 0.9397 (ttp80) cc_final: 0.8853 (ttm-80) REVERT: B 589 ASP cc_start: 0.9327 (m-30) cc_final: 0.9111 (m-30) REVERT: B 591 GLN cc_start: 0.9460 (tt0) cc_final: 0.9198 (tm-30) REVERT: B 595 ILE cc_start: 0.9562 (pt) cc_final: 0.9315 (tt) REVERT: B 622 ILE cc_start: 0.9328 (mp) cc_final: 0.8907 (mp) REVERT: B 634 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8667 (tp30) REVERT: B 651 ASN cc_start: 0.8878 (t0) cc_final: 0.8672 (t0) REVERT: B 654 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 664 ASP cc_start: 0.7670 (t0) cc_final: 0.6919 (p0) REVERT: C 39 TYR cc_start: 0.8062 (m-80) cc_final: 0.7519 (m-10) REVERT: C 40 TYR cc_start: 0.9250 (t80) cc_final: 0.8960 (t80) REVERT: C 116 LEU cc_start: 0.9573 (tp) cc_final: 0.9084 (tp) REVERT: C 191 TYR cc_start: 0.8477 (m-80) cc_final: 0.7854 (m-80) REVERT: C 319 TYR cc_start: 0.9160 (p90) cc_final: 0.8460 (p90) REVERT: C 434 MET cc_start: 0.8941 (tpp) cc_final: 0.8280 (tpt) REVERT: C 477 ASP cc_start: 0.9551 (m-30) cc_final: 0.9148 (p0) REVERT: E 536 THR cc_start: 0.9238 (p) cc_final: 0.8874 (t) REVERT: E 584 GLU cc_start: 0.9316 (tt0) cc_final: 0.8912 (tm-30) REVERT: E 589 ASP cc_start: 0.9393 (m-30) cc_final: 0.9063 (p0) REVERT: E 595 ILE cc_start: 0.9666 (tt) cc_final: 0.9402 (tp) REVERT: E 603 ILE cc_start: 0.9187 (mt) cc_final: 0.8883 (mt) REVERT: E 607 ASN cc_start: 0.8789 (m-40) cc_final: 0.8569 (m-40) REVERT: E 620 SER cc_start: 0.8365 (m) cc_final: 0.8066 (p) REVERT: E 646 LEU cc_start: 0.9854 (mt) cc_final: 0.9640 (mt) REVERT: E 654 GLU cc_start: 0.9275 (tp30) cc_final: 0.8733 (tp30) REVERT: E 655 LYS cc_start: 0.9318 (tptp) cc_final: 0.8967 (tppt) REVERT: E 659 ASP cc_start: 0.9200 (m-30) cc_final: 0.8795 (t0) REVERT: D 121 LYS cc_start: 0.9256 (pptt) cc_final: 0.8889 (ptmm) REVERT: D 210 PHE cc_start: 0.8558 (m-80) cc_final: 0.8351 (m-80) REVERT: D 376 PHE cc_start: 0.8705 (p90) cc_final: 0.7780 (p90) REVERT: D 383 PHE cc_start: 0.9364 (m-80) cc_final: 0.8725 (m-80) REVERT: D 424 ILE cc_start: 0.8918 (tp) cc_final: 0.8333 (tp) REVERT: F 535 MET cc_start: 0.7872 (mpp) cc_final: 0.7595 (mpp) REVERT: F 539 VAL cc_start: 0.9573 (t) cc_final: 0.9280 (p) REVERT: F 574 LYS cc_start: 0.9427 (mttt) cc_final: 0.9097 (ptmm) REVERT: F 590 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8412 (mp10) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1105 time to fit residues: 42.1292 Evaluate side-chains 190 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 10.0000 chunk 134 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 4 optimal weight: 40.0000 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN D 114 GLN D 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049699 restraints weight = 92906.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051199 restraints weight = 53903.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.052288 restraints weight = 36252.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.053046 restraints weight = 26763.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053619 restraints weight = 21147.496| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15965 Z= 0.228 Angle : 0.778 10.732 21901 Z= 0.373 Chirality : 0.047 0.532 2771 Planarity : 0.004 0.065 2623 Dihedral : 8.385 62.719 4042 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: -0.20 (0.20), residues: 1620 helix: 0.76 (0.26), residues: 397 sheet: 0.22 (0.23), residues: 464 loop : -0.78 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 327 TYR 0.029 0.002 TYR A 217 PHE 0.021 0.002 PHE C 382 TRP 0.016 0.002 TRP E 631 HIS 0.007 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00489 (15832) covalent geometry : angle 0.72693 (21535) SS BOND : bond 0.00420 ( 33) SS BOND : angle 1.38805 ( 66) hydrogen bonds : bond 0.04773 ( 565) hydrogen bonds : angle 5.86409 ( 1569) link_ALPHA1-3 : bond 0.01190 ( 3) link_ALPHA1-3 : angle 2.62628 ( 9) link_ALPHA1-6 : bond 0.00885 ( 3) link_ALPHA1-6 : angle 1.78041 ( 9) link_BETA1-4 : bond 0.00420 ( 39) link_BETA1-4 : angle 2.05696 ( 117) link_NAG-ASN : bond 0.00574 ( 55) link_NAG-ASN : angle 2.64758 ( 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 247 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.449 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 98 ASN cc_start: 0.9326 (t0) cc_final: 0.8848 (t0) REVERT: A 136 ASN cc_start: 0.8922 (m-40) cc_final: 0.8590 (p0) REVERT: A 217 TYR cc_start: 0.7784 (m-80) cc_final: 0.7471 (m-80) REVERT: A 271 ILE cc_start: 0.8702 (mt) cc_final: 0.8467 (tp) REVERT: A 345 VAL cc_start: 0.9641 (t) cc_final: 0.9270 (p) REVERT: A 427 TRP cc_start: 0.8786 (m100) cc_final: 0.8548 (m100) REVERT: A 484 TYR cc_start: 0.9428 (p90) cc_final: 0.9041 (p90) REVERT: A 492 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8214 (mm-30) REVERT: B 584 GLU cc_start: 0.8506 (pp20) cc_final: 0.7730 (pp20) REVERT: B 585 HIS cc_start: 0.8544 (m90) cc_final: 0.8045 (m-70) REVERT: B 588 ARG cc_start: 0.9427 (ttp80) cc_final: 0.8815 (ttm-80) REVERT: B 589 ASP cc_start: 0.9271 (m-30) cc_final: 0.9069 (m-30) REVERT: B 591 GLN cc_start: 0.9466 (tt0) cc_final: 0.9046 (tm-30) REVERT: B 603 ILE cc_start: 0.8255 (pt) cc_final: 0.7784 (pt) REVERT: B 634 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8635 (tp30) REVERT: B 647 GLU cc_start: 0.8323 (pp20) cc_final: 0.8115 (pp20) REVERT: B 651 ASN cc_start: 0.8904 (t0) cc_final: 0.8538 (t0) REVERT: B 654 GLU cc_start: 0.8874 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 39 TYR cc_start: 0.8077 (m-80) cc_final: 0.7471 (m-10) REVERT: C 40 TYR cc_start: 0.9239 (t80) cc_final: 0.8590 (t80) REVERT: C 116 LEU cc_start: 0.9573 (tp) cc_final: 0.9145 (tp) REVERT: C 191 TYR cc_start: 0.8501 (m-80) cc_final: 0.7867 (m-80) REVERT: C 217 TYR cc_start: 0.7282 (m-10) cc_final: 0.6906 (m-80) REVERT: C 319 TYR cc_start: 0.9089 (p90) cc_final: 0.8330 (p90) REVERT: C 434 MET cc_start: 0.8767 (tpp) cc_final: 0.8417 (tpp) REVERT: C 477 ASP cc_start: 0.9525 (m-30) cc_final: 0.9178 (p0) REVERT: E 536 THR cc_start: 0.9197 (p) cc_final: 0.8866 (t) REVERT: E 537 LEU cc_start: 0.9069 (mt) cc_final: 0.8867 (mt) REVERT: E 571 TRP cc_start: 0.8680 (m100) cc_final: 0.8321 (m100) REVERT: E 575 GLN cc_start: 0.9325 (tt0) cc_final: 0.8706 (tp40) REVERT: E 584 GLU cc_start: 0.9303 (tt0) cc_final: 0.9027 (tm-30) REVERT: E 589 ASP cc_start: 0.9342 (m-30) cc_final: 0.9030 (p0) REVERT: E 595 ILE cc_start: 0.9663 (tt) cc_final: 0.9448 (tp) REVERT: E 603 ILE cc_start: 0.9161 (mt) cc_final: 0.8856 (mt) REVERT: E 607 ASN cc_start: 0.8845 (m-40) cc_final: 0.8591 (m-40) REVERT: E 632 ASP cc_start: 0.9242 (t0) cc_final: 0.8833 (p0) REVERT: E 654 GLU cc_start: 0.9288 (tp30) cc_final: 0.8803 (tp30) REVERT: E 655 LYS cc_start: 0.9310 (tptp) cc_final: 0.9082 (tppt) REVERT: D 121 LYS cc_start: 0.9278 (pptt) cc_final: 0.9053 (ptmm) REVERT: D 210 PHE cc_start: 0.8578 (m-80) cc_final: 0.8335 (m-80) REVERT: D 376 PHE cc_start: 0.8705 (p90) cc_final: 0.7731 (p90) REVERT: D 383 PHE cc_start: 0.9253 (m-80) cc_final: 0.8692 (m-80) REVERT: D 424 ILE cc_start: 0.8953 (tp) cc_final: 0.7658 (tp) REVERT: F 535 MET cc_start: 0.8104 (mpp) cc_final: 0.7624 (mpp) REVERT: F 539 VAL cc_start: 0.9495 (t) cc_final: 0.9195 (p) REVERT: F 574 LYS cc_start: 0.9314 (mttt) cc_final: 0.8901 (ptmm) REVERT: F 589 ASP cc_start: 0.9086 (m-30) cc_final: 0.8840 (m-30) REVERT: F 601 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8740 (tppt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1093 time to fit residues: 40.6771 Evaluate side-chains 190 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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: 7.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 650 GLN E 653 GLN D 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050690 restraints weight = 91962.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052208 restraints weight = 53319.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053324 restraints weight = 36013.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054129 restraints weight = 26514.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054700 restraints weight = 20825.723| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15965 Z= 0.154 Angle : 0.698 10.544 21901 Z= 0.334 Chirality : 0.047 0.754 2771 Planarity : 0.004 0.063 2623 Dihedral : 7.816 59.716 4042 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.07 % Allowed : 1.49 % Favored : 98.45 % 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: -0.15 (0.20), residues: 1620 helix: 1.00 (0.26), residues: 399 sheet: 0.24 (0.24), residues: 460 loop : -0.87 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 327 TYR 0.021 0.002 TYR A 217 PHE 0.016 0.002 PHE A 383 TRP 0.019 0.002 TRP C 112 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00334 (15832) covalent geometry : angle 0.64511 (21535) SS BOND : bond 0.00314 ( 33) SS BOND : angle 1.18531 ( 66) hydrogen bonds : bond 0.04375 ( 565) hydrogen bonds : angle 5.58514 ( 1569) link_ALPHA1-3 : bond 0.01079 ( 3) link_ALPHA1-3 : angle 2.43510 ( 9) link_ALPHA1-6 : bond 0.00866 ( 3) link_ALPHA1-6 : angle 1.81118 ( 9) link_BETA1-4 : bond 0.00388 ( 39) link_BETA1-4 : angle 1.87939 ( 117) link_NAG-ASN : bond 0.00374 ( 55) link_NAG-ASN : angle 2.59280 ( 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 245 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9334 (mm) cc_final: 0.9127 (mm) REVERT: A 98 ASN cc_start: 0.9364 (t0) cc_final: 0.8901 (t0) REVERT: A 109 ILE cc_start: 0.9723 (mt) cc_final: 0.9234 (mt) REVERT: A 136 ASN cc_start: 0.8914 (m-40) cc_final: 0.8553 (p0) REVERT: A 217 TYR cc_start: 0.7591 (m-80) cc_final: 0.7196 (m-80) REVERT: A 244 THR cc_start: 0.8994 (m) cc_final: 0.8597 (t) REVERT: A 427 TRP cc_start: 0.8896 (m100) cc_final: 0.8577 (m100) REVERT: A 492 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8309 (mm-30) REVERT: B 543 ASN cc_start: 0.9440 (m-40) cc_final: 0.8236 (t0) REVERT: B 584 GLU cc_start: 0.8649 (pp20) cc_final: 0.7958 (pp20) REVERT: B 585 HIS cc_start: 0.8557 (m90) cc_final: 0.8031 (m-70) REVERT: B 588 ARG cc_start: 0.9407 (ttp80) cc_final: 0.8812 (ttm-80) REVERT: B 591 GLN cc_start: 0.9505 (tt0) cc_final: 0.9051 (tm-30) REVERT: B 603 ILE cc_start: 0.8199 (pt) cc_final: 0.7791 (pt) REVERT: B 622 ILE cc_start: 0.9453 (mp) cc_final: 0.9248 (mp) REVERT: B 629 LEU cc_start: 0.9185 (pp) cc_final: 0.8675 (tp) REVERT: B 634 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8603 (tp30) REVERT: B 651 ASN cc_start: 0.8904 (t0) cc_final: 0.8524 (t0) REVERT: B 654 GLU cc_start: 0.8933 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 39 TYR cc_start: 0.8026 (m-80) cc_final: 0.7451 (m-10) REVERT: C 40 TYR cc_start: 0.9240 (t80) cc_final: 0.8777 (t80) REVERT: C 116 LEU cc_start: 0.9584 (tp) cc_final: 0.9130 (tp) REVERT: C 191 TYR cc_start: 0.8466 (m-80) cc_final: 0.7755 (m-80) REVERT: C 319 TYR cc_start: 0.9118 (p90) cc_final: 0.8369 (p90) REVERT: C 434 MET cc_start: 0.8706 (tpp) cc_final: 0.8473 (tpp) REVERT: C 477 ASP cc_start: 0.9539 (m-30) cc_final: 0.9170 (p0) REVERT: E 536 THR cc_start: 0.9149 (p) cc_final: 0.8939 (t) REVERT: E 571 TRP cc_start: 0.8800 (m100) cc_final: 0.8305 (m100) REVERT: E 575 GLN cc_start: 0.9323 (tt0) cc_final: 0.8717 (tp40) REVERT: E 584 GLU cc_start: 0.9318 (tt0) cc_final: 0.9028 (tm-30) REVERT: E 589 ASP cc_start: 0.9323 (m-30) cc_final: 0.9001 (p0) REVERT: E 603 ILE cc_start: 0.9175 (mt) cc_final: 0.8801 (mt) REVERT: E 632 ASP cc_start: 0.9105 (t0) cc_final: 0.8715 (p0) REVERT: E 654 GLU cc_start: 0.9279 (tp30) cc_final: 0.8780 (tp30) REVERT: D 376 PHE cc_start: 0.8698 (p90) cc_final: 0.7864 (p90) REVERT: D 383 PHE cc_start: 0.9197 (m-80) cc_final: 0.8687 (m-80) REVERT: D 424 ILE cc_start: 0.8923 (tp) cc_final: 0.7777 (tp) REVERT: F 535 MET cc_start: 0.8194 (mpp) cc_final: 0.7685 (mpp) REVERT: F 539 VAL cc_start: 0.9465 (t) cc_final: 0.9154 (p) REVERT: F 574 LYS cc_start: 0.9293 (mttt) cc_final: 0.8837 (ptmm) REVERT: F 589 ASP cc_start: 0.9098 (m-30) cc_final: 0.8833 (m-30) REVERT: F 601 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8718 (tppt) REVERT: F 633 LYS cc_start: 0.9321 (mmmm) cc_final: 0.9109 (mmmm) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.1099 time to fit residues: 40.8794 Evaluate side-chains 194 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 50.0000 chunk 137 optimal weight: 0.0070 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 21 optimal weight: 0.0050 chunk 23 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050850 restraints weight = 91633.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052358 restraints weight = 53902.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.053429 restraints weight = 36530.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054230 restraints weight = 27238.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054778 restraints weight = 21549.670| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15965 Z= 0.137 Angle : 0.679 10.796 21901 Z= 0.325 Chirality : 0.046 0.614 2771 Planarity : 0.004 0.059 2623 Dihedral : 7.445 57.950 4042 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 0.98 (0.27), residues: 397 sheet: 0.19 (0.23), residues: 466 loop : -0.80 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 327 TYR 0.018 0.002 TYR A 217 PHE 0.016 0.002 PHE A 383 TRP 0.021 0.002 TRP C 69 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00299 (15832) covalent geometry : angle 0.63096 (21535) SS BOND : bond 0.00328 ( 33) SS BOND : angle 0.93932 ( 66) hydrogen bonds : bond 0.04100 ( 565) hydrogen bonds : angle 5.42226 ( 1569) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 2.24015 ( 9) link_ALPHA1-6 : bond 0.00943 ( 3) link_ALPHA1-6 : angle 1.89161 ( 9) link_BETA1-4 : bond 0.00416 ( 39) link_BETA1-4 : angle 1.82449 ( 117) link_NAG-ASN : bond 0.00355 ( 55) link_NAG-ASN : angle 2.46789 ( 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 246 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.523 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 53 PHE cc_start: 0.8466 (m-80) cc_final: 0.7846 (m-80) REVERT: A 136 ASN cc_start: 0.8895 (m-40) cc_final: 0.8540 (p0) REVERT: A 217 TYR cc_start: 0.7480 (m-80) cc_final: 0.7228 (m-80) REVERT: A 244 THR cc_start: 0.9018 (m) cc_final: 0.8576 (t) REVERT: A 427 TRP cc_start: 0.8903 (m100) cc_final: 0.8575 (m100) REVERT: A 477 ASP cc_start: 0.9212 (m-30) cc_final: 0.8931 (m-30) REVERT: A 492 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 543 ASN cc_start: 0.9326 (m-40) cc_final: 0.8251 (t0) REVERT: B 584 GLU cc_start: 0.8640 (pp20) cc_final: 0.7892 (pp20) REVERT: B 585 HIS cc_start: 0.8494 (m90) cc_final: 0.7875 (m-70) REVERT: B 588 ARG cc_start: 0.9374 (ttp80) cc_final: 0.8780 (ttm-80) REVERT: B 591 GLN cc_start: 0.9501 (tt0) cc_final: 0.9032 (tm-30) REVERT: B 595 ILE cc_start: 0.9601 (pt) cc_final: 0.9364 (pt) REVERT: B 603 ILE cc_start: 0.8151 (pt) cc_final: 0.7780 (pt) REVERT: B 622 ILE cc_start: 0.9503 (mp) cc_final: 0.9113 (mp) REVERT: B 634 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8603 (tp30) REVERT: B 647 GLU cc_start: 0.8170 (pp20) cc_final: 0.7938 (pp20) REVERT: B 654 GLU cc_start: 0.8963 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 39 TYR cc_start: 0.8027 (m-80) cc_final: 0.7436 (m-10) REVERT: C 40 TYR cc_start: 0.9178 (t80) cc_final: 0.8469 (t80) REVERT: C 116 LEU cc_start: 0.9599 (tp) cc_final: 0.9090 (tp) REVERT: C 191 TYR cc_start: 0.8453 (m-80) cc_final: 0.7715 (m-80) REVERT: C 319 TYR cc_start: 0.9090 (p90) cc_final: 0.8327 (p90) REVERT: C 434 MET cc_start: 0.8692 (tpp) cc_final: 0.8449 (tpp) REVERT: C 477 ASP cc_start: 0.9540 (m-30) cc_final: 0.9165 (p0) REVERT: E 536 THR cc_start: 0.9108 (p) cc_final: 0.8722 (t) REVERT: E 575 GLN cc_start: 0.9295 (tt0) cc_final: 0.8724 (tp40) REVERT: E 584 GLU cc_start: 0.9390 (tt0) cc_final: 0.8997 (tm-30) REVERT: E 603 ILE cc_start: 0.9101 (mt) cc_final: 0.8735 (mt) REVERT: E 632 ASP cc_start: 0.9145 (t0) cc_final: 0.8704 (p0) REVERT: E 648 GLU cc_start: 0.9529 (pm20) cc_final: 0.8713 (pm20) REVERT: E 653 GLN cc_start: 0.9571 (tt0) cc_final: 0.9316 (tt0) REVERT: E 654 GLU cc_start: 0.9242 (tp30) cc_final: 0.8766 (tp30) REVERT: D 376 PHE cc_start: 0.8712 (p90) cc_final: 0.7937 (p90) REVERT: D 383 PHE cc_start: 0.9163 (m-80) cc_final: 0.8659 (m-80) REVERT: D 424 ILE cc_start: 0.8945 (tp) cc_final: 0.7683 (tp) REVERT: F 535 MET cc_start: 0.8222 (mpp) cc_final: 0.7687 (mpp) REVERT: F 539 VAL cc_start: 0.9471 (t) cc_final: 0.9260 (t) REVERT: F 589 ASP cc_start: 0.9078 (m-30) cc_final: 0.8786 (m-30) REVERT: F 601 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8695 (tppt) REVERT: F 617 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8071 (mtp85) REVERT: F 633 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9084 (mmmm) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1160 time to fit residues: 43.2479 Evaluate side-chains 194 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 4.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 0.0370 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 HIS E 607 ASN E 625 ASN D 114 GLN D 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.048026 restraints weight = 95807.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.049441 restraints weight = 56956.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.050439 restraints weight = 38934.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051168 restraints weight = 29267.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051696 restraints weight = 23436.875| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15965 Z= 0.303 Angle : 0.891 12.104 21901 Z= 0.427 Chirality : 0.051 0.725 2771 Planarity : 0.005 0.058 2623 Dihedral : 8.179 59.362 4042 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.77 (0.20), residues: 1620 helix: 0.28 (0.25), residues: 392 sheet: -0.10 (0.23), residues: 477 loop : -1.17 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 166 TYR 0.047 0.003 TYR C 217 PHE 0.034 0.003 PHE B 522 TRP 0.018 0.003 TRP C 479 HIS 0.006 0.002 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00651 (15832) covalent geometry : angle 0.83983 (21535) SS BOND : bond 0.00481 ( 33) SS BOND : angle 1.40555 ( 66) hydrogen bonds : bond 0.04819 ( 565) hydrogen bonds : angle 5.98020 ( 1569) link_ALPHA1-3 : bond 0.00860 ( 3) link_ALPHA1-3 : angle 2.83660 ( 9) link_ALPHA1-6 : bond 0.00861 ( 3) link_ALPHA1-6 : angle 2.00075 ( 9) link_BETA1-4 : bond 0.00508 ( 39) link_BETA1-4 : angle 2.12920 ( 117) link_NAG-ASN : bond 0.00597 ( 55) link_NAG-ASN : angle 2.94102 ( 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 215 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.639 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 53 PHE cc_start: 0.8710 (m-80) cc_final: 0.8205 (m-80) REVERT: A 136 ASN cc_start: 0.9032 (m-40) cc_final: 0.8674 (p0) REVERT: A 217 TYR cc_start: 0.7654 (m-80) cc_final: 0.7329 (m-80) REVERT: A 475 MET cc_start: 0.9283 (mmp) cc_final: 0.8992 (mmp) REVERT: A 477 ASP cc_start: 0.9144 (m-30) cc_final: 0.8846 (m-30) REVERT: A 484 TYR cc_start: 0.9311 (p90) cc_final: 0.9103 (p90) REVERT: A 492 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 543 ASN cc_start: 0.9497 (m-40) cc_final: 0.9059 (m-40) REVERT: B 585 HIS cc_start: 0.8563 (m90) cc_final: 0.8071 (m90) REVERT: B 586 TYR cc_start: 0.9086 (t80) cc_final: 0.8644 (t80) REVERT: B 588 ARG cc_start: 0.9431 (ttp80) cc_final: 0.8760 (ttm-80) REVERT: B 591 GLN cc_start: 0.9500 (tt0) cc_final: 0.9008 (tm-30) REVERT: B 622 ILE cc_start: 0.9586 (mp) cc_final: 0.9283 (mp) REVERT: B 634 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8582 (tp30) REVERT: B 647 GLU cc_start: 0.8477 (pp20) cc_final: 0.8197 (pp20) REVERT: B 654 GLU cc_start: 0.8842 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 39 TYR cc_start: 0.8201 (m-80) cc_final: 0.7361 (m-10) REVERT: C 116 LEU cc_start: 0.9589 (tp) cc_final: 0.9108 (tp) REVERT: C 191 TYR cc_start: 0.8600 (m-80) cc_final: 0.8018 (m-80) REVERT: C 252 LYS cc_start: 0.9216 (mttt) cc_final: 0.8992 (mttt) REVERT: C 319 TYR cc_start: 0.9137 (p90) cc_final: 0.8414 (p90) REVERT: C 434 MET cc_start: 0.8900 (tpp) cc_final: 0.8599 (tpp) REVERT: C 475 MET cc_start: 0.8728 (mmm) cc_final: 0.8205 (mmt) REVERT: C 477 ASP cc_start: 0.9508 (m-30) cc_final: 0.9237 (p0) REVERT: E 571 TRP cc_start: 0.8617 (m100) cc_final: 0.8346 (m100) REVERT: E 575 GLN cc_start: 0.9326 (tt0) cc_final: 0.8720 (tp40) REVERT: E 584 GLU cc_start: 0.9315 (tt0) cc_final: 0.9055 (tm-30) REVERT: E 603 ILE cc_start: 0.9195 (mt) cc_final: 0.8828 (mt) REVERT: E 632 ASP cc_start: 0.9261 (t0) cc_final: 0.8867 (p0) REVERT: E 653 GLN cc_start: 0.9535 (tt0) cc_final: 0.8852 (pt0) REVERT: E 655 LYS cc_start: 0.9535 (tptp) cc_final: 0.8858 (tppt) REVERT: E 658 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8953 (tm-30) REVERT: D 251 ILE cc_start: 0.9317 (tp) cc_final: 0.9050 (tp) REVERT: D 376 PHE cc_start: 0.8812 (p90) cc_final: 0.7825 (p90) REVERT: D 383 PHE cc_start: 0.9239 (m-80) cc_final: 0.8728 (m-80) REVERT: D 424 ILE cc_start: 0.8916 (tp) cc_final: 0.7798 (tp) REVERT: F 535 MET cc_start: 0.8266 (mpp) cc_final: 0.7579 (mpp) REVERT: F 539 VAL cc_start: 0.9535 (t) cc_final: 0.9321 (t) REVERT: F 589 ASP cc_start: 0.9097 (m-30) cc_final: 0.8863 (m-30) REVERT: F 601 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8671 (tppt) REVERT: F 648 GLU cc_start: 0.9251 (pp20) cc_final: 0.9039 (pp20) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1167 time to fit residues: 37.7594 Evaluate side-chains 169 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 6.9990 chunk 174 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.049098 restraints weight = 94649.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050536 restraints weight = 56225.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051557 restraints weight = 38358.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.052239 restraints weight = 28725.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052796 restraints weight = 23336.127| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15965 Z= 0.217 Angle : 0.762 11.388 21901 Z= 0.367 Chirality : 0.048 0.686 2771 Planarity : 0.004 0.057 2623 Dihedral : 7.933 58.848 4042 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -0.78 (0.20), residues: 1620 helix: 0.40 (0.26), residues: 387 sheet: -0.23 (0.23), residues: 484 loop : -1.14 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 617 TYR 0.041 0.002 TYR D 217 PHE 0.019 0.002 PHE B 522 TRP 0.031 0.002 TRP E 628 HIS 0.012 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00470 (15832) covalent geometry : angle 0.71580 (21535) SS BOND : bond 0.00433 ( 33) SS BOND : angle 1.12403 ( 66) hydrogen bonds : bond 0.04444 ( 565) hydrogen bonds : angle 5.75137 ( 1569) link_ALPHA1-3 : bond 0.00749 ( 3) link_ALPHA1-3 : angle 2.31744 ( 9) link_ALPHA1-6 : bond 0.00960 ( 3) link_ALPHA1-6 : angle 2.06236 ( 9) link_BETA1-4 : bond 0.00419 ( 39) link_BETA1-4 : angle 1.90295 ( 117) link_NAG-ASN : bond 0.00430 ( 55) link_NAG-ASN : angle 2.58202 ( 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 221 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8763 (m-80) cc_final: 0.8273 (m-80) REVERT: A 136 ASN cc_start: 0.9020 (m-40) cc_final: 0.8694 (p0) REVERT: A 161 MET cc_start: 0.8745 (tpt) cc_final: 0.8479 (tpp) REVERT: A 217 TYR cc_start: 0.7577 (m-80) cc_final: 0.7122 (m-80) REVERT: A 477 ASP cc_start: 0.9187 (m-30) cc_final: 0.8882 (m-30) REVERT: A 492 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 543 ASN cc_start: 0.9492 (m-40) cc_final: 0.9207 (m-40) REVERT: B 584 GLU cc_start: 0.8644 (pp20) cc_final: 0.7891 (pp20) REVERT: B 585 HIS cc_start: 0.8512 (m90) cc_final: 0.7927 (m-70) REVERT: B 586 TYR cc_start: 0.9020 (t80) cc_final: 0.8538 (t80) REVERT: B 588 ARG cc_start: 0.9427 (ttp80) cc_final: 0.8747 (ttm-80) REVERT: B 591 GLN cc_start: 0.9514 (tt0) cc_final: 0.9011 (tm-30) REVERT: B 634 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8499 (tp30) REVERT: B 654 GLU cc_start: 0.8854 (mt-10) cc_final: 0.7723 (mt-10) REVERT: C 39 TYR cc_start: 0.8135 (m-80) cc_final: 0.7303 (m-10) REVERT: C 40 TYR cc_start: 0.8881 (t80) cc_final: 0.8665 (t80) REVERT: C 45 TRP cc_start: 0.8298 (p90) cc_final: 0.7951 (p90) REVERT: C 116 LEU cc_start: 0.9598 (tp) cc_final: 0.9055 (tp) REVERT: C 191 TYR cc_start: 0.8556 (m-80) cc_final: 0.7852 (m-80) REVERT: C 252 LYS cc_start: 0.9166 (mttt) cc_final: 0.8960 (mttt) REVERT: C 319 TYR cc_start: 0.9117 (p90) cc_final: 0.8374 (p90) REVERT: C 434 MET cc_start: 0.8798 (tpp) cc_final: 0.8494 (tpp) REVERT: C 475 MET cc_start: 0.8630 (mmm) cc_final: 0.8110 (mmt) REVERT: C 477 ASP cc_start: 0.9469 (m-30) cc_final: 0.9236 (p0) REVERT: E 536 THR cc_start: 0.9268 (p) cc_final: 0.8793 (t) REVERT: E 539 VAL cc_start: 0.8829 (t) cc_final: 0.8488 (t) REVERT: E 575 GLN cc_start: 0.9293 (tt0) cc_final: 0.8694 (tp40) REVERT: E 584 GLU cc_start: 0.9335 (tt0) cc_final: 0.8873 (tm-30) REVERT: E 603 ILE cc_start: 0.9127 (mt) cc_final: 0.8803 (mt) REVERT: E 632 ASP cc_start: 0.9222 (t0) cc_final: 0.8861 (p0) REVERT: E 653 GLN cc_start: 0.9489 (tt0) cc_final: 0.8794 (pt0) REVERT: E 654 GLU cc_start: 0.9242 (tp30) cc_final: 0.8957 (tp30) REVERT: E 655 LYS cc_start: 0.9568 (tptp) cc_final: 0.8994 (tppt) REVERT: E 658 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8967 (tm-30) REVERT: D 376 PHE cc_start: 0.8767 (p90) cc_final: 0.7956 (p90) REVERT: D 383 PHE cc_start: 0.9079 (m-80) cc_final: 0.8615 (m-80) REVERT: D 424 ILE cc_start: 0.8934 (tp) cc_final: 0.7877 (tp) REVERT: F 535 MET cc_start: 0.8329 (mpp) cc_final: 0.7638 (mpp) REVERT: F 539 VAL cc_start: 0.9491 (t) cc_final: 0.9143 (p) REVERT: F 589 ASP cc_start: 0.9137 (m-30) cc_final: 0.8906 (m-30) REVERT: F 601 LYS cc_start: 0.9137 (mtpt) cc_final: 0.8711 (tppt) REVERT: F 633 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9127 (mmmm) REVERT: F 648 GLU cc_start: 0.9252 (pp20) cc_final: 0.9028 (pp20) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1094 time to fit residues: 36.7876 Evaluate side-chains 172 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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: 8.9990 chunk 2 optimal weight: 30.0000 chunk 82 optimal weight: 0.0980 chunk 154 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 363 GLN ** 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 585 HIS E 607 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 = 0.3180 r_free = 0.3180 target = 0.060539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051060 restraints weight = 92350.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052570 restraints weight = 54438.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053640 restraints weight = 36956.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054434 restraints weight = 27494.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054955 restraints weight = 21749.347| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15965 Z= 0.125 Angle : 0.705 11.527 21901 Z= 0.333 Chirality : 0.047 0.636 2771 Planarity : 0.004 0.055 2623 Dihedral : 7.369 57.641 4042 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.48 (0.21), residues: 1620 helix: 0.68 (0.26), residues: 391 sheet: -0.08 (0.23), residues: 498 loop : -0.96 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 327 TYR 0.030 0.002 TYR C 217 PHE 0.014 0.001 PHE A 383 TRP 0.022 0.002 TRP C 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00270 (15832) covalent geometry : angle 0.65676 (21535) SS BOND : bond 0.00269 ( 33) SS BOND : angle 0.94267 ( 66) hydrogen bonds : bond 0.04014 ( 565) hydrogen bonds : angle 5.40861 ( 1569) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 1.85866 ( 9) link_ALPHA1-6 : bond 0.01082 ( 3) link_ALPHA1-6 : angle 2.05307 ( 9) link_BETA1-4 : bond 0.00449 ( 39) link_BETA1-4 : angle 1.75688 ( 117) link_NAG-ASN : bond 0.00373 ( 55) link_NAG-ASN : angle 2.60028 ( 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 244 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.440 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 53 PHE cc_start: 0.8642 (m-80) cc_final: 0.8306 (m-80) REVERT: A 136 ASN cc_start: 0.9019 (m-40) cc_final: 0.8678 (p0) REVERT: A 217 TYR cc_start: 0.7301 (m-80) cc_final: 0.6968 (m-80) REVERT: A 244 THR cc_start: 0.8923 (m) cc_final: 0.8570 (t) REVERT: A 477 ASP cc_start: 0.9193 (m-30) cc_final: 0.8912 (m-30) REVERT: A 492 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 543 ASN cc_start: 0.9443 (m-40) cc_final: 0.8594 (t0) REVERT: B 584 GLU cc_start: 0.8535 (pp20) cc_final: 0.7729 (pp20) REVERT: B 585 HIS cc_start: 0.8544 (m90) cc_final: 0.7899 (m-70) REVERT: B 586 TYR cc_start: 0.8887 (t80) cc_final: 0.8442 (t80) REVERT: B 588 ARG cc_start: 0.9386 (ttp80) cc_final: 0.8681 (ttm-80) REVERT: B 591 GLN cc_start: 0.9508 (tt0) cc_final: 0.9010 (tm-30) REVERT: B 634 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8428 (tp30) REVERT: B 648 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8793 (tm-30) REVERT: B 654 GLU cc_start: 0.8959 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 39 TYR cc_start: 0.7975 (m-80) cc_final: 0.7162 (m-10) REVERT: C 45 TRP cc_start: 0.8156 (p90) cc_final: 0.7879 (p90) REVERT: C 106 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9025 (mp0) REVERT: C 116 LEU cc_start: 0.9579 (tp) cc_final: 0.9224 (tp) REVERT: C 191 TYR cc_start: 0.8444 (m-80) cc_final: 0.7702 (m-80) REVERT: C 319 TYR cc_start: 0.9191 (p90) cc_final: 0.8462 (p90) REVERT: C 434 MET cc_start: 0.8703 (tpp) cc_final: 0.7881 (tpp) REVERT: C 475 MET cc_start: 0.8553 (mmm) cc_final: 0.8123 (mmt) REVERT: C 477 ASP cc_start: 0.9497 (m-30) cc_final: 0.9192 (p0) REVERT: E 536 THR cc_start: 0.9222 (p) cc_final: 0.8795 (t) REVERT: E 538 THR cc_start: 0.8306 (p) cc_final: 0.7837 (p) REVERT: E 542 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7266 (ptm160) REVERT: E 584 GLU cc_start: 0.9307 (tt0) cc_final: 0.9056 (tm-30) REVERT: E 632 ASP cc_start: 0.9172 (t0) cc_final: 0.8795 (p0) REVERT: E 653 GLN cc_start: 0.9504 (tt0) cc_final: 0.8763 (pt0) REVERT: E 654 GLU cc_start: 0.9253 (tp30) cc_final: 0.8861 (tp30) REVERT: E 655 LYS cc_start: 0.9538 (tptp) cc_final: 0.9312 (tppt) REVERT: D 42 VAL cc_start: 0.9600 (m) cc_final: 0.9286 (p) REVERT: D 256 SER cc_start: 0.8350 (p) cc_final: 0.7588 (t) REVERT: D 376 PHE cc_start: 0.8680 (p90) cc_final: 0.7896 (p90) REVERT: D 383 PHE cc_start: 0.9013 (m-80) cc_final: 0.8524 (m-80) REVERT: D 424 ILE cc_start: 0.8900 (tp) cc_final: 0.7915 (tp) REVERT: F 535 MET cc_start: 0.8265 (mpp) cc_final: 0.7631 (mpp) REVERT: F 539 VAL cc_start: 0.9417 (t) cc_final: 0.9212 (t) REVERT: F 589 ASP cc_start: 0.9089 (m-30) cc_final: 0.8861 (m-30) REVERT: F 593 LEU cc_start: 0.9679 (mm) cc_final: 0.9166 (tp) REVERT: F 601 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8571 (tppt) REVERT: F 633 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9095 (mmmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1081 time to fit residues: 40.0544 Evaluate side-chains 194 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 9.9990 chunk 168 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 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 = 0.3122 r_free = 0.3122 target = 0.058242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.048925 restraints weight = 95483.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050359 restraints weight = 56733.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051362 restraints weight = 38826.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052108 restraints weight = 29146.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.052545 restraints weight = 23297.323| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15965 Z= 0.237 Angle : 0.797 13.760 21901 Z= 0.382 Chirality : 0.048 0.672 2771 Planarity : 0.005 0.058 2623 Dihedral : 7.697 57.964 4042 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -0.74 (0.21), residues: 1620 helix: 0.37 (0.26), residues: 391 sheet: -0.15 (0.23), residues: 490 loop : -1.14 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 617 TYR 0.029 0.002 TYR A 384 PHE 0.026 0.002 PHE B 522 TRP 0.022 0.002 TRP E 628 HIS 0.005 0.001 HIS E 570 Details of bonding type rmsd covalent geometry : bond 0.00515 (15832) covalent geometry : angle 0.74322 (21535) SS BOND : bond 0.00413 ( 33) SS BOND : angle 1.14441 ( 66) hydrogen bonds : bond 0.04495 ( 565) hydrogen bonds : angle 5.75427 ( 1569) link_ALPHA1-3 : bond 0.00757 ( 3) link_ALPHA1-3 : angle 2.35440 ( 9) link_ALPHA1-6 : bond 0.00902 ( 3) link_ALPHA1-6 : angle 2.10876 ( 9) link_BETA1-4 : bond 0.00441 ( 39) link_BETA1-4 : angle 1.96477 ( 117) link_NAG-ASN : bond 0.00534 ( 55) link_NAG-ASN : angle 2.90474 ( 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 220 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.533 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: A 53 PHE cc_start: 0.8731 (m-80) cc_final: 0.8409 (m-80) REVERT: A 136 ASN cc_start: 0.9121 (m-40) cc_final: 0.8369 (t0) REVERT: A 161 MET cc_start: 0.8541 (tpt) cc_final: 0.8315 (tpp) REVERT: A 217 TYR cc_start: 0.7519 (m-80) cc_final: 0.7140 (m-80) REVERT: A 477 ASP cc_start: 0.9164 (m-30) cc_final: 0.8865 (m-30) REVERT: A 484 TYR cc_start: 0.9283 (p90) cc_final: 0.8969 (p90) REVERT: A 492 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 542 ARG cc_start: 0.8937 (ptt90) cc_final: 0.8721 (ttp80) REVERT: B 543 ASN cc_start: 0.9516 (m-40) cc_final: 0.9211 (m-40) REVERT: B 584 GLU cc_start: 0.8685 (pp20) cc_final: 0.7963 (pp20) REVERT: B 585 HIS cc_start: 0.8600 (m90) cc_final: 0.7959 (m-70) REVERT: B 586 TYR cc_start: 0.9031 (t80) cc_final: 0.8620 (t80) REVERT: B 588 ARG cc_start: 0.9450 (ttp80) cc_final: 0.8746 (ttm-80) REVERT: B 591 GLN cc_start: 0.9532 (tt0) cc_final: 0.8984 (tm-30) REVERT: B 634 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8543 (tp30) REVERT: B 654 GLU cc_start: 0.8874 (mt-10) cc_final: 0.7830 (mt-10) REVERT: C 39 TYR cc_start: 0.8132 (m-80) cc_final: 0.7384 (m-10) REVERT: C 40 TYR cc_start: 0.9003 (t80) cc_final: 0.8778 (t80) REVERT: C 104 MET cc_start: 0.8962 (tpp) cc_final: 0.8683 (tpp) REVERT: C 116 LEU cc_start: 0.9597 (tp) cc_final: 0.9058 (tp) REVERT: C 191 TYR cc_start: 0.8551 (m-80) cc_final: 0.7864 (m-80) REVERT: C 319 TYR cc_start: 0.9155 (p90) cc_final: 0.8456 (p90) REVERT: C 434 MET cc_start: 0.8803 (tpp) cc_final: 0.8479 (tpp) REVERT: C 475 MET cc_start: 0.8686 (mmm) cc_final: 0.8159 (mmt) REVERT: C 477 ASP cc_start: 0.9481 (m-30) cc_final: 0.9245 (p0) REVERT: E 536 THR cc_start: 0.9241 (p) cc_final: 0.8874 (t) REVERT: E 575 GLN cc_start: 0.9355 (tt0) cc_final: 0.8830 (tp40) REVERT: E 584 GLU cc_start: 0.9349 (tt0) cc_final: 0.9117 (tm-30) REVERT: E 632 ASP cc_start: 0.9247 (t0) cc_final: 0.8853 (p0) REVERT: E 653 GLN cc_start: 0.9502 (tt0) cc_final: 0.8785 (pt0) REVERT: E 654 GLU cc_start: 0.9323 (tp30) cc_final: 0.9015 (tp30) REVERT: E 655 LYS cc_start: 0.9566 (tptp) cc_final: 0.8976 (tppt) REVERT: E 658 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8958 (tm-30) REVERT: D 97 LYS cc_start: 0.9115 (mppt) cc_final: 0.8865 (mppt) REVERT: D 256 SER cc_start: 0.8549 (p) cc_final: 0.7666 (t) REVERT: D 376 PHE cc_start: 0.8736 (p90) cc_final: 0.7919 (p90) REVERT: D 383 PHE cc_start: 0.9136 (m-80) cc_final: 0.8642 (m-80) REVERT: D 424 ILE cc_start: 0.8875 (tp) cc_final: 0.7862 (tp) REVERT: F 535 MET cc_start: 0.8364 (mpp) cc_final: 0.7854 (mpp) REVERT: F 539 VAL cc_start: 0.9460 (t) cc_final: 0.9179 (p) REVERT: F 589 ASP cc_start: 0.9095 (m-30) cc_final: 0.8879 (m-30) REVERT: F 601 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8692 (tppt) REVERT: F 633 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9117 (mmmm) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1053 time to fit residues: 35.4303 Evaluate side-chains 173 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 chunk 165 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 95 optimal weight: 0.0040 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 300 ASN C 411 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN E 625 ASN D 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050780 restraints weight = 92084.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.052249 restraints weight = 54456.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053305 restraints weight = 37205.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.054018 restraints weight = 27698.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054591 restraints weight = 22434.267| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15965 Z= 0.129 Angle : 0.700 13.027 21901 Z= 0.333 Chirality : 0.047 0.632 2771 Planarity : 0.004 0.055 2623 Dihedral : 7.220 56.687 4042 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.14 % Allowed : 0.20 % 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: -0.55 (0.21), residues: 1620 helix: 0.62 (0.26), residues: 392 sheet: -0.14 (0.23), residues: 504 loop : -1.00 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 273 TYR 0.049 0.002 TYR D 217 PHE 0.019 0.002 PHE A 383 TRP 0.023 0.002 TRP C 69 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00292 (15832) covalent geometry : angle 0.65063 (21535) SS BOND : bond 0.00268 ( 33) SS BOND : angle 0.93027 ( 66) hydrogen bonds : bond 0.04035 ( 565) hydrogen bonds : angle 5.48333 ( 1569) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 1.96559 ( 9) link_ALPHA1-6 : bond 0.00978 ( 3) link_ALPHA1-6 : angle 2.12076 ( 9) link_BETA1-4 : bond 0.00410 ( 39) link_BETA1-4 : angle 1.76212 ( 117) link_NAG-ASN : bond 0.00375 ( 55) link_NAG-ASN : angle 2.61899 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.11 seconds wall clock time: 35 minutes 22.06 seconds (2122.06 seconds total)