Starting phenix.real_space_refine on Wed Mar 4 19:23:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l88_23225/03_2026/7l88_23225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l88_23225/03_2026/7l88_23225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l88_23225/03_2026/7l88_23225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l88_23225/03_2026/7l88_23225.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l88_23225/03_2026/7l88_23225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l88_23225/03_2026/7l88_23225.map" } resolution = 3.6 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= 0.003 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 9734 2.51 5 N 2622 2.21 5 O 3179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 15634 Number of models: 1 Model: "" Number of chains: 43 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" 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: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 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: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" 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: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "L" 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: "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: 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: 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: "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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "D" 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: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 Time building chain proxies: 3.85, per 1000 atoms: 0.25 Number of scatterers: 15634 At special positions: 0 Unit cell: (131.84, 122.57, 145.23, 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 3179 8.00 N 2622 7.00 C 9734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.08 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.06 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 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 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 M 3 " - " MAN M 4 " " BMA X 3 " - " MAN X 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA g 3 " - " MAN g 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 448 " " NAG A 607 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 88 " " NAG C 608 " - " ASN C 137 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 301 " " NAG D 603 " - " ASN D 339 " " NAG D 604 " - " ASN D 448 " " NAG D 605 " - " ASN D 355 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN D 133 " " NAG I 1 " - " ASN D 156 " " NAG J 1 " - " ASN D 197 " " NAG K 1 " - " ASN D 234 " " NAG M 1 " - " ASN D 262 " " NAG N 1 " - " ASN D 276 " " NAG O 1 " - " ASN D 295 " " NAG P 1 " - " ASN D 332 " " NAG Q 1 " - " ASN D 386 " " NAG R 1 " - " ASN D 392 " " NAG S 1 " - " ASN D 88 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 234 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 276 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 88 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 276 " " NAG i 1 " - " ASN C 295 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 386 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 603.1 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3586 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 38 sheets defined 27.1% alpha, 65.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.750A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 115 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.070A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.517A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.509A pdb=" N LYS F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.137A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) 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 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.909A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 597 Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.734A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.089A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.053A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.531A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.080A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 256 through 257 removed outlier: 3.586A pdb=" N SER D 375 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.884A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 393 through 396 removed outlier: 6.441A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 271 through 273 removed outlier: 7.315A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 375 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.884A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.486A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.844A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AB8, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.042A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.706A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.812A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.745A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.706A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.812A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.412A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.731A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AD1, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.608A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.797A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.552A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.609A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.797A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.552A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AE1, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.775A pdb=" N UNK L 11 " --> pdb=" O UNK L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 703 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2602 1.31 - 1.45: 4695 1.45 - 1.59: 8403 1.59 - 1.73: 72 1.73 - 1.87: 130 Bond restraints: 15902 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.390 -0.064 1.10e-02 8.26e+03 3.40e+01 bond pdb=" C GLU E 621 " pdb=" O GLU E 621 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.28e-02 6.10e+03 3.04e+01 bond pdb=" CA ASN E 618 " pdb=" C ASN E 618 " ideal model delta sigma weight residual 1.526 1.453 0.074 1.37e-02 5.33e+03 2.89e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.70e+01 ... (remaining 15897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 20307 3.35 - 6.70: 1254 6.70 - 10.06: 62 10.06 - 13.41: 9 13.41 - 16.76: 1 Bond angle restraints: 21633 Sorted by residual: angle pdb=" N HIS F 585 " pdb=" CA HIS F 585 " pdb=" C HIS F 585 " ideal model delta sigma weight residual 110.35 97.38 12.97 1.38e+00 5.25e-01 8.83e+01 angle pdb=" N SER B 599 " pdb=" CA SER B 599 " pdb=" C SER B 599 " ideal model delta sigma weight residual 112.68 124.03 -11.35 1.33e+00 5.65e-01 7.29e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.55 -7.99 1.02e+00 9.61e-01 6.13e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.02e+00 9.61e-01 6.01e+01 ... (remaining 21628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 10481 21.79 - 43.58: 199 43.58 - 65.37: 51 65.37 - 87.16: 33 87.16 - 108.95: 12 Dihedral angle restraints: 10776 sinusoidal: 5270 harmonic: 5506 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.93 -61.93 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" C ASN E 618 " pdb=" N ASN E 618 " pdb=" CA ASN E 618 " pdb=" CB ASN E 618 " ideal model delta harmonic sigma weight residual -122.60 -104.93 -17.67 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.13 -60.13 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 10773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1964 0.121 - 0.242: 446 0.242 - 0.364: 232 0.364 - 0.485: 117 0.485 - 0.606: 5 Chirality restraints: 2764 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.76e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2761 not shown) Planarity restraints: 2705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 703 " 0.295 2.00e-02 2.50e+03 2.50e-01 7.80e+02 pdb=" C7 NAG B 703 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B 703 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 703 " -0.429 2.00e-02 2.50e+03 pdb=" O7 NAG B 703 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.238 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG A 607 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.305 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " 0.140 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" C7 NAG F 702 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " -0.188 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.112 2.00e-02 2.50e+03 ... (remaining 2702 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 80 2.58 - 3.16: 12863 3.16 - 3.74: 21756 3.74 - 4.32: 33588 4.32 - 4.90: 52100 Nonbonded interactions: 120387 Sorted by model distance: nonbonded pdb=" O ASN D 80 " pdb=" OD1 ASN D 80 " model vdw 2.004 3.040 nonbonded pdb=" O3 NAG C 601 " pdb=" O7 NAG C 601 " model vdw 2.052 3.040 nonbonded pdb=" O4 NAG C 601 " pdb=" O6 NAG C 601 " model vdw 2.166 3.040 nonbonded pdb=" N HIS F 585 " pdb=" O HIS F 585 " model vdw 2.244 2.496 nonbonded pdb=" OD1 ASN A 137 " pdb=" C1 NAG A 606 " model vdw 2.255 3.470 ... (remaining 120382 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 33 through 605) selection = (chain 'C' and resid 33 through 605) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 519 through 702) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } ncs_group { reference = (chain 'H' and resid 10 through 116) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.060 Find NCS groups from input model: 0.500 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 0.132 16027 Z= 1.193 Angle : 1.775 18.582 21975 Z= 1.090 Chirality : 0.149 0.606 2764 Planarity : 0.011 0.250 2650 Dihedral : 11.037 108.954 7091 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.28 % 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: 0.89 (0.20), residues: 1635 helix: 0.12 (0.23), residues: 423 sheet: 0.88 (0.23), residues: 477 loop : 0.92 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 500 TYR 0.044 0.007 TYR A 40 PHE 0.030 0.005 PHE A 383 TRP 0.060 0.009 TRP C 69 HIS 0.010 0.003 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.02194 (15902) covalent geometry : angle 1.72954 (21633) SS BOND : bond 0.01267 ( 33) SS BOND : angle 2.55866 ( 66) hydrogen bonds : bond 0.17249 ( 547) hydrogen bonds : angle 8.01398 ( 1893) link_ALPHA1-3 : bond 0.08561 ( 3) link_ALPHA1-3 : angle 4.32041 ( 9) link_ALPHA1-6 : bond 0.05224 ( 2) link_ALPHA1-6 : angle 2.60905 ( 6) link_BETA1-4 : bond 0.07161 ( 32) link_BETA1-4 : angle 4.84189 ( 96) link_NAG-ASN : bond 0.07515 ( 55) link_NAG-ASN : angle 3.17052 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: D 373 THR cc_start: 0.8943 (t) cc_final: 0.8740 (p) REVERT: F 577 GLN cc_start: 0.8350 (mt0) cc_final: 0.8060 (tt0) REVERT: A 150 MET cc_start: 0.8269 (mmm) cc_final: 0.8040 (mmp) REVERT: A 167 ASP cc_start: 0.8389 (p0) cc_final: 0.8081 (p0) REVERT: A 180 ASP cc_start: 0.7828 (p0) cc_final: 0.7432 (p0) REVERT: A 467 THR cc_start: 0.7868 (m) cc_final: 0.7506 (m) REVERT: B 535 MET cc_start: 0.8243 (mmp) cc_final: 0.7945 (mmp) REVERT: B 622 ILE cc_start: 0.8887 (mt) cc_final: 0.8666 (mt) REVERT: C 161 MET cc_start: 0.8588 (tpt) cc_final: 0.8141 (tpt) REVERT: C 198 THR cc_start: 0.9078 (p) cc_final: 0.8767 (p) REVERT: C 199 SER cc_start: 0.8764 (t) cc_final: 0.8362 (m) REVERT: E 590 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8971 (mm-40) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1421 time to fit residues: 75.8914 Evaluate side-chains 177 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 HIS D 425 ASN F 590 GLN F 607 ASN C 33 ASN C 67 ASN C 195 ASN C 216 HIS C 422 GLN C 425 ASN E 570 HIS E 658 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113006 restraints weight = 25791.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116043 restraints weight = 14187.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118074 restraints weight = 9624.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119393 restraints weight = 7388.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120264 restraints weight = 6164.829| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16027 Z= 0.166 Angle : 0.750 12.692 21975 Z= 0.366 Chirality : 0.047 0.241 2764 Planarity : 0.005 0.082 2650 Dihedral : 8.049 81.745 3926 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 7.30 % Favored : 90.56 % 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: 0.88 (0.20), residues: 1635 helix: 1.44 (0.26), residues: 417 sheet: 0.66 (0.24), residues: 411 loop : 0.21 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 178 TYR 0.021 0.002 TYR A 217 PHE 0.012 0.002 PHE C 53 TRP 0.020 0.001 TRP C 112 HIS 0.005 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00360 (15902) covalent geometry : angle 0.69734 (21633) SS BOND : bond 0.00320 ( 33) SS BOND : angle 1.32946 ( 66) hydrogen bonds : bond 0.06100 ( 547) hydrogen bonds : angle 5.64290 ( 1893) link_ALPHA1-3 : bond 0.01723 ( 3) link_ALPHA1-3 : angle 2.28087 ( 9) link_ALPHA1-6 : bond 0.01070 ( 2) link_ALPHA1-6 : angle 1.97626 ( 6) link_BETA1-4 : bond 0.00434 ( 32) link_BETA1-4 : angle 2.29946 ( 96) link_NAG-ASN : bond 0.00386 ( 55) link_NAG-ASN : angle 2.64972 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.8920 (t) cc_final: 0.8565 (p) REVERT: D 434 MET cc_start: 0.8851 (tmm) cc_final: 0.8354 (ttp) REVERT: F 542 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.8307 (ttp80) REVERT: A 150 MET cc_start: 0.8116 (mmm) cc_final: 0.7638 (mmp) REVERT: A 323 ILE cc_start: 0.7699 (mt) cc_final: 0.6894 (mm) REVERT: B 590 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8325 (mm110) REVERT: C 150 MET cc_start: 0.8594 (mmp) cc_final: 0.7853 (mmp) REVERT: C 161 MET cc_start: 0.8462 (tpt) cc_final: 0.8094 (tpt) REVERT: C 199 SER cc_start: 0.8587 (t) cc_final: 0.8251 (m) REVERT: E 571 TRP cc_start: 0.7382 (m100) cc_final: 0.6943 (m100) REVERT: E 632 ASP cc_start: 0.8979 (t0) cc_final: 0.8725 (t0) outliers start: 32 outliers final: 19 residues processed: 258 average time/residue: 0.1193 time to fit residues: 46.3443 Evaluate side-chains 195 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS C 33 ASN C 195 ASN C 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111249 restraints weight = 26079.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114311 restraints weight = 14333.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116302 restraints weight = 9725.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117623 restraints weight = 7505.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118531 restraints weight = 6280.866| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16027 Z= 0.143 Angle : 0.653 11.468 21975 Z= 0.318 Chirality : 0.044 0.240 2764 Planarity : 0.004 0.047 2650 Dihedral : 7.208 75.499 3926 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 9.37 % Favored : 88.22 % 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: 0.72 (0.20), residues: 1635 helix: 1.61 (0.27), residues: 417 sheet: 0.32 (0.23), residues: 465 loop : 0.04 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 308 TYR 0.020 0.001 TYR B 586 PHE 0.010 0.001 PHE D 53 TRP 0.012 0.001 TRP C 112 HIS 0.007 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00317 (15902) covalent geometry : angle 0.60994 (21633) SS BOND : bond 0.00432 ( 33) SS BOND : angle 1.46937 ( 66) hydrogen bonds : bond 0.05268 ( 547) hydrogen bonds : angle 5.12360 ( 1893) link_ALPHA1-3 : bond 0.01426 ( 3) link_ALPHA1-3 : angle 1.22265 ( 9) link_ALPHA1-6 : bond 0.01165 ( 2) link_ALPHA1-6 : angle 1.72719 ( 6) link_BETA1-4 : bond 0.00556 ( 32) link_BETA1-4 : angle 1.79585 ( 96) link_NAG-ASN : bond 0.00377 ( 55) link_NAG-ASN : angle 2.24289 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: D 373 THR cc_start: 0.9017 (t) cc_final: 0.8759 (p) REVERT: D 434 MET cc_start: 0.8793 (tmm) cc_final: 0.8248 (ttp) REVERT: F 542 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8136 (ttp80) REVERT: A 150 MET cc_start: 0.8159 (mmm) cc_final: 0.7537 (mmt) REVERT: A 323 ILE cc_start: 0.7596 (mt) cc_final: 0.6800 (mm) REVERT: B 535 MET cc_start: 0.7679 (mmp) cc_final: 0.7462 (mmp) REVERT: B 648 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6692 (mt-10) REVERT: C 199 SER cc_start: 0.8379 (t) cc_final: 0.7993 (m) REVERT: E 571 TRP cc_start: 0.7370 (m100) cc_final: 0.7158 (m100) outliers start: 36 outliers final: 21 residues processed: 224 average time/residue: 0.1203 time to fit residues: 41.3031 Evaluate side-chains 186 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain E residue 612 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS C 33 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109962 restraints weight = 26183.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113009 restraints weight = 14587.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115022 restraints weight = 9948.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116295 restraints weight = 7674.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117144 restraints weight = 6449.490| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16027 Z= 0.142 Angle : 0.619 10.610 21975 Z= 0.300 Chirality : 0.044 0.263 2764 Planarity : 0.004 0.039 2650 Dihedral : 6.494 67.766 3926 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.61 % Allowed : 9.24 % Favored : 88.15 % 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: 0.65 (0.20), residues: 1635 helix: 1.63 (0.27), residues: 417 sheet: 0.36 (0.24), residues: 447 loop : -0.10 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 151 TYR 0.015 0.001 TYR B 586 PHE 0.010 0.001 PHE E 522 TRP 0.012 0.001 TRP D 96 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00323 (15902) covalent geometry : angle 0.58277 (21633) SS BOND : bond 0.00366 ( 33) SS BOND : angle 1.13916 ( 66) hydrogen bonds : bond 0.04763 ( 547) hydrogen bonds : angle 4.84449 ( 1893) link_ALPHA1-3 : bond 0.01331 ( 3) link_ALPHA1-3 : angle 1.50098 ( 9) link_ALPHA1-6 : bond 0.01240 ( 2) link_ALPHA1-6 : angle 1.86410 ( 6) link_BETA1-4 : bond 0.00441 ( 32) link_BETA1-4 : angle 1.58489 ( 96) link_NAG-ASN : bond 0.00204 ( 55) link_NAG-ASN : angle 2.08641 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7508 (ttp80) REVERT: D 373 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8764 (p) REVERT: D 434 MET cc_start: 0.8773 (tmm) cc_final: 0.8236 (ttp) REVERT: A 35 TRP cc_start: 0.8852 (m100) cc_final: 0.8505 (m100) REVERT: A 150 MET cc_start: 0.8225 (mmm) cc_final: 0.7591 (mmt) REVERT: A 323 ILE cc_start: 0.7554 (mt) cc_final: 0.6763 (mm) REVERT: C 199 SER cc_start: 0.8223 (t) cc_final: 0.7804 (m) REVERT: E 633 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8390 (mmtm) outliers start: 39 outliers final: 27 residues processed: 208 average time/residue: 0.1101 time to fit residues: 36.0850 Evaluate side-chains 186 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 85 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105833 restraints weight = 26352.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108726 restraints weight = 14779.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110639 restraints weight = 10174.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111870 restraints weight = 7904.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112709 restraints weight = 6672.768| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16027 Z= 0.225 Angle : 0.693 10.577 21975 Z= 0.335 Chirality : 0.046 0.292 2764 Planarity : 0.004 0.043 2650 Dihedral : 6.505 61.214 3926 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.81 % Allowed : 10.44 % Favored : 86.75 % 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: 1635 helix: 1.49 (0.27), residues: 417 sheet: 0.62 (0.25), residues: 381 loop : -0.43 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 151 TYR 0.014 0.002 TYR B 586 PHE 0.016 0.002 PHE E 522 TRP 0.011 0.001 TRP D 96 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00537 (15902) covalent geometry : angle 0.65871 (21633) SS BOND : bond 0.00456 ( 33) SS BOND : angle 1.43859 ( 66) hydrogen bonds : bond 0.05181 ( 547) hydrogen bonds : angle 4.91552 ( 1893) link_ALPHA1-3 : bond 0.01359 ( 3) link_ALPHA1-3 : angle 1.57902 ( 9) link_ALPHA1-6 : bond 0.01201 ( 2) link_ALPHA1-6 : angle 2.01930 ( 6) link_BETA1-4 : bond 0.00467 ( 32) link_BETA1-4 : angle 1.60857 ( 96) link_NAG-ASN : bond 0.00269 ( 55) link_NAG-ASN : angle 2.11188 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.8898 (p) cc_final: 0.8680 (m) REVERT: D 373 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8808 (p) REVERT: D 434 MET cc_start: 0.8783 (tmm) cc_final: 0.8281 (ttp) REVERT: A 150 MET cc_start: 0.8047 (mmm) cc_final: 0.7410 (mmt) REVERT: A 195 ASN cc_start: 0.9108 (p0) cc_final: 0.8743 (p0) REVERT: C 199 SER cc_start: 0.8469 (t) cc_final: 0.7944 (m) REVERT: E 622 ILE cc_start: 0.8958 (mt) cc_final: 0.8705 (mt) REVERT: E 633 LYS cc_start: 0.8703 (mttm) cc_final: 0.8396 (mmtm) outliers start: 42 outliers final: 31 residues processed: 199 average time/residue: 0.1012 time to fit residues: 32.5153 Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 19 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108326 restraints weight = 26005.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111257 restraints weight = 14460.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113218 restraints weight = 9905.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114465 restraints weight = 7650.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115279 restraints weight = 6433.775| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16027 Z= 0.126 Angle : 0.594 9.482 21975 Z= 0.287 Chirality : 0.044 0.272 2764 Planarity : 0.004 0.039 2650 Dihedral : 5.973 58.177 3926 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.34 % Allowed : 11.91 % Favored : 85.74 % 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: 0.46 (0.20), residues: 1635 helix: 1.60 (0.27), residues: 417 sheet: 0.51 (0.25), residues: 387 loop : -0.43 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.024 0.001 TYR A 173 PHE 0.009 0.001 PHE E 522 TRP 0.031 0.001 TRP E 571 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00282 (15902) covalent geometry : angle 0.56075 (21633) SS BOND : bond 0.00462 ( 33) SS BOND : angle 1.14775 ( 66) hydrogen bonds : bond 0.04469 ( 547) hydrogen bonds : angle 4.66107 ( 1893) link_ALPHA1-3 : bond 0.01318 ( 3) link_ALPHA1-3 : angle 1.57632 ( 9) link_ALPHA1-6 : bond 0.01332 ( 2) link_ALPHA1-6 : angle 1.84052 ( 6) link_BETA1-4 : bond 0.00426 ( 32) link_BETA1-4 : angle 1.37857 ( 96) link_NAG-ASN : bond 0.00209 ( 55) link_NAG-ASN : angle 1.97014 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.8896 (p) cc_final: 0.8694 (m) REVERT: D 373 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8737 (p) REVERT: D 434 MET cc_start: 0.8751 (tmm) cc_final: 0.8233 (ttp) REVERT: A 150 MET cc_start: 0.7831 (mmm) cc_final: 0.7180 (mmt) REVERT: A 195 ASN cc_start: 0.9087 (p0) cc_final: 0.8734 (p0) REVERT: A 323 ILE cc_start: 0.7676 (mt) cc_final: 0.6765 (mm) REVERT: C 199 SER cc_start: 0.8110 (t) cc_final: 0.7622 (m) REVERT: E 571 TRP cc_start: 0.6404 (m100) cc_final: 0.5779 (m-10) REVERT: E 633 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8361 (mmtm) outliers start: 35 outliers final: 27 residues processed: 196 average time/residue: 0.1020 time to fit residues: 31.7688 Evaluate side-chains 190 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** 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 = 0.3583 r_free = 0.3583 target = 0.127352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105517 restraints weight = 26592.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108281 restraints weight = 15033.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110081 restraints weight = 10324.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111184 restraints weight = 8047.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112056 restraints weight = 6832.514| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16027 Z= 0.154 Angle : 0.612 9.010 21975 Z= 0.297 Chirality : 0.044 0.277 2764 Planarity : 0.004 0.041 2650 Dihedral : 5.838 54.657 3926 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.74 % Allowed : 12.38 % Favored : 84.87 % 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: 0.43 (0.20), residues: 1635 helix: 1.67 (0.27), residues: 417 sheet: 0.49 (0.25), residues: 387 loop : -0.50 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 178 TYR 0.022 0.001 TYR A 173 PHE 0.011 0.001 PHE A 317 TRP 0.026 0.001 TRP E 571 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00362 (15902) covalent geometry : angle 0.57971 (21633) SS BOND : bond 0.00411 ( 33) SS BOND : angle 1.28351 ( 66) hydrogen bonds : bond 0.04501 ( 547) hydrogen bonds : angle 4.64148 ( 1893) link_ALPHA1-3 : bond 0.01127 ( 3) link_ALPHA1-3 : angle 1.42212 ( 9) link_ALPHA1-6 : bond 0.01340 ( 2) link_ALPHA1-6 : angle 1.91963 ( 6) link_BETA1-4 : bond 0.00452 ( 32) link_BETA1-4 : angle 1.39732 ( 96) link_NAG-ASN : bond 0.00230 ( 55) link_NAG-ASN : angle 1.92936 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.8894 (p) cc_final: 0.8684 (m) REVERT: D 373 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8808 (p) REVERT: D 434 MET cc_start: 0.8754 (tmm) cc_final: 0.8269 (ttp) REVERT: A 150 MET cc_start: 0.7865 (mmm) cc_final: 0.7505 (mmt) REVERT: A 195 ASN cc_start: 0.9064 (p0) cc_final: 0.8692 (p0) REVERT: A 323 ILE cc_start: 0.7562 (mt) cc_final: 0.6711 (mm) REVERT: C 199 SER cc_start: 0.8365 (t) cc_final: 0.7867 (m) REVERT: C 434 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8437 (ttp) REVERT: E 571 TRP cc_start: 0.6778 (m100) cc_final: 0.6251 (m-10) REVERT: E 633 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8392 (mmtm) outliers start: 41 outliers final: 31 residues processed: 196 average time/residue: 0.0993 time to fit residues: 31.2413 Evaluate side-chains 191 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN E 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104019 restraints weight = 26664.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106732 restraints weight = 15152.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108512 restraints weight = 10492.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109702 restraints weight = 8216.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110526 restraints weight = 6937.414| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16027 Z= 0.181 Angle : 0.646 12.984 21975 Z= 0.311 Chirality : 0.045 0.378 2764 Planarity : 0.004 0.047 2650 Dihedral : 5.931 50.012 3926 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.74 % Allowed : 13.12 % Favored : 84.14 % 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: 0.32 (0.20), residues: 1635 helix: 1.65 (0.27), residues: 414 sheet: 0.45 (0.26), residues: 387 loop : -0.63 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 178 TYR 0.020 0.001 TYR A 173 PHE 0.011 0.002 PHE E 522 TRP 0.022 0.001 TRP E 571 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00430 (15902) covalent geometry : angle 0.61529 (21633) SS BOND : bond 0.00423 ( 33) SS BOND : angle 1.24447 ( 66) hydrogen bonds : bond 0.04720 ( 547) hydrogen bonds : angle 4.69053 ( 1893) link_ALPHA1-3 : bond 0.01217 ( 3) link_ALPHA1-3 : angle 1.44993 ( 9) link_ALPHA1-6 : bond 0.01317 ( 2) link_ALPHA1-6 : angle 1.99821 ( 6) link_BETA1-4 : bond 0.00428 ( 32) link_BETA1-4 : angle 1.41655 ( 96) link_NAG-ASN : bond 0.00243 ( 55) link_NAG-ASN : angle 1.95258 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8847 (p) REVERT: D 434 MET cc_start: 0.8746 (tmm) cc_final: 0.8297 (ttp) REVERT: A 163 THR cc_start: 0.9154 (p) cc_final: 0.8704 (t) REVERT: A 195 ASN cc_start: 0.9125 (p0) cc_final: 0.8741 (p0) REVERT: B 660 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8533 (tt) REVERT: C 199 SER cc_start: 0.8345 (t) cc_final: 0.7826 (m) REVERT: E 571 TRP cc_start: 0.7335 (m100) cc_final: 0.7072 (m100) REVERT: E 633 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8390 (mmtm) outliers start: 41 outliers final: 33 residues processed: 193 average time/residue: 0.1116 time to fit residues: 34.3519 Evaluate side-chains 192 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 249 HIS ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105037 restraints weight = 26674.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107771 restraints weight = 15073.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109575 restraints weight = 10401.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110766 restraints weight = 8089.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111534 restraints weight = 6833.487| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16027 Z= 0.150 Angle : 0.612 11.508 21975 Z= 0.296 Chirality : 0.044 0.365 2764 Planarity : 0.004 0.041 2650 Dihedral : 5.738 48.456 3926 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.48 % Allowed : 14.12 % Favored : 83.40 % 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: 0.30 (0.20), residues: 1635 helix: 1.69 (0.27), residues: 414 sheet: 0.31 (0.25), residues: 417 loop : -0.62 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 178 TYR 0.020 0.001 TYR A 173 PHE 0.009 0.001 PHE E 522 TRP 0.020 0.001 TRP E 571 HIS 0.012 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00351 (15902) covalent geometry : angle 0.58177 (21633) SS BOND : bond 0.00398 ( 33) SS BOND : angle 1.17140 ( 66) hydrogen bonds : bond 0.04437 ( 547) hydrogen bonds : angle 4.60416 ( 1893) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 1.38062 ( 9) link_ALPHA1-6 : bond 0.01310 ( 2) link_ALPHA1-6 : angle 1.93688 ( 6) link_BETA1-4 : bond 0.00423 ( 32) link_BETA1-4 : angle 1.33536 ( 96) link_NAG-ASN : bond 0.00218 ( 55) link_NAG-ASN : angle 1.93477 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8844 (p) REVERT: D 434 MET cc_start: 0.8722 (tmm) cc_final: 0.8301 (ttp) REVERT: A 163 THR cc_start: 0.9127 (p) cc_final: 0.8678 (t) REVERT: A 195 ASN cc_start: 0.9086 (p0) cc_final: 0.8707 (p0) REVERT: C 199 SER cc_start: 0.8390 (t) cc_final: 0.7884 (m) REVERT: E 633 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8301 (mmtm) outliers start: 37 outliers final: 31 residues processed: 191 average time/residue: 0.1047 time to fit residues: 32.1220 Evaluate side-chains 189 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 71 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 374 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.128232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106237 restraints weight = 26465.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109137 restraints weight = 14573.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111041 restraints weight = 9863.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112261 restraints weight = 7604.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113004 restraints weight = 6367.449| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16027 Z= 0.121 Angle : 0.579 11.469 21975 Z= 0.281 Chirality : 0.043 0.397 2764 Planarity : 0.004 0.039 2650 Dihedral : 5.433 46.574 3926 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.94 % Allowed : 14.66 % Favored : 83.40 % 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: 0.31 (0.20), residues: 1635 helix: 1.61 (0.27), residues: 423 sheet: 0.36 (0.25), residues: 417 loop : -0.62 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.020 0.001 TYR A 173 PHE 0.008 0.001 PHE E 522 TRP 0.012 0.001 TRP C 112 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00277 (15902) covalent geometry : angle 0.55040 (21633) SS BOND : bond 0.00361 ( 33) SS BOND : angle 1.14108 ( 66) hydrogen bonds : bond 0.04116 ( 547) hydrogen bonds : angle 4.47632 ( 1893) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 1.31132 ( 9) link_ALPHA1-6 : bond 0.01347 ( 2) link_ALPHA1-6 : angle 1.84652 ( 6) link_BETA1-4 : bond 0.00417 ( 32) link_BETA1-4 : angle 1.27625 ( 96) link_NAG-ASN : bond 0.00201 ( 55) link_NAG-ASN : angle 1.80984 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8823 (p) REVERT: D 434 MET cc_start: 0.8717 (tmm) cc_final: 0.8267 (ttp) REVERT: A 163 THR cc_start: 0.9124 (p) cc_final: 0.8665 (t) REVERT: A 195 ASN cc_start: 0.9048 (p0) cc_final: 0.8665 (p0) REVERT: C 199 SER cc_start: 0.8216 (t) cc_final: 0.7730 (m) outliers start: 29 outliers final: 28 residues processed: 187 average time/residue: 0.0921 time to fit residues: 28.3968 Evaluate side-chains 185 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 173 optimal weight: 30.0000 chunk 70 optimal weight: 0.0070 chunk 185 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 302 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103445 restraints weight = 26488.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106168 restraints weight = 14964.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107964 restraints weight = 10328.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109137 restraints weight = 8041.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109877 restraints weight = 6784.340| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16027 Z= 0.183 Angle : 0.644 11.502 21975 Z= 0.310 Chirality : 0.045 0.362 2764 Planarity : 0.004 0.043 2650 Dihedral : 5.714 44.593 3926 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.34 % Allowed : 14.12 % Favored : 83.53 % 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: 0.39 (0.20), residues: 1635 helix: 1.69 (0.27), residues: 414 sheet: 0.47 (0.25), residues: 387 loop : -0.55 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 542 TYR 0.028 0.001 TYR B 586 PHE 0.012 0.002 PHE E 522 TRP 0.010 0.001 TRP C 112 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00434 (15902) covalent geometry : angle 0.61405 (21633) SS BOND : bond 0.00447 ( 33) SS BOND : angle 1.30201 ( 66) hydrogen bonds : bond 0.04584 ( 547) hydrogen bonds : angle 4.63539 ( 1893) link_ALPHA1-3 : bond 0.01130 ( 3) link_ALPHA1-3 : angle 1.32325 ( 9) link_ALPHA1-6 : bond 0.01304 ( 2) link_ALPHA1-6 : angle 1.97388 ( 6) link_BETA1-4 : bond 0.00437 ( 32) link_BETA1-4 : angle 1.39495 ( 96) link_NAG-ASN : bond 0.00255 ( 55) link_NAG-ASN : angle 1.93288 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2238.62 seconds wall clock time: 39 minutes 37.01 seconds (2377.01 seconds total)