Starting phenix.real_space_refine on Sat Jun 14 05:46:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l88_23225/06_2025/7l88_23225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l88_23225/06_2025/7l88_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7l88_23225/06_2025/7l88_23225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l88_23225/06_2025/7l88_23225.map" model { file = "/net/cci-nas-00/data/ceres_data/7l88_23225/06_2025/7l88_23225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l88_23225/06_2025/7l88_23225.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.46, per 1000 atoms: 0.67 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: 4.88 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.42 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: 6.14 Time building geometry restraints manager: 5.63 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 503 or resid 601 through 605)) selection = (chain 'C' and (resid 33 through 503 or resid 601 through 605)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 519 through 664 or resid 701 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.900 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- 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 : 2.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.060 0.009 TRP C 69 HIS 0.010 0.003 HIS D 374 PHE 0.030 0.005 PHE A 383 TYR 0.044 0.007 TYR A 40 ARG 0.006 0.001 ARG C 500 Details of bonding type rmsd link_NAG-ASN : bond 0.07515 ( 55) link_NAG-ASN : angle 3.17052 ( 165) 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_ALPHA1-3 : bond 0.08561 ( 3) link_ALPHA1-3 : angle 4.32041 ( 9) hydrogen bonds : bond 0.17249 ( 547) hydrogen bonds : angle 8.01398 ( 1893) SS BOND : bond 0.01267 ( 33) SS BOND : angle 2.55866 ( 66) covalent geometry : bond 0.02194 (15902) covalent geometry : angle 1.72954 (21633) *********************** 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 : 1.638 Fit side-chains revert: symmetry clash REVERT: D 373 THR cc_start: 0.8943 (t) cc_final: 0.8739 (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: 0.7431 (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: 0.7946 (mmp) REVERT: B 622 ILE cc_start: 0.8886 (mt) cc_final: 0.8666 (mt) REVERT: C 161 MET cc_start: 0.8588 (tpt) cc_final: 0.8124 (tpt) REVERT: C 198 THR cc_start: 0.9078 (p) cc_final: 0.8766 (p) REVERT: C 199 SER cc_start: 0.8764 (t) cc_final: 0.8359 (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: 0.3056 time to fit residues: 163.1532 Evaluate side-chains 175 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 607 ASN C 33 ASN C 67 ASN C 195 ASN C 216 HIS C 422 GLN E 570 HIS E 658 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112777 restraints weight = 25618.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115822 restraints weight = 14071.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117815 restraints weight = 9565.318| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16027 Z= 0.167 Angle : 0.750 12.951 21975 Z= 0.369 Chirality : 0.047 0.234 2764 Planarity : 0.005 0.086 2650 Dihedral : 8.115 83.683 3926 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.14 % Allowed : 7.43 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1635 helix: 1.48 (0.26), residues: 417 sheet: 0.70 (0.24), residues: 411 loop : 0.27 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.004 0.001 HIS B 570 PHE 0.012 0.002 PHE C 53 TYR 0.023 0.002 TYR A 217 ARG 0.009 0.001 ARG D 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 55) link_NAG-ASN : angle 2.66045 ( 165) link_ALPHA1-6 : bond 0.01100 ( 2) link_ALPHA1-6 : angle 1.75235 ( 6) link_BETA1-4 : bond 0.00603 ( 32) link_BETA1-4 : angle 2.32191 ( 96) link_ALPHA1-3 : bond 0.01817 ( 3) link_ALPHA1-3 : angle 1.90487 ( 9) hydrogen bonds : bond 0.06309 ( 547) hydrogen bonds : angle 5.70466 ( 1893) SS BOND : bond 0.00470 ( 33) SS BOND : angle 1.48735 ( 66) covalent geometry : bond 0.00351 (15902) covalent geometry : angle 0.69561 (21633) *********************** 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 264 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 229 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7847 (ptpt) REVERT: D 373 THR cc_start: 0.8918 (t) cc_final: 0.8534 (p) REVERT: F 542 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8267 (ttp80) REVERT: A 150 MET cc_start: 0.8079 (mmm) cc_final: 0.7613 (mmp) REVERT: A 247 CYS cc_start: 0.5605 (OUTLIER) cc_final: 0.5259 (p) REVERT: A 323 ILE cc_start: 0.7665 (mt) cc_final: 0.6878 (mm) REVERT: C 150 MET cc_start: 0.8531 (mmp) cc_final: 0.7836 (mmp) REVERT: C 161 MET cc_start: 0.8392 (tpt) cc_final: 0.7991 (tpt) REVERT: C 199 SER cc_start: 0.8527 (t) cc_final: 0.8180 (m) REVERT: E 571 TRP cc_start: 0.7387 (m100) cc_final: 0.7172 (m100) REVERT: E 632 ASP cc_start: 0.8891 (t0) cc_final: 0.8661 (t0) outliers start: 32 outliers final: 18 residues processed: 257 average time/residue: 0.2610 time to fit residues: 102.0607 Evaluate side-chains 196 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 229 LYS 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 247 CYS 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 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 175 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 102 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 0.0000 chunk 116 optimal weight: 4.9990 chunk 166 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 216 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 = 0.3565 r_free = 0.3565 target = 0.126142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103609 restraints weight = 26251.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106451 restraints weight = 14794.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108329 restraints weight = 10206.656| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 16027 Z= 0.324 Angle : 0.851 13.266 21975 Z= 0.413 Chirality : 0.051 0.308 2764 Planarity : 0.005 0.060 2650 Dihedral : 7.877 69.935 3926 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.95 % Allowed : 9.24 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1635 helix: 1.22 (0.26), residues: 417 sheet: 0.53 (0.25), residues: 387 loop : -0.35 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 96 HIS 0.008 0.002 HIS A 249 PHE 0.025 0.003 PHE E 522 TYR 0.024 0.002 TYR B 586 ARG 0.007 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 55) link_NAG-ASN : angle 2.45737 ( 165) link_ALPHA1-6 : bond 0.01111 ( 2) link_ALPHA1-6 : angle 2.03639 ( 6) link_BETA1-4 : bond 0.00621 ( 32) link_BETA1-4 : angle 2.02376 ( 96) link_ALPHA1-3 : bond 0.01639 ( 3) link_ALPHA1-3 : angle 1.27543 ( 9) hydrogen bonds : bond 0.06367 ( 547) hydrogen bonds : angle 5.47546 ( 1893) SS BOND : bond 0.00809 ( 33) SS BOND : angle 1.98882 ( 66) covalent geometry : bond 0.00777 (15902) covalent geometry : angle 0.81122 (21633) *********************** 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 217 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.9152 (t) cc_final: 0.8877 (p) REVERT: A 150 MET cc_start: 0.8476 (mmm) cc_final: 0.8063 (mmt) REVERT: C 161 MET cc_start: 0.8297 (tpt) cc_final: 0.8059 (tpt) REVERT: C 199 SER cc_start: 0.8784 (t) cc_final: 0.8200 (m) REVERT: E 622 ILE cc_start: 0.9007 (mt) cc_final: 0.8779 (mt) outliers start: 44 outliers final: 32 residues processed: 207 average time/residue: 0.2677 time to fit residues: 85.4397 Evaluate side-chains 180 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 325 ASP 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 75 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR 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 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 66 HIS 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 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 171 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 33 ASN C 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107792 restraints weight = 25939.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110727 restraints weight = 14414.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112627 restraints weight = 9852.410| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16027 Z= 0.135 Angle : 0.627 10.056 21975 Z= 0.305 Chirality : 0.044 0.268 2764 Planarity : 0.004 0.039 2650 Dihedral : 6.708 64.539 3926 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.48 % Allowed : 10.24 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1635 helix: 1.52 (0.27), residues: 417 sheet: 0.54 (0.25), residues: 381 loop : -0.37 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.003 0.001 HIS A 249 PHE 0.009 0.001 PHE D 53 TYR 0.013 0.001 TYR B 586 ARG 0.004 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 55) link_NAG-ASN : angle 2.13497 ( 165) link_ALPHA1-6 : bond 0.01255 ( 2) link_ALPHA1-6 : angle 1.88155 ( 6) link_BETA1-4 : bond 0.00437 ( 32) link_BETA1-4 : angle 1.49135 ( 96) link_ALPHA1-3 : bond 0.01394 ( 3) link_ALPHA1-3 : angle 1.70867 ( 9) hydrogen bonds : bond 0.04913 ( 547) hydrogen bonds : angle 4.90972 ( 1893) SS BOND : bond 0.00426 ( 33) SS BOND : angle 1.36302 ( 66) covalent geometry : bond 0.00301 (15902) covalent geometry : angle 0.58882 (21633) *********************** 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 215 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.8946 (p) cc_final: 0.8704 (m) REVERT: D 434 MET cc_start: 0.8781 (tmm) cc_final: 0.8297 (ttp) REVERT: A 150 MET cc_start: 0.8022 (mmm) cc_final: 0.7750 (mmt) REVERT: A 195 ASN cc_start: 0.9017 (p0) cc_final: 0.8664 (p0) REVERT: B 601 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8640 (mttm) REVERT: C 161 MET cc_start: 0.8232 (tpt) cc_final: 0.8031 (tpt) REVERT: C 199 SER cc_start: 0.8288 (t) cc_final: 0.7801 (m) REVERT: C 426 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8005 (mmp) REVERT: E 633 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8420 (mmtm) outliers start: 37 outliers final: 25 residues processed: 203 average time/residue: 0.2361 time to fit residues: 74.6272 Evaluate side-chains 180 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 VAL 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 141 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 182 VAL 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 342 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 601 LYS 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 196 CYS Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 633 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 17 optimal weight: 0.0370 chunk 108 optimal weight: 4.9990 chunk 178 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- 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 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099526 restraints weight = 27189.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102191 restraints weight = 15616.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103944 restraints weight = 10907.499| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 16027 Z= 0.325 Angle : 0.819 11.308 21975 Z= 0.393 Chirality : 0.051 0.318 2764 Planarity : 0.005 0.057 2650 Dihedral : 7.305 58.200 3926 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.68 % Allowed : 10.84 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1635 helix: 1.11 (0.26), residues: 417 sheet: 0.05 (0.24), residues: 417 loop : -0.69 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 571 HIS 0.007 0.002 HIS A 249 PHE 0.019 0.002 PHE E 522 TYR 0.016 0.002 TYR A 217 ARG 0.009 0.001 ARG D 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 55) link_NAG-ASN : angle 2.34980 ( 165) link_ALPHA1-6 : bond 0.01140 ( 2) link_ALPHA1-6 : angle 2.22172 ( 6) link_BETA1-4 : bond 0.00535 ( 32) link_BETA1-4 : angle 1.83206 ( 96) link_ALPHA1-3 : bond 0.01393 ( 3) link_ALPHA1-3 : angle 1.82133 ( 9) hydrogen bonds : bond 0.05983 ( 547) hydrogen bonds : angle 5.28358 ( 1893) SS BOND : bond 0.00627 ( 33) SS BOND : angle 1.82435 ( 66) covalent geometry : bond 0.00776 (15902) covalent geometry : angle 0.78164 (21633) *********************** 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 213 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 657 GLU cc_start: 0.7822 (tt0) cc_final: 0.7614 (tt0) REVERT: A 141 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: A 195 ASN cc_start: 0.9051 (p0) cc_final: 0.8692 (p0) REVERT: A 323 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7267 (mt) REVERT: A 484 TYR cc_start: 0.8487 (p90) cc_final: 0.8196 (p90) REVERT: B 660 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8709 (tp) REVERT: C 199 SER cc_start: 0.8696 (t) cc_final: 0.8079 (m) REVERT: E 571 TRP cc_start: 0.6738 (m100) cc_final: 0.6336 (m-10) REVERT: E 633 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8399 (mptt) outliers start: 55 outliers final: 40 residues processed: 199 average time/residue: 0.2315 time to fit residues: 72.6757 Evaluate side-chains 192 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 106 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP 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 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ILE 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 534 SER 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 154 LEU Chi-restraints excluded: chain C residue 172 VAL 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 243 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 503 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3541 r_free = 0.3541 target = 0.124257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102661 restraints weight = 26798.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105336 restraints weight = 15141.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107078 restraints weight = 10447.470| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16027 Z= 0.179 Angle : 0.661 10.503 21975 Z= 0.320 Chirality : 0.045 0.280 2764 Planarity : 0.004 0.044 2650 Dihedral : 6.608 56.028 3926 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.01 % Allowed : 11.85 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1635 helix: 1.38 (0.27), residues: 414 sheet: 0.05 (0.24), residues: 423 loop : -0.67 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 571 HIS 0.004 0.001 HIS A 249 PHE 0.011 0.002 PHE E 522 TYR 0.012 0.001 TYR B 586 ARG 0.004 0.000 ARG D 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 55) link_NAG-ASN : angle 2.09666 ( 165) link_ALPHA1-6 : bond 0.01275 ( 2) link_ALPHA1-6 : angle 1.96276 ( 6) link_BETA1-4 : bond 0.00434 ( 32) link_BETA1-4 : angle 1.47105 ( 96) link_ALPHA1-3 : bond 0.01357 ( 3) link_ALPHA1-3 : angle 1.78836 ( 9) hydrogen bonds : bond 0.05014 ( 547) hydrogen bonds : angle 4.93337 ( 1893) SS BOND : bond 0.00453 ( 33) SS BOND : angle 1.39131 ( 66) covalent geometry : bond 0.00420 (15902) covalent geometry : angle 0.62647 (21633) *********************** 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 214 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: D 434 MET cc_start: 0.8801 (tmm) cc_final: 0.8416 (ttp) REVERT: A 141 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: A 150 MET cc_start: 0.7910 (mmm) cc_final: 0.7507 (mmt) REVERT: A 195 ASN cc_start: 0.9042 (p0) cc_final: 0.8803 (p0) REVERT: A 484 TYR cc_start: 0.8425 (p90) cc_final: 0.8208 (p90) REVERT: B 660 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8402 (tt) REVERT: C 199 SER cc_start: 0.8494 (t) cc_final: 0.7910 (m) REVERT: E 571 TRP cc_start: 0.6854 (m100) cc_final: 0.6421 (m-10) REVERT: E 633 LYS cc_start: 0.8764 (mttm) cc_final: 0.8360 (mptt) outliers start: 45 outliers final: 34 residues processed: 204 average time/residue: 0.2289 time to fit residues: 73.7307 Evaluate side-chains 189 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 443 ILE 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 639 THR 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 141 ASP 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 342 LEU 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 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 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 626 MET 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 120 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 C 33 ASN C 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102353 restraints weight = 26857.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105024 restraints weight = 15204.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106799 restraints weight = 10490.236| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16027 Z= 0.197 Angle : 0.678 11.269 21975 Z= 0.326 Chirality : 0.046 0.296 2764 Planarity : 0.004 0.043 2650 Dihedral : 6.462 53.485 3926 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.48 % Allowed : 12.65 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1635 helix: 1.43 (0.27), residues: 414 sheet: 0.18 (0.24), residues: 411 loop : -0.72 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.004 0.001 HIS A 249 PHE 0.012 0.002 PHE E 522 TYR 0.012 0.001 TYR B 586 ARG 0.005 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 55) link_NAG-ASN : angle 2.07943 ( 165) link_ALPHA1-6 : bond 0.01276 ( 2) link_ALPHA1-6 : angle 2.00166 ( 6) link_BETA1-4 : bond 0.00445 ( 32) link_BETA1-4 : angle 1.49397 ( 96) link_ALPHA1-3 : bond 0.01372 ( 3) link_ALPHA1-3 : angle 1.76672 ( 9) hydrogen bonds : bond 0.04969 ( 547) hydrogen bonds : angle 4.90718 ( 1893) SS BOND : bond 0.00558 ( 33) SS BOND : angle 1.36310 ( 66) covalent geometry : bond 0.00466 (15902) covalent geometry : angle 0.64446 (21633) *********************** 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 214 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: 0.8789 (tmm) cc_final: 0.8404 (ttp) REVERT: F 530 MET cc_start: 0.8955 (mtp) cc_final: 0.8745 (mtp) REVERT: A 69 TRP cc_start: 0.8272 (OUTLIER) cc_final: 0.7943 (m100) REVERT: A 107 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7734 (t70) REVERT: A 141 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: A 150 MET cc_start: 0.7940 (mmm) cc_final: 0.7450 (mmt) REVERT: A 195 ASN cc_start: 0.9018 (p0) cc_final: 0.8762 (p0) REVERT: A 323 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7191 (mt) REVERT: B 660 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8462 (tt) REVERT: C 199 SER cc_start: 0.8590 (t) cc_final: 0.7973 (m) REVERT: E 571 TRP cc_start: 0.7117 (m100) cc_final: 0.6683 (m-10) REVERT: E 633 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8337 (mptt) outliers start: 52 outliers final: 38 residues processed: 199 average time/residue: 0.2339 time to fit residues: 73.3730 Evaluate side-chains 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 443 ILE 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 639 THR 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 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP 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 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU 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 33 ASN 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 172 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 475 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 114 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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 33 ASN C 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102947 restraints weight = 26674.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105693 restraints weight = 14764.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107525 restraints weight = 10102.620| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16027 Z= 0.168 Angle : 0.643 10.192 21975 Z= 0.310 Chirality : 0.045 0.313 2764 Planarity : 0.004 0.042 2650 Dihedral : 6.250 51.875 3926 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.15 % Allowed : 12.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1635 helix: 1.54 (0.27), residues: 414 sheet: 0.18 (0.24), residues: 411 loop : -0.71 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 112 HIS 0.003 0.001 HIS A 249 PHE 0.010 0.001 PHE E 522 TYR 0.011 0.001 TYR B 586 ARG 0.005 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 55) link_NAG-ASN : angle 2.01891 ( 165) link_ALPHA1-6 : bond 0.01291 ( 2) link_ALPHA1-6 : angle 1.95658 ( 6) link_BETA1-4 : bond 0.00431 ( 32) link_BETA1-4 : angle 1.42821 ( 96) link_ALPHA1-3 : bond 0.01300 ( 3) link_ALPHA1-3 : angle 1.66193 ( 9) hydrogen bonds : bond 0.04768 ( 547) hydrogen bonds : angle 4.81594 ( 1893) SS BOND : bond 0.00435 ( 33) SS BOND : angle 1.37753 ( 66) covalent geometry : bond 0.00393 (15902) covalent geometry : angle 0.61029 (21633) *********************** 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 203 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: 0.8771 (tmm) cc_final: 0.8367 (ttp) REVERT: A 69 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7834 (m100) REVERT: A 107 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7234 (t0) REVERT: A 141 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: A 150 MET cc_start: 0.7849 (mmm) cc_final: 0.7368 (mmt) REVERT: A 195 ASN cc_start: 0.9003 (p0) cc_final: 0.8745 (p0) REVERT: A 323 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7161 (mt) REVERT: B 660 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 199 SER cc_start: 0.8518 (t) cc_final: 0.7908 (m) REVERT: E 571 TRP cc_start: 0.7226 (m100) cc_final: 0.6780 (m-10) outliers start: 47 outliers final: 39 residues processed: 190 average time/residue: 0.2438 time to fit residues: 72.4741 Evaluate side-chains 194 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 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 426 MET Chi-restraints excluded: chain D residue 443 ILE 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 639 THR 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 69 TRP 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 107 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU 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 33 ASN 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 172 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET 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 135 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 63 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105349 restraints weight = 26605.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108071 restraints weight = 14871.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109875 restraints weight = 10176.602| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16027 Z= 0.117 Angle : 0.600 9.759 21975 Z= 0.291 Chirality : 0.044 0.299 2764 Planarity : 0.004 0.041 2650 Dihedral : 5.874 50.659 3926 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.68 % Allowed : 13.25 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1635 helix: 1.67 (0.27), residues: 414 sheet: 0.14 (0.24), residues: 417 loop : -0.66 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 112 HIS 0.003 0.001 HIS A 216 PHE 0.009 0.001 PHE D 53 TYR 0.011 0.001 TYR B 586 ARG 0.006 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 55) link_NAG-ASN : angle 1.92516 ( 165) link_ALPHA1-6 : bond 0.01332 ( 2) link_ALPHA1-6 : angle 1.82928 ( 6) link_BETA1-4 : bond 0.00420 ( 32) link_BETA1-4 : angle 1.32370 ( 96) link_ALPHA1-3 : bond 0.01306 ( 3) link_ALPHA1-3 : angle 1.53701 ( 9) hydrogen bonds : bond 0.04340 ( 547) hydrogen bonds : angle 4.64673 ( 1893) SS BOND : bond 0.00376 ( 33) SS BOND : angle 1.17586 ( 66) covalent geometry : bond 0.00259 (15902) covalent geometry : angle 0.56853 (21633) *********************** 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 210 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: 0.8731 (tmm) cc_final: 0.8340 (ttp) REVERT: D 475 MET cc_start: 0.8276 (mmm) cc_final: 0.7826 (mmm) REVERT: A 69 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7779 (m100) REVERT: A 107 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7163 (t0) REVERT: A 141 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: A 150 MET cc_start: 0.7718 (mmm) cc_final: 0.7151 (mmt) REVERT: A 195 ASN cc_start: 0.8961 (p0) cc_final: 0.8651 (p0) REVERT: C 199 SER cc_start: 0.8495 (t) cc_final: 0.7924 (m) REVERT: E 571 TRP cc_start: 0.7307 (m100) cc_final: 0.6699 (m-10) outliers start: 40 outliers final: 29 residues processed: 196 average time/residue: 0.2405 time to fit residues: 73.0183 Evaluate side-chains 187 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 171 LYS 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 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE 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 172 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET 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 81 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 171 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** B 652 GLN 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 = 0.3583 r_free = 0.3583 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105974 restraints weight = 26658.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108727 restraints weight = 15049.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110559 restraints weight = 10334.002| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16027 Z= 0.118 Angle : 0.592 10.678 21975 Z= 0.287 Chirality : 0.043 0.291 2764 Planarity : 0.004 0.041 2650 Dihedral : 5.549 48.330 3926 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.48 % Allowed : 13.79 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1635 helix: 1.74 (0.27), residues: 414 sheet: 0.20 (0.24), residues: 417 loop : -0.65 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 571 HIS 0.004 0.001 HIS A 216 PHE 0.009 0.001 PHE D 53 TYR 0.024 0.001 TYR B 586 ARG 0.007 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 55) link_NAG-ASN : angle 1.86267 ( 165) link_ALPHA1-6 : bond 0.01289 ( 2) link_ALPHA1-6 : angle 1.83112 ( 6) link_BETA1-4 : bond 0.00431 ( 32) link_BETA1-4 : angle 1.30459 ( 96) link_ALPHA1-3 : bond 0.01216 ( 3) link_ALPHA1-3 : angle 1.39169 ( 9) hydrogen bonds : bond 0.04191 ( 547) hydrogen bonds : angle 4.54964 ( 1893) SS BOND : bond 0.00355 ( 33) SS BOND : angle 1.23769 ( 66) covalent geometry : bond 0.00267 (15902) covalent geometry : angle 0.56181 (21633) ********************** 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 204 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 434 MET cc_start: 0.8712 (tmm) cc_final: 0.8301 (ttp) REVERT: A 69 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.7831 (m100) REVERT: A 95 MET cc_start: 0.8630 (ptm) cc_final: 0.8163 (ttp) REVERT: A 107 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7142 (t0) REVERT: A 141 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: A 150 MET cc_start: 0.7641 (mmm) cc_final: 0.7116 (mmt) REVERT: A 195 ASN cc_start: 0.8877 (p0) cc_final: 0.8540 (p0) REVERT: A 359 ILE cc_start: 0.8261 (mm) cc_final: 0.8027 (mm) REVERT: B 660 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8304 (tt) REVERT: C 199 SER cc_start: 0.8419 (t) cc_final: 0.7775 (m) REVERT: C 482 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7304 (mt-10) outliers start: 37 outliers final: 27 residues processed: 194 average time/residue: 0.2298 time to fit residues: 70.3468 Evaluate side-chains 191 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 443 ILE 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 639 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 171 LYS 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 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 172 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET 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 115 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 183 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.125182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103615 restraints weight = 26417.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106338 restraints weight = 14881.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108118 restraints weight = 10251.320| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4539 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= 0.161 Angle : 0.622 10.286 21975 Z= 0.301 Chirality : 0.044 0.273 2764 Planarity : 0.004 0.041 2650 Dihedral : 5.658 46.215 3926 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.28 % Allowed : 13.86 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1635 helix: 1.74 (0.27), residues: 414 sheet: 0.27 (0.24), residues: 411 loop : -0.68 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 112 HIS 0.003 0.001 HIS A 216 PHE 0.011 0.001 PHE E 522 TYR 0.025 0.001 TYR B 586 ARG 0.006 0.000 ARG E 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 55) link_NAG-ASN : angle 1.89056 ( 165) link_ALPHA1-6 : bond 0.01271 ( 2) link_ALPHA1-6 : angle 1.92724 ( 6) link_BETA1-4 : bond 0.00430 ( 32) link_BETA1-4 : angle 1.36591 ( 96) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 1.42136 ( 9) hydrogen bonds : bond 0.04469 ( 547) hydrogen bonds : angle 4.62261 ( 1893) SS BOND : bond 0.00442 ( 33) SS BOND : angle 1.38469 ( 66) covalent geometry : bond 0.00380 (15902) covalent geometry : angle 0.59110 (21633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4486.41 seconds wall clock time: 78 minutes 56.00 seconds (4736.00 seconds total)